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Our 800 MHz Avance III Spectrometer is our highest field and most modern instrument. It is equipped 24/7 with a Bruker TCI cryoprobe that provides about a 4:1 Signal-to-Noise improvement over conventional probes.  It is highly suited for metabolomic studies, the study of complex biomolecules like proteins and nucleic acids, and routine 1H and 13C NMR experiments on small molecules.

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• Protein conformational dynamics determined by NMR relaxation dispersion analysis.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092842/
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• NMR structure and function of cyanobacteriochromes.   http://link.springer.com/article/10.1007%2Fs12104-013-9496-0

32 physics experiments that changed the world

From the discovery of gravity to the first mission to defend Earth from an asteroid, here are the most important physics experiments that changed the world.

Physics experiments have changed the world irrevocably, altering our reality and enabling us to take gigantic leaps in technology. From ancient times to now, here's a look at some of the greatest physics experiments of all time.

Conservation of energy

Energy conservation — the idea that energy cannot be created or destroyed, only transformed — is one of the most important laws of physics. James Prescott Joule demonstrated this rule, the first law of thermodynamics , when he filled a large container with water and fixed a paddle wheel inside it. The wheel was held in place by an axle with a string around it and then looped over a pulley and attached to a weight, which, when dropped, caused the wheel to spin. By sloshing the water with the wheel, Joule demonstrated that the heat energy gained by the water from the wheel's movement was equal to the potential energy lost by dropping the weight.

Measurement of the electron's charge

As the fundamental carriers of electric charge, electrons carry the smallest amount of electricity possible. But the particles are truly tiny, with a mass 1,838 times smaller than the already-minuscule proton.

So how could you measure the charge on something so small? Physicist Robert Millikan's answer was to drop electrically charged oil drops through the plates of a capacitor and adjust the voltage of the capacitor until the electric field it emitted produced a force on some of the drops that balanced out gravity — thus suspending them in the air. Repeating the experiment for different voltages revealed that, no matter the size of the drops, the total charge it carried was a multiple of a base number. Millikan had found the fundamental charge of the electron.

 "Gold foil experiment" revealing the structure of the atom

Once thought to be indivisible, the atom was slowly divided and split by a series of experiments during the late 19th and early 20th centuries. These included J.J. Thomson's 1897 discovery of the electron and James Chadwick's 1932 identification of the neutron. But perhaps the most famous of these experiments was Hans Geiger and Ernest Marsden's " gold foil experiment ." Under the direction of Ernest Rutherford, the students fired positively charged alpha particles at a thin sheet of gold foil. To their surprise, the particles passed through, revealing that atoms consisted of a positively charged nucleus separated by a significant empty space by their orbiting electrons.

Nuclear chain reaction

By the mid-20th century, scientists were aware of the basic structure of the atom and that, according to Einstein, matter and energy were different forms of the same thing. This set the stage for the wartime work of Enrico Fermi, who in 1942 demonstrated that atoms could be split to release enormous quantities of energy.

While working at the University of Chicago with an experimental setup he called an "atomic pile," Fermi demonstrated the first-ever controlled nuclear fission reaction. Fermi fired neutrons at the unstable isotope uranium-235, causing it to split and release more neutrons in a growing chain reaction. The experiment paved the way for the development of nuclear reactors and was used by J. Robert Oppenheimer and the Manhattan Project to build the first atomic bombs.

Wave-particle duality

One of the most famous experiments in physics is also one that illustrates, with disturbing simplicity, the bizarreness of the quantum world. The experiment consisted of two slits, through which electrons would travel to create an interference pattern on a screen, like waves. Scientists were stunned when they placed a detector near the screen and found that its presence caused the electrons to switch their behavior to act instead as particles.

First performed by Thomas Young to demonstrate the wave nature of light, the experiment was later used by physicists in the 20th century to show that all particles, including photons , were both waves and particles at the same time — and they acted more like particles when they were being measured directly.

Splitting of white light into colors

White light is a mixture of all the colors of the rainbow, but before 1672, the composite nature of light was completely unknown. Isaac Newton determined this by using a prism that bent light of different wavelengths, or colors, by different amounts, decomposing white light into its composite colors. The result was one of the most famous experiments in scientific history and a discovery that, alongside other contributions by Newton, gave birth to the modern field of optics.

Discovery of gravity

In perhaps the most widely repeated story in all of science, Newton is said to have chanced upon the theory of gravity while contemplating under the shade of an apple tree. According to the legend, when an apple fell and struck him on the head, he supposedly yelled "Eureka!" as he realized that the same force that brought the apple tumbling to Earth also kept the moon in orbit around our planet and Earth circling the sun. That force, of course, would become known as gravity .

The story is slightly embellished, however. According to Newton's own account, the apple did not strike him on the head, and there's no record of what he said or if he said anything, at the moment of discovery. Nonetheless, the realization led Newton to develop his theory of gravity in 1687, which was updated by Einstein's theory of general relativity 228 years later.

Blackbody radiation

By the turn of the 20th century, many physicists — having advanced theories that explained gravity, mechanics, thermodynamics and the behavior of electromagnetic fields — were confident that they had conquered the vast majority of their field. But one troubling source of doubt remained: Theories predicted the existence of a "blackbody" — an object capable of absorbing and then remitting all incident radiation. The problem was that physicists couldn't find it.

In fact, data from experiments conducted with close approximations of black bodies — a box with a single hole whose inside walls are black — revealed that significantly less energy was emitted from blackbodies than classical theories led scientists to believe, especially at shorter wavelengths. The contradiction between experiment and theory became known as the "ultraviolet catastrophe."

The discovery prompted Max Planck to propose that the energy emitted by blackbodies wasn't continuous but rather split into discrete integer chunks called quanta. His radical proposal catalyzed the development of quantum mechanics , whose bizarre rules are completely unintuitive to observers living in the macroscopic world.

Einstein and the eclipse

Following its publication in 1915, Einstein's groundbreaking theory of general relativity briefly remained just that — a theory. Then, in 1919, astronomer Sir Arthur Eddington devised and completed stunning proof using that year's total solar eclipse .

Key to Einstein's theory was the notion that space — and, therefore, the path that light would follow through it — was warped by powerful gravitational forces. So, as the moon's shadow passed in front of the sun, Eddington recorded the position of nearby stars from his vantage point on the island of Principe in the Gulf of Guinea. By comparing these positions to those he had recorded at night without the sun in the sky, Eddington observed that they had been shifted slightly by the sun's gravity, completing his stunning proof of Einstein's theory.

Higgs boson

In 1964, Peter Higgs suggested that matter gets its mass from a field that permeates all of space, imparting particles with mass through their interactions with a particle known as the Higgs boson .

To search for the boson, thousands of particle physicists planned, constructed and fired up the Large Hadron Collider . In 2012, after trillions upon trillions of collisions in which two protons are smashed together at near light speed, the physicists finally spotted the telltale signature of the boson.

Weighing the world

Although he's perhaps best known for his discovery of hydrogen, 18th-century physicist Henry Cavendish's most ingenious experiment accurately estimated the weight of our entire planet. Using a special piece of equipment known as a torsion balance (two rods with one smaller and one larger pair of lead balls attached to the end), Cavendish measured the minuscule force of gravitational attraction between the masses. Then, by measuring the weight of one of the small balls, he measured the gravitational force between it and Earth, giving him an easy formula for calculating our planet's density and — therefore, its weight — that remains accurate to this day.

Conservation of mass

Much like energy, matter in our universe is finite and cannot be created or destroyed, only rearranged. In 1789, to arrive at this startling conclusion, French chemist Antoine Lavoisier placed a burning candle inside a sealed glass jar. After the candle had burned and melted into a puddle of wax, Lavoisier weighed the jar and its contents, finding that it had not changed

Leaning Tower of Pisa experiment

Greek philosopher Aristotle believed that objects fall at different rates because the force acting upon them was stronger for heavier objects — a claim that went unchallenged for more than a millennium.

Then came the Italian polymath Galileo Galilei, who corrected Aristotle's false claim by showing that two objects with different masses fall at exactly the same rate. Some claim Galileo's famous experiment was conducted by dropping two spheres from the Leaning Tower of Pisa, but others say this part of the story is apocryphal. Nonetheless, the experiment was perhaps most famously demonstrated by Apollo 15 astronaut David Scott, who, while dropping a feather and a hammer on the moon, showed that without air, the two objects fell at the same speed.

Detection of gravitational waves

If gravity warps space-time as Einstein predicted, then the collision of two extremely dense objects, such as neutron stars or black holes , should also create detectable shock waves in space that could reveal physics unseen by light. The problem is that these gravitational waves are tiny, often the size of a few thousandths of a proton or neutron, so detecting them requires an extremely sensitive experiment.

Enter LIGO, the Laser Interferometer Gravitational-Wave Observatory. The L-shaped detector has two 2.5-mile-long (4 km) arms containing two identical laser beams. When a gravitational wave laps at our cosmic shores, the laser in one arm is compressed and the other expands, alerting scientists to the wave's presence. In 2015, LIGO achieved its task, making the first-ever direct detection of gravitational waves and opening up an entirely new window to the cosmos.

Destruction of heliocentrism

The idea that Earth orbits the sun goes back to the fifth century B.C. to Greek philosophers Hicetas and Philolaus. Nonetheless, Claudius Ptolemy's belief that Earth was the center of the universe later took root and dominated scientific thought for more than a millennium.

Then came Nicolaus Copernicus, who proposed that Earth did, in fact, revolve around the sun and not the other way around. Concrete evidence for this was later offered by Galileo, who in 1610 peered through his telescope to observe the planet Venus moving through distinct phases — proof that it, too, orbited the sun. Galileo's discovery did not win him any friends with the Catholic Church, which tried him for heresy for his unorthodox proposal.

Foucault's pendulum

First used by French physicist Jean Bernard Léon Foucault in 1851, the famous pendulum consisted of a brass bob containing sand and suspended by a cable from the ceiling. As it swung back and forth, the angle of the line traced out by the sand changed subtly over time — clear evidence that some unknown rotation was causing it to shift. This rotation was the spinning of Earth on its axis.

Discovery of the electron

In the 19th century, physicists found that by creating a vacuum inside a glass tube and sending electricity through it, they could make the tube give off a fluorescent glow. But exactly what caused this effect, called a cathode ray, was unclear.

Then, in 1897, physicist J.J. Thomson discovered that by applying a magnetic field to the rays inside the tube, he could control the direction in which they traveled. This revelation showed Thomson that the charge within the tube came from tiny particles 1,000 times smaller than hydrogen atoms. The tiny electron had finally been found.

Deflection of an asteroid

In 2022, NASA scientists hit an astronomical "bull's-eye" by intentionally steering the 1,210-pound (550 kilograms), $314 million Double Asteroid Redirection Test (DART) spacecraft into the asteroid Dimorphos just 56 feet (17 meters) from its center. The test was designed to see if a small spacecraft propelled along a planned trajectory could, if given enough lead time, redirect an asteroid from a potentially catastrophic impact with Earth.

DART was a smashing success . The probe's original goal was to change the orbit of Dimorphos around its larger partner — the 2,560-foot-wide (780 m) asteroid Didymos — by at least 73 seconds, but the spacecraft actually altered Dimorphos' orbit by a stunning 32 minutes. NASA hailed the collision as a watershed moment for planetary defense, marking the first time that humans proved capable of diverting Armageddon, and without any assistance from Bruce Willis.

Faraday induction

In 1831, Michael Faraday, the self-taught son of a blacksmith born in rural south England, proposed the law of electromagnetic induction. The law was the result of three experiments by Faraday, the most notable of which involved the movement of a magnet inside a coil made by wrapping a wire around a paper cylinder. As the magnet moved inside the cylinder, it induced an electric current through the coil — proving that electric and magnetic fields were inextricably linked and paving the way for electric generators and devices.

Measurement of the speed of light

Light is the fastest thing in our universe, which makes measuring its speed a unique challenge. In 1676, Danish astronomer Ole Roemer chanced upon the first estimate for light's propagation while studying Io, Jupiter's innermost moon. By timing the eclipses of Io by Jupiter, Roemer was hoping to find the moon's orbital period.

What he noticed instead was that, as Earth's orbit moved closer to Jupiter, the time intervals between successive eclipses became shorter. Roemer's crucial insight was that this was due to a finite speed of light, which he roughly calculated based on Earth's orbit. Other methods later refined the measurement of light's speed, eventually arriving at its current value of 2.98 × 10^8 meters per second (about 186,282 miles per second).

Disproof of the "luminiferous ether"

Most waves, such as sound waves and water waves, require a medium to travel through. In the 19th century, physicists thought the same rule applied to light, too, with electromagnetic waves traveling through a ubiquitous medium dubbed the "luminiferous ether."

Albert Michelson and Edward W. Morley set out to prove this conjecture with a remarkably ingenious hypothesis: As the sun moves through the ether, it should displace some of the strange substance, meaning light should travel detectably faster when it moves with the ether wind than against it. They set up an interferometer experiment that used mirrors to split light beams along two opposing directions before bouncing them back with distant mirrors. If the light beams returned at different times, then the ether was real.

But the light beams inside their interferometer did not vary. Michelson and Morley concluded that their experiment had failed and moved on to other projects. But the result — which had conclusively disproved the ether theory — was later used by Einstein in his theory of special relativity to correctly state that light's speed through a fixed medium does not change, even if its source is moving.

Discovery of radioactivity

In 1897, while working in a converted shed with her husband Pierre, Marie Curie began to investigate the source of a strange new type of radiation emitted from the elements thorium and uranium. Marie Curie discovered that the radiation these elements emitted did not depend on any other factors, such as their temperature or molecular structure, but changed purely based on their quantities. While grinding up an even more radioactive substance known as pitchblende, she also discovered that it consisted of two elements that she dubbed radium and polonium.

Curie's work revealed the nature of radioactivity, a truly random property of atoms that comes from their internal structure. Curie won the Nobel Prize (twice) for her discoveries — making her the first woman to do so — and later trained doctors to use X-rays to image broken bones and bullet wounds. She died of aplastic pernicious anemia, a disease caused by radiation exposure, in 1934.

Expansion of the universe

While using the 100-inch Hooker telescope in California to study the light glimmering from distant galaxies in 1929, Edwin Hubble made a surprising observation: The light from the distant galaxies appeared to be shifted toward the red end of the spectrum — an indication that they were receding from Earth and each other. The farther away a galaxy was, the faster it was moving away.

Hubble's observation became a crucial piece of evidence for the Big Bang theory of our universe. Yet precise measurements for galaxies' recession, known as the Hubble constant, still confound scientists to this day .

Put simply, the universe is indeed expanding, but depending on where cosmologists look, it's doing so at different rates. In the past, the two best experiments to measure the expansion rate were the European Space Agency 's Planck satellite and the Hubble Space Telescope . The two observatories, each of which used a different method to measure the expansion rate, arrived at different results. These conflicting measurements have led to what some call a "cosmology crisis" that could reveal new physics or even replace the standard model of cosmology.

Ignition of nuclear fusion

In 2022, scientists at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory in California used the world's most powerful laser to achieve something physicists have been dreaming about for nearly a century: the ignition of a pellet of fuel by nuclear fusion .

The demonstration marked the first time that the energy going out of the plasma in the nuclear reactor's fiery core exceeded the energy beamed in by the laser, and has been a rallying call for fusion scientists that the distant goal of near-limitless and clean power is, in fact, achievable.

However, scientists have cautioned that the energy from the plasma exceeds only that from the lasers, and not from the energy from the whole reactor. Additionally, the laser-confinement method used by the NIF reactor, built to test thermonuclear explosions for bomb development, will be difficult to scale up.

Measurement of Earth's circumference

By roughly 500 B.C., most ancient Greeks believed the world was round — citing evidence provided by Aristotle and guided by a suggestion from Pythagoras, who believed a sphere was the most aesthetically pleasing shape for our planet.

Then, around 245 B.C., Eratosthenes of Cyrene thought of a way to make the measurement directly. Eratosthenes hired a team of bematists (professional surveyors who measured distances by walking in equal-length steps called stadia) to walk from Syene to Alexandria. They found that the distance between the two cities was roughly 5,000 stadia.

Eratosthenes then visited a well in Syene that had been reported to have an interesting property: At noon on the summer solstice each year, the sun illuminated the well's bottom without casting any shadows. Eratosthenes went to Alexandria during the solstice, stuck a pole in the ground and measured the shadow from it to be about one-fiftieth of a complete circle. Pairing this with his measurement of the distance between the two cities, he determined that Earth's circumference was about 250,000 stadia, or 24,497 miles (39,424 km). Earth is now known to measure 24,901 miles (40,074 km) around the equator, making the ancient Greeks' measurements remarkably accurate.

Discovery of black holes

The acceptance of Einstein's theory of general relativity led to some startling predictions about our universe and the nature of reality. In 1915, Karl Schwarzschild's solutions to Einstein's field equations predicted that it was possible for mass to be compressed into such a small radius that it would collapse into a gravitational singularity from which not even light could escape — a black hole.

Schwarzschild's solution remained speculation until 1971, when Paul Murdin and Louise Webster used NASA's Uhuru X-ray Explorer Satellite to identify a bright X-ray source in the constellation Cygnus that they correctly contended was a black hole.

More conclusive evidence came in 2015, when the LIGO experiment detected gravitational waves from two of the colliding cosmic monsters. Then, in 2019, the Event Horizon Telescope captured the first image of the accretion disk of superheated matter surrounding the supermassive black hole at the center of the galaxy M87.

Discovery of X-rays

While testing whether the radiation produced by cathode rays could escape through glass in 1895, German physicist Wilhelm Conrad Röntgen saw that the radiation could not only do so, but it could also zip through very thick objects, leaving a shadow on a lead screen placed behind them. He quickly realized the medical potential of these rays — later known as X-rays — for imaging skeletons and organs. His observations gave birth to the field of radiology, enabling doctors to safely and noninvasively scan for tumors, broken bones and organ failure.

The Bell test

In 1964, physicist John Stewart Bell proposed a test to prove that quantum entanglement — the weird instantaneous connection between two far-apart particles that Einstein objected to as "spooky action at a distance" — was required by quantum theory.

The test has taken many experimental forms since Bell first proposed it, but the findings remain the same: Despite what our intuition tells us, what happens in one part of the universe can instantaneously affect what happens in another, provided the objects in each region are entangled.

Detection of the quark

In 1968, experiments at the Stanford Linear Accelerator Center found that electrons and their lepton cousins, muons, were scattering from protons in a distinct way that could only be explained by the protons being composed of smaller components. These findings matched predictions by physicist Murray Gell-Mann, who dubbed them "quarks" after a line in James Joyce's "Finnegans Wake."

Archimedes' naked leap from his bathtub

First recorded in the first century B.C. by Roman architect Vitruvius, Archimedes' discovery of buoyancy is one of the most famous stories in science. The prompting for Archimedes' finding came from King Hieron of Syracuse, who suspected that a pure-gold crown a blacksmith made for him actually contained silver. To get an answer, Hieron enlisted Archimedes' help.

The problem stumped Archimedes, but not long after, as the story goes, he filled up a bathtub with water and noticed that the water spilled out as he got in. This caused him to realize that the water displaced by his body was equal to his weight — and because gold weighed more than silver, he had found a method for judging the authenticity of the crown. "Eureka!" ("I've got it!") Archimedes is said to have cried, leaping from his bathtub to announce his discovery to the king.

Deepest and most detailed photo of the universe

In 2022, the James Webb Space Telescope unveiled the deepest and most detailed picture of the universe ever taken . Called "Webb's First Deep Field," the image captures light as it appeared when our universe was just a few hundred million years old, right when galaxies began to form and light from the first stars started flickering.

The image contains an overwhelmingly dense collection of galaxies, the light from which, on its way to us, was warped by the gravitational pull of a galaxy cluster. This process, known as gravitational lensing, brings the fainter light into focus. Despite the dizzying number of galaxies in view, the image represents just a tiny sliver of sky — the speck of sky blocked out by a grain of sand held on the tip of a finger at arm's length.

OSIRIS-REx asteroid-sampling mission

In 2023, NASA's OSIRIS-REx spacecraft came hurtling back through Earth's atmosphere after a years-long journey to Bennu, a " potentially hazardous asteroid " with a 1-in-2,700 chance of smashing cataclysmically into Earth — the highest odds of any identified space object.

The goal of the mission was to see whether the building blocks for life on Earth came from outer space. OSIRIS-REx circled the asteroid for 22 months to search for a landing spot, touching down to collect a 2-ounce (60 grams) sample from Bennu's surface that could contain the extraterrestrial precursors to life on our planet. Scientists have already found many surprising details that have the potential to rewrite the history of our solar system .

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Ben Turner is a U.K. based staff writer at Live Science. He covers physics and astronomy, among other topics like tech and climate change. He graduated from University College London with a degree in particle physics before training as a journalist. When he's not writing, Ben enjoys reading literature, playing the guitar and embarrassing himself with chess.

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1.6: Scientific Experiments

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Seeing Spots

The spots on this child's tongue are an early sign of vitamin C deficiency , which is also called scurvy. This disorder, which may be fatal, is uncommon today because foods high in vitamin C are readily available. They include tomatoes, peppers, and citrus fruits such as oranges, lemons, and limes. However, scurvy was a well-known problem on navy ships in the 1700s. It was said that scurvy caused more deaths in the British fleet than French and Spanish arms. At that time, the cause of scurvy was unknown and vitamins had not yet been discovered. Anecdotal evidence suggested that eating citrus fruits might cure scurvy. However, no one knew for certain until 1747, when a Scottish naval physician named John Lind did an experiment to test the idea. Lind's experiment was one of the first clinical experiments in the history of medicine.

What Is an Experiment?

An experiment is a special type of scientific investigation that is performed under controlled conditions. Like all investigations, an experiment generates evidence to test a hypothesis. But unlike some other types of investigations, an experiment involves manipulating some factors in a system in order to see how it affects the outcome. Ideally, experiments also involve controlling as many other factors as possible in order to isolate the cause of the experimental results.

An experiment generally tests how one particular variable is affected by some other specific variable. The affected variable is called the dependent variable  or outcome variable. The variable that affects the dependent variable is called the independent variable. It is also called the manipulated variable because this is the variable that is manipulated by the researcher. Any other variables ( control variable ) that might also affect the dependent variable are held constant, so the effects of the independent variable alone are measured.

Lind's Scurvy Experiment

Lind began his scurvy experiment onboard a British ship after it had been at sea for two months and sailors had started showing signs of scurvy. He chose a group of 12 sailors with scurvy and divided the group into 6 pairs. All 12 sailors received the same diet, but each pair also received a different daily supplement to the diet (Table \(\PageIndex{1}\)).

Lind's experiment ended after just five days when the fresh citrus fruits ran out for pair 5. However, the two sailors in this pair had already fully recovered or greatly improved. The sailors in pair 1 (receiving the quart of cider) also showed some improvement, but sailors in the other pairs showed none.

Can you identify the independent and dependent variables in Lind's experiment? The independent variable is the daily supplement received by the pairs. The dependent variable is the improvement/no improvement in scurvy symptoms. Lind's results supported the citrus fruit cure for scurvy, and it was soon adopted by the British navy with good results. However, the fact that scurvy is caused by a vitamin C deficiency was not discovered until almost 200 years later.

Lind's scurvy experiment included just 12 subjects. This is a very small sample by modern scientific standards. The sample in an experiment or other investigation consists of the individuals or events that are actually studied. It rarely includes the entire population because doing so would likely be impractical or even impossible.

There are two types of errors that may occur by studying a sample instead of the entire population: chance error and bias.

• A chance error occurs if the sample is too small. The smaller the sample is, the greater the chance that it does not fairly represent the whole population. Chance error is mitigated by using a larger sample.
• Bias occurs if the sample is not selected randomly with respect to a variable in the study. This problem is mitigated by taking care to choose a randomized sample.

A reliable experiment must be designed to minimize both of these potential sources of error. You can see how the sources of error were addressed in another landmark experiment: Jonas Salk's famous 1953 trial of his newly developed polio vaccine. Salk's massive experiment has been called the "greatest public health experiment in history."

Salk's Polio Vaccine Experiment

Imagine a nationwide epidemic of a contagious flu-like illness that attacks mainly children and often causes paralysis. That's exactly what happened in the U.S. during the first half of the 20th century. Starting in the early 1900s, there were repeated cycles of polio epidemics, and each seemed to be stronger than the one before. Many children ended up on life support in so-called "iron lungs" (see photo below) because their breathing muscles were paralyzed by the disease.

Polio is caused by a virus, and there is still no cure for this potentially devastating illness. Fortunately, it can now be prevented with vaccines. The first polio vaccine was discovered by Jonas Salk in 1952. After testing the vaccine on himself and his family members to assess its safety, Salk undertook a nationwide experiment to test the effectiveness of the vaccine using more than a million schoolchildren as subjects. It's hard to imagine a nationwide trial of an experimental vaccine using children as "guinea pigs." It would never happen today. However, in 1953, polio struck such fear in the hearts of parents that they accepted Salk's word that the vaccine was safe and gladly permitted their children to participate in the study.

Salk's experiment was very well designed. First, it included two very large, random samples of children — 600,000 in the treatment group, called the experimental group , and 600,000 in the untreated group, called the control group . Using very large and randomized samples reduced the potential for chance error and bias in the experiment. Children in the experimental group were injected with the experimental polio vaccine. Children in the control group were injected with a harmless saline (saltwater) solution. The saline injection was a placebo. A placebo is a "fake" treatment that actually has no effect on health. It is included in trials of vaccines and other medical treatments, so subjects will not know in which group (control or experimental) they have been placed. The use of a placebo helps researchers control for the placebo effect . This is a psychologically-based reaction to a treatment that occurs just because the subject is treated, even if the treatment has no real effect.

Experiments in which a placebo is used are generally blind experiments because the subjects are "blind" to their experimental group. This helps prevent bias in the experiment. Often, even the researchers do not know which subjects are in each group. This type of experiment is called a double-blind experiment because both subjects and researchers are "blind" to which subjects are in each group. Salk's vaccine trial was a double-blind experiment, and double-blind experiments are now considered the gold standard of clinical trials of vaccines, therapeutic drugs, and other medical treatments.

Salk's polio vaccine proved to be highly successful. Analysis of data from his study revealed that the vaccine was 80 to 90 percent effective in preventing polio. Almost overnight, Salk was hailed as a national hero. He appeared on the cover of Time magazine and was invited to the White House. Within a few years, millions of children had received the polio vaccine. By 1961, the incidence of polio in the U.S. had been reduced by 96 percent.

Limits on Experimentation

Well-done experiments are generally the most rigorous and reliable scientific investigations. However, their hallmark feature of manipulating variables to test outcomes is not possible, practical, or ethical in all investigations. As a result, many ideas cannot be tested through experimentation. For example, experiments cannot be used to test ideas about what our ancestors ate millions of years ago or how long-term cigarette smoking contributes to lung cancer. In the case of our ancestors, it is impossible to study them directly. Researchers must rely instead on indirect evidence, such as detailed observations of their fossilized teeth. In the case of smoking, it is unethical to expose human subjects to harmful cigarette smoke. Instead, researchers may use large observational studies of people who are already smokers, with nonsmokers as controls, to look for correlations between smoking habits and lung cancer.

Feature: Human Biology in the News

Lind undertook his experiment to test the effects of citrus fruits on scurvy at a time when seamen were dying by the thousands from this nutritional disease as he explored the world. Today's explorers are astronauts in space, and their nutrition is also crucial to the success of their missions. However, maintaining good nutrition in astronauts in space can be challenging. One problem is that astronauts tend to eat less while in space. Not only are they very busy on their missions, but they may also get tired of the space food rations. The environment of space is another problem. Factors such as microgravity and higher radiation exposure can have major effects on human health and require nutritional adjustments to help counteract them. A novel way of studying astronaut nutrition and health is provided by identical twin astronauts Scott and Mark Kelly (Figure \(\PageIndex{3}\)).

The Kellys are the first identical twin astronauts, but twin studies are nothing new. Scientists have used identical (homozygotic) twins as research subjects for many decades. Identical twins have the same genes, so any differences between them generally can be attributed to environmental influences rather than genetic causes. Mark Kelly spent almost a full year on the International Space Station (ISS) between 2015 and 2016, while his twin, Scott Kelly, stayed on the ground, serving as a control in the experiment. You may have noticed a lot of media coverage of Mark Kelly's return to Earth in March 2016 because his continuous sojourn in space was the longest of any American astronaut at that time. NASA is learning a great deal about the effects of long-term space travel on the human body by measuring and comparing nutritional indicators and other health data in the twins.

• How do experiments differ from other types of scientific investigations?
• Identify the independent and dependent variables in Salk's nationwide polio vaccine trial.
• Compare and contrast chance error and bias in sampling. How can each type of error be minimized?
• What is the placebo effect? Explain how Salk's experimental design controlled for it.
• Fill in the blanks. The _____________ variable is manipulated to see the effects on the ___________ variable.
• True or False. In studies of identical twins, the independent variable is their genetics.
• True or False. Experiments cannot be done on humans.
• True or False. Larger sample sizes are generally better than smaller ones in scientific experiments.
• Why do you think it was important that the sailors’ diets were all kept the same, other than the daily supplement?
• Can you think of some factors other than diet that could have potentially been different between the sailors that might have affected the outcome of the experiment?
• Why do you think the sailors who drank cider had some improvement in their scurvy symptoms?
• Explain why double-blind experiments are considered to be more rigorous than regular blind experiments.
• Why are studies using identical twins so useful?
• Do you think it is necessary to include a placebo (such as an injection with saline in a drug testing experiment) in experiments that use animals? Why or why not?

Explore More

Watch this entertaining TED talk, in which biochemist, Kary Mullis, talks about the experiment as the basis of modern science.

Check out this video to learn more about conducting scientific experiments:

Attributions

• Scorbutic tongue by CDC, public domain via Wikimedia Commons
• Iron lung ward by Food and Drug Administration, public domain via Wikimedia Commons
• Mark and Scott Kelly by NASA/Robert Markowitz, public domain via Wikimedia Commons
• Text adapted from Human Biology by CK-12 licensed CC BY-NC 3.0

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• Published: 19 March 2018

The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development

• Maria A. Schumacher 1   na1 ,
• Chris D. den Hengst 2   na1 ,
• Matthew J. Bush 2 ,
• T. B. K. Le   ORCID: orcid.org/0000-0003-4764-8851 2 ,
• Ngat T. Tran 2 ,
• Govind Chandra 2 ,
• Wenjie Zeng 1 ,
• Brady Travis 1 ,
• Richard G. Brennan 1 &
• Mark J. Buttner 2  

Nature Communications volume  9 , Article number:  1139 ( 2018 ) Cite this article

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• Bacterial transcription
• DNA-binding proteins
• Transcription factors
• X-ray crystallography

Streptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putative DNA-binding protein related to MerR regulators, but lacks coiled-coil dimerization and effector-binding domains characteristic of classical MerR proteins. Hence, the molecular function of the protein has been unclear. Here we show that BldC is indeed a DNA-binding protein and controls a regulon that includes other key developmental regulators. Intriguingly, BldC DNA-binding sites vary significantly in length. Our BldC-DNA structures explain this DNA-binding capability by revealing that BldC utilizes a DNA-binding mode distinct from MerR and other known regulators, involving asymmetric head-to-tail oligomerization on DNA direct repeats that results in dramatic DNA distortion. Notably, BldC-like proteins radiate throughout eubacteria, establishing BldC as the founding member of a new structural family of regulators.

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Introduction.

S treptomyces are ubiquitous, primarily soil-dwelling filamentous bacteria that undergo a complex developmental transition from vegetative growth to the production of reproductive aerial hyphae, which differentiate into chains of exospores 1 , 2 , 3 , 4 , 5 . Entry into development coincides with the biosynthesis of numerous secondary metabolites that serve as our most abundant source of clinically important antibiotics and provide other medically important drugs such as anticancer agents and immunosuppressants 6 , 7 , 8 . As a consequence, there is considerable interest in understanding the mechanisms that control this developmental transition. Genetic studies identified the regulatory loci that control entry into development, which are called bld (bald) genes because null mutations in these loci prevent the formation of fuzzy aerial hyphae for one of two diametrically opposite reasons: either because they block differentiation (mutations in activators) or because they cause precocious hyper-sporulation, bypassing the formation of aerial hyphae (mutations in repressors). The three Bld regulators that fall into this latter class are BldD, BldO, and BldC 4 , 9 , 10 , 11 , 12 . BldD is a transcriptional repressor that sits at the top of the developmental hierarchy and is regulated by cyclic-di-GMP (c-di-GMP). c-di-GMP mediates the dimerization of two BldD protomers, leading to DNA binding 4 , 9 , 13 , 14 , 15 . In this way, c-di-GMP drives repression of the large BldD regulon of sporulation genes, extending vegetative growth and inhibiting the hypha-to-spore transition 4 , 9 , 13 , 15 . Unlike the pleiotropic regulator BldD, BldO prevents entry into development by acting as the dedicated repressor of a single key developmental target, whiB 10 , 11 . Like BldD and BldO, BldC acts as a repressor to sustain vegetative growth, and so deletion of bldC causes the premature onset of sporulation 12 . To date, however, there has been no mechanistic insight into the way BldC prevents entry into development.

bldC encodes a 68-residue protein that is predicted to contain a winged helix-turn-helix (wHTH) motif, suggesting it may be involved in DNA binding. This wHTH shows the strongest sequence similarity to those of the MerR family of transcriptional activators 16 . The basic structure of classical MerR proteins is a dimer consisting of two identical subunits, each composed of an N-terminal wHTH DNA-binding domain, a C-terminal effector-recognition domain and an interconnecting linker region that consists of a long α helix that interacts with the same helix in the other subunit, forming an antiparallel coiled-coil responsible for homodimerization 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 . MerR proteins share significant sequence similarity only within their DNA-binding domains; as different family members bind different effectors, their C-terminal domains are variable and show little, if any, similarity to one another. Promoters controlled by classical MerR family regulators have unusually long (19–20 base pairs (bp) vs. 17 bp) spacers between their −10 and −35 promoter elements such that these motifs are misaligned for binding by the σ factor of the RNA polymerase (RNAP) holoenzyme, rendering the promoters inactive for transcription. Structures for several canonical MerR proteins have been solved in their apo and DNA-bound activated forms and reveal a conserved mode of transcription activation. Specifically, classical MerR proteins bind operators in the spacer between the −10 and −35 regions and when the C-terminal effector-recognition domain binds its cognate ligand, the transcription factor untwists and shortens the DNA, realigning the −10 and −35 sequences to allow RNAP holoenzyme to bind and activate transcription 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 .

While BldC appears to contain a MerR-like wHTH, it is to date, the only known MerR-like protein that consists entirely of a wHTH with no obvious effector or oligomerization domain. Interestingly, bioinformatic analysis shows that there are numerous BldC homologs in both Gram-negative and Gram-positive bacteria, suggesting that BldC represents a large family of putative DNA-binding proteins 16 . Despite this, the roles of BldC and its homologs remain unknown. Using a battery of structural, biochemical, and in vivo approaches, we show here that BldC functions as a pleotropic regulator of Streptomyces development by employing a unique mode of DNA binding for a transcription factor that involves asymmetric head-to-tail oligomerization on DNA direct repeats of varying number with concomitant distortion of the DNA. This mode of DNA binding defines a new family of transcription regulatory proteins that we designate the BldC family.

Identification of BldC binding sites in vivo

The presence of a putative wHTH in BldC suggests it functions in DNA binding and transcription regulation. Therefore, to identify possible BldC binding sites in vivo, we performed chromatin immunoprecipitation-microarray (ChIP-chip) using a polyclonal BldC antibody 16 . Figure 1a,b and Supplementary Data  1 present the results from two independent biological experiments. A congenic bldC null mutant was used as a control to eliminate any potential signals that might arise from cross-reaction of the antibody with other transcription factors. ~280 BldC-specific peaks were detected ( P -value <= 0.05, P -value based on empirical Bayes moderated t -statistic test), scattered across the genome (Fig.  1a and Supplementary Data  1 ). 25 BldC target genes encode regulatory proteins themselves (Supplementary Table  1 ), implying a pleiotropic role for BldC in Streptomyces development. Indeed, promoter sites bound by BldC are found upstream of genes encoding many key transcriptional regulators of the Streptomyces developmental cascade including bldM , whiB , whiD , whiH , whiI , sigF , and bldC itself, in addition to others encoding proteins involved in chromosome segregation and condensation during sporulation such as smeA - sffA 25 and hupS 26 (Fig.  1b and Supplementary Data  1 ) and genes that influence antibiotic production, specifically the conservon cvnA1 (ref. 27 ) and the serine-threonine protein kinase, afsK 28 . In parallel work, we used qRT-PCR to examine the expression of 5 key BldC targets ( whiI , smeA , whiD , sigF , and hupS ) in Streptomyces venezuelae comparing the wild type (WT) and a congenic bldC mutant. In each case, the gene was expressed earlier in the bldC mutant than in the WT, indicating that the transcription of these genes is directly regulated by BldC 12 . Both BldC and BldD inhibit entry into development 4 , 9 , 12 , and previously we identified ~160 genes controlled by BldD using ChIP-chip 4 , 9 , 15 . Comparison of genes bound by BldC or BldD showed only a small overlap of 15 genes/operons bound by both proteins (Supplementary Table  2 ). However, these include the key developmental genes whiB , whiD , bldM , smeA-sffA , bldC , and cvnA1 .

The S. coelicolor BldC regulon. a Chromosome-wide distribution of BldC binding sites identified by ChIP-chip analysis. DNA obtained from immunoprecipitation of BldC was labeled with Cy3 and hybridized to DNA microarrays together with a total DNA control labeled with Cy5. Data are plotted as Cy3/Cy5 ratios ( y -axis), as a function of chromosome location ( x -axis). b ChIP-chip data for nine selected BldC targets in WT S. coelicolor and the S. coelicolor ΔbldC mutant (blue and red dots, respectively). Plots span approximately 8 kb of DNA sequence. Gene names or identifiers (SCO numbers) are indicated below the arrows, which indicate gene orientation

BldC binding to the whiI promoter

To glean insight into the DNA binding mode of BldC, we performed DNase I protection studies on the promoter regions of two important BldC-regulated loci: whiI and the smeA-ssfA operon. whiI is among the key developmental targets of BldC (Fig.  1b and Supplementary Data  1 ), being essential for the late stages of sporulation 4 , 29 , 30 . whiI encodes an orphan response regulator that activates its regulon by forming a functional heterodimer with a second orphan response regulator, BldM 4 , 30 . DNase I protection studies on the whiI promoter show that BldC protects an ~30 bp region from –50 to –80, an unusual location from which to exert repression. Nevertheless, RNA analysis shows that whiI transcription comes on much earlier in a bldC mutant than in the WT 12 indicating it is regulated by BldC. The BldC-protected region harbors an imperfect direct repeat and two sites of enhanced DNase I cleavage are observed on the top strand, suggesting that BldC binding may distort DNA (Fig.  2 ). Notably, the enhanced cleavages also appear periodic in nature, falling on approximately the same face of the DNA and within the imperfect direct repeats (Fig.  2 ). To gain more insight into the specific sequence and minimal length requirement for high affinity DNA binding by BldC, we performed EMSA analyses employing a variety of DNA duplexes based on the whiI site that ranged from 16 to 30 bp (Supplementary Fig.  1 ). These analyses identified the 22-bp sequence, top strand 5′-TGTGTCCGAATTGCTCGGATTG-3′ as the shortest DNA duplex that bound BldC. Binding to this sequence by BldC was subsequently optimized by introducing 3 base changes, which also allowed the DNA duplex to be shortened to 20 bp, 20R sym, with a top strand sequence, 5′-TGTCCGAATTGTCCGAATTG-3′ (Supplementary Fig.  1 ). Two of these changes are naturally present in the whiI promoter of the alternative model species S. venezuelae and the amino acid sequences of BldC from Streptomyces coelicolor and S. venezuelae are identical.

BldC binding to the whiI promoter region. a DNase I footprinting analysis. 5′ end-labeled probes were incubated with increasing amounts of BldC (indicated in µM above the lanes) and subjected to DNase I footprinting analysis as described in Methods. Footprints are flanked on the left-hand side by Maxam and Gilbert sequence ladders (AG). Horizontal black arrows indicate sites of enhanced DNase I cleavage on the forward strand and the vertical bar indicates the region of DNase I protection on the reverse strand. b Summary of DNase I footprinting results presented in a . The bracket indicates the protected region and the vertical black arrows indicate sites of enhanced DNase I cleavage. The numbers indicate the distance to the 5′ end of the whiI transcript. The direct repeats shown to be bound by BldC in a head-tail orientation are indicated by arrows (with arrows pointing in the head-tail direction)

BldC binding to the smeA-sffA promoter

Another key target regulated by BldC is the smeA-sffA operon (Fig.  1b and Supplementary Data  1 ). The smeA-sffA operon encodes a DNA translocase (SffA) involved in chromosome segregation during sporulation that is specifically targeted to septa by the small membrane protein SmeA 25 . Deletion of smeA-sffA results in a defect in spore chromosome segregation and has pleiotropic effects on spore maturation 25 . Strikingly, in contrast to the ~30 bp BldC-protected region in the whiI promoter, BldC protects a much larger region of the smeA-sffA promoter, extending approximately from –60 to –10 relative to the transcription start site. A regular pattern of hypersensitive sites on the top strand is observed in the footprint (Fig.  3a,b ). While the BldC-binding site in the whiI promoter contains two direct repeat elements, the BldC binding site within the smeA-sffA promoter reveals four similar repeats, but arranged in the opposite orientation, 5′ to 3′ (see Fig.  3a,b ). To explore BldC binding to the smeA-sffA promoter further, a finer analysis was undertaken using hydroxyl radical footprinting. BldC protects four regularly spaced 5-bp tracts, with one helical turn of the DNA between one tract and the next (Fig.  3b,c ), suggesting that four molecules of BldC bind the smeA-ssfA promoter. However, only one shift is observed in EMSA analyses of BldC binding to the smeA-sffA site, suggesting that BldC binds this extended site cooperatively (Supplementary Fig.  2 ).

BldC binding to the smeA-ssfA promoter region. a DNase I and b hydroxyl radical footprinting analysis. 5′ end-labeled probes were incubated in the presence (1 µM) or absence of BldC and subjected to footprinting analysis as described in Methods. Footprints are flanked on the left-hand side by Maxam and Gilbert sequence ladders (AG). Horizontal black arrows indicate sites of enhanced cleavage and vertical bars indicate regions of DNase I protection. c Summary of the footprinting results presented in a and b . The filled black circles indicate the repeat pattern of bases protected from hydroxyl radical attack. The bases colored red and blue indicate the DNase I-protected sequences on the forward and reverse strands, respectively, and the vertical black arrows indicate the repeat pattern of DNase I hypersensitive sites seen on the top strand in the presence of BldC. The numbers indicate the distance to the 5′ end of the smeA transcript. Direct repeat motifs are indicated by head-to-tail arrows

BldC-DNA structure reveals MerR-like structural family

The mechanism by which BldC binds sites with variable numbers of direct repeat elements is unclear, but it is likely to differ from that used by other MerR transcriptional regulators, which function as symmetric dimers that bind palindromic DNA sites. Consistent with this hypothesis, the BldC protein does not contain a canonical MerR family dimerization domain. Further, unlike classical MerR proteins, size exclusion chromatography (SEC) studies showed that apo BldC is a monomer (Supplementary Fig.  3 ). Thus, to deduce the molecular mechanism underlying DNA binding and recognition by BldC, we determined the structure of S. coelicolor BldC bound to a 22 bp double-stranded DNA based on the optimized whiI binding site ( whiI opt). The structure was solved by single wavelength anomalous diffraction (SAD) using data collected from a selenomethionine-substituted BldC(L43M-L58M)- whiI opt DNA crystal (WT BldC- whiI opt produced the same crystals) and refined to R work / R free values of 22.3%/26.8% to 3.28 Å resolution (Supplementary Table  3 and Supplementary Fig.  4 ). Notably, the structure reveals that BldC forms a head to tail (head-tail) dimer on the DNA whereby each BldC protomer binds to a 9 bp direct repeat with the recognition helix of the HTH motif interacting in the major groove and the wing in the minor groove (Fig.  4a,b ). Because the BldC dimer is asymmetric it binds head-tail with a specific directionality, which is 5′ to 3′ with the sequence, 5′-CAATTCGGACAATTCGGACA-3′ (Fig.  4d,e and Supplementary Fig.  1 ). Formation of the head-tail BldC dimer buries ~600 Å 2 of protein surface from solvent. The oligomer interface is largely hydrophobic with residues Phe21, Val23, and Trp31 packing against the side chains of Leu11′, Ile 40′, Thr42′, Leu43′, and Gly44′ (where ′ indicates the other subunit of the DNA-stabilized dimer) (Fig.  4c and Supplementary Fig.  5 ). Hydrogen bonds/electrostatic contacts between the side chains of Arg22 and Glu16′ help fasten the two subunits together (Fig.  4c and Supplementary Fig.  5 ). While the buried surface area of the DNA-bound BldC dimer is significant for such a small protein it is much less than that observed in stable dimers, likely explaining why BldC must be anchored to its cognate DNA to assemble the asymmetric dimer.

Structure of the BldC- whiI opt DNA complex. a Overall BldC- whiI opt structure with one BldC subunit colored cyan and the other magenta. The secondary structural elements are labeled. The head-tail directionality of BldC binding is indicated by an arrow. b Electrostatic surface representation of the structure rotated by 90° relative to a . Blue and red represent electropositive and electronegative regions, respectively. c Contacts important in BldC head-tail dimerization on the DNA. The side chains that mediate dimer formation are shown as sticks. The contacts between Arg22 and Glu16 from apposing subunits are shown as dashed lines. d BldC-DNA contacts. Residues that contact the DNA are shown as sticks and labeled. e Schematic ladder diagram showing the contacts between BldC and DNA. Note, for clarity, the 2 bp overhangs that are not contacted by BldC are not included. f FP binding isotherms of various BldC proteins binding to a fluorescently labeled whiI opt 22mer. Experiments were preformed in technical triplicate and the error between measurements noted. Shown are representative binding isotherms for WT His 6 -BldC (red squares), His 6 -Semet BldC(L43M-L58M) (green diamonds), Tag-free WT BldC (blue circles), His 6 -BldC(E16R) (black crosses), His 6 -BldC(G44E) (orange squares), His 6 -BldC(H46A) (light blue triangles) and His 6 -BldC(R30A) (yellow diamonds). The resulting K d s for these curves are 18.2 nM ± 4.8 nM, 19.6 nM ± 4.8 nM, 16.5 nM ± 4.0 nM, 140 nM ± 63 nM, no saturable binding (NB), NB and NB, respectively. The y -axis and x -axis are mP and BldC concentration (nM), respectively

The DNA binding mode exhibited by BldC is notably distinct from that used by classical MerR proteins, all of which bind palindromic DNA sites as symmetric dimers 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 (Supplementary Fig.  6a ). The head-tail binding of the two BldC protomers bends the whiI site by ~50°. The helical twist (35.1°) and rise per base pair (3.25 Å) of the BldC-bound DNA remains similar to B-DNA (36.0° and 3.32 Å, respectively). However, the minor and major groove widths are significantly distorted: the wing-bound, AT-rich minor groove has an average width of 9.3 Å (compared to 12.0 Å for B-DNA) whereas the minor groove outside this region is widened significantly (14.5 Å). The major groove in which the recognition helix docks is expanded to 19.4 Å compared 17.2 Å for B-DNA. Despite employing a DNA binding mode different from classical MerR proteins, the BldC wHTH indeed harbors a fold that is highly similar to these proteins. The BldC structure follows the typical MerR topology: α1 (BldC residues 14–21), α2 (25–34), β1 (38–42), β2 (45–48), and α3 (51–60) (Fig.  4a ). Moreover, DALI searches indicate that the BldC wHTH shows significant structural similarity to the wHTH domains of the MerR proteins with which it superimposes with root mean square deviations (rmsds) of 1.7–2.2 Å for 45–58 corresponding Cα atoms. The superimposition of BldC onto the wHTH of the MerR protein MtaN underscores the homology between the wHTHs but also the lack of the dimerization coiled-coil in BldC (Supplementary Fig.  6b ).

Molecular basis of DNA binding specificity of BldC

Each BldC subunit makes a large number of phosphate and base contacts, allowing for high affinity BldC binding. The side chains of BldC residues Thr27, Thr29, and Lys33 and the amide nitrogens of Ala15 and Asp24 from the HTH anchor the wHTH on the DNA via phosphate contacts to both DNA strands. The Trp31 side chain also interacts with the phosphate backbone via its Nε and induces a kink in the DNA (Fig.  4d,e ). The BldC wing is particularly rich in basic residues with Arg47 and Arg48 providing key contacts that aid in docking the wing into the minor groove. The combined DNA-binding region of the two interacting BldC subunits also presents a striking electropositive surface that complements the bound DNA (Fig.  4b ).

The DNA-binding specificity of BldC is mediated by residues from both its wing and its HTH. Residues from the wing recognize the AT-rich narrowed minor groove. The His46 side chain fits within the narrowed groove and makes numerous hydrogen bonds and van der Waals contacts with sugar and phosphate moieties (Fig.  4d ). The importance of the AT-rich motif in BldC binding sites was assessed by fluorescence polarization (FP) binding assays. These studies showed that replacement of the AATT motif with GGCC abrogated DNA binding (Supplementary Fig.  7 ). Major groove base contacts are provided by BldC residues Arg30 and Lys26, both located on the recognition helix of the HTH. The relatively low resolution of the structure prevents a highly detailed description of protein-DNA contacts and the possible role of waters in the protein-DNA interface. However, despite the low resolution, the electron density for the Arg30 side chain is clear and reveals that it provides highly specific, bidentate hydrogen bonds to Gua2′ and Gua11′ (Fig.  4d,e and Supplementary Fig.  8 ). Simultaneously, the Arg30 guanidinium groups stack with the bases of Thy1′ and Thy10′, which are located 5′ of the contacted guanine (Fig.  4d,e and Supplementary Fig.  9 ). This type of specific protein-DNA contact has been called a 5′-pyrimidine-guanine-3′ (5′-YpG-3′) interaction and it arises from the inherent flexibility of pyrimidine-guanine steps. A survey of the protein database by Glover and coworkers showed that diverse classes of DNA-binding motifs utilize this DNA recognition element 31 , 32 , 33 . This type of contact mediates specific binding to two bases whereby an arginine side chains interacts with the major groove face of the 5′-guanine nucleobase and also contacts the unstacked preceding pyrimidine 31 , 32 . The side chain of BldC residue Lys26 also makes base contacts. However, the electron density for the Lys26 side chain is less well resolved than that of the Arg30 side chain suggesting it is conformationally flexible. Moreover, while the Lys26 side chain is within hydrogen bonding distance of major groove guanines from bps 7, 8, and 17 (Fig.  4e ), it could also interact with thymine O4 atoms in other sequences, suggesting that it may not dictate complete readout specificity of major groove bases. Indeed, binding studies revealed that replacement of the guanines at bp8 and bp17 with thymine (Fig.  4e ) had little effect on binding (app K d of WT = 20 nM compared to 50 nM ± 1.1 nM for the T mutant), while replacement of the guanines with cytosines resulted in a nearly 6-fold reduction in binding (app K d  = 115 nM ± 10 nM) (Supplementary Fig.  7 ). Hence, the flexible contacts provided by this residue may contribute to the range of sequences that BldC can bind within select promoters.

Thus, the analysis of the BldC- whiI opt structure indicates that there are two main DNA elements specifically recognized by BldC; an AT-rich region and a C-G, 4 base pairs downstream from the AT-rich region, which is recognized by Arg30. The consensus direct repeat for binding by each BldC protomer is, therefore, AATTXXXX(C), where the C represents the C-G bp containing the guanine recognized by Arg30. Because the BldC dimer binds direct repeats in a head-tail manner, its interaction with the DNA is also directional. As a result, BldC binds whiI opt and the WT whiI promoter in a reverse orientation, i.e., the BldC dimer is arranged head-tail, 5′ to 3′ on the bottom strand of the DNA (Figs.  2 , 4a ).

Probing the BldC-DNA structural model

The BldC-DNA structure revealed several unexpected findings for a MerR-like protein, in particular a direct repeat DNA binding mode involving the formation of a head-tail dimer. Thus, to further test the structural model, we mutated several residues observed to be important for DNA binding in the structure as well as those involved in dimer formation and carried out FP DNA binding assays. The WT protein, with or without the his 6 -tag, and the selenomethionine BldC(L43M-L58M) protein bound the 22 bp whiI opt DNA with essentially the same K d (~20 nM) (Fig.  4f ). An E16R mutation, which would disrupt the dimer stabilizing contact with Arg22 (Fig.  4c ), resulted in a ~10-fold reduction in DNA binding while a G44E substitution, which places a large, negatively, charged residue at the hydrophobic interface of the dimer and hence is predicted to disrupt the head-tail dimer, led to complete loss of DNA binding (Fig.  4f ). Individual substitution of residues His46 and Arg30, which make key contacts to the minor and major grooves, respectively, with a glutamate (H46E) or an alanine (R30A), also essentially abrogated DNA binding (Fig.  4f ). Thus, these combined data support the unusual mode of DNA binding observed in the BldC-DNA structure. Importantly, circular dichroism (CD) analyses showed that all mutant BldC proteins were properly folded and exhibited the same CD spectrum as WT BldC (Supplementary Fig.  10 ).

BldC- smeA-ssfA structure shows extended protein-DNA filament

The head-tail mode of DNA binding observed in the BldC- whiI opt structure (Fig.  4 ) could permit the formation of continuous protein–DNA complexes through extension at one or both ends of the asymmetric dimer, which could explain the mechanism which BldC utilizes to interact with longer DNA binding sites such as that of the smeA-sffA promoter. The BldC protected region in the smeA-ssfA promoter region contains four AATTXXXX(C) motifs similar those in the whiI site (5′-AATTCGGT C -3′, 5′-GATTTCCC C -3′, 5′-CATTTGCA C -3′, and 5′-CTTTTATC G -3′, where the C-G bp recognized by Arg30 is underlined) (Fig.  3 ). But, in the smeA-ssfA promoter these repeats proceed in a 5′ to 3′ direction and the last repeat does not conform to the consensus (Fig.  2 ). However, conservation of the exact consensus sequence does not appear to be critical for specific binding, in particular for the AT-rich region, as it is the narrowing of the minor groove caused by the AT-rich nature of that sequence that is important. This so-called indirect readout 33 based on the shape of the minor groove as well as the pliability in contacts afforded by the Lys36 side chain in the major groove likely allows BldC to bind DNA sites that harbor differences from the consensus. As a result, BldC might be able to interact with sites that contain repeats that diverge from the consensus in longer DNA sites provided there are consensus sites to enable the docking of subunits that can then enable binding by other protomers. This binding mode predicts that multiple BldC subunits might bind a DNA site such as the smeA-ssfA operator. To address this issue, we determined the K d and stoichiometry of BldC binding to the 22mer whiI opt site, to an extended 36-mer opt site that contains four perfect direct repeats and to the smeA-ssfA site. BldC bound these DNA sites with apparent affinities ( K d s) of 20, 20, and 60 nM, respectively, and displayed binding stoichiometries (BldC subunits per DNA duplex) of 2:1, 4:1, and 4:1, respectively (Fig.  5a ). These data, therefore, support the hypothesis that multiple BldC subunits can bind cooperatively to extended DNA sites.

BldC binds DNA to form extended protein-nucleic acid superstructural filaments. a FP-based stoichiometry binding experiments performed with fluoresceinated 22mer opt, 36mer opt (containing 4 binding repeats), and the smeA-ssfA BldC site, each experiment was conducted in technical triplicate with a representative analysis shown for each. For the experiments, DNA was present at a concentration 10-fold above the K d s, which are 20, 20, and 60 nM, respectively. Binding was observed as increasing mPs until saturation, at which the mPs no longer increase. The inflection point of each binding isotherm represents the subunit protein concentration at saturation. This occurred at BldC: DNA duplex stoichiometries of 2:1, 4:1, and 4:1, respectively. b Structure of the BldC- smeA-ssfA promoter complex. The DNA packs pseudo-continuously. The unit corresponding to the BldC- smeA-ssfA complex is boxed. Two views are shown. Left is a view looking down the axis of the structure and right shows the view rotated 90°. The structure shows how BldC could bind promoters with longer sites than present in the smeA-ssfA promoter. c Electrostatic representation of the structure with blue and red, representing electropositive and electronegative regions. Notably, the continuous protein superstructure also forms a continuous electropositive stripe that tracks along the DNA

To deduce the molecular basis for this extended binding we next determined the structure of BldC in complex with an 18mer smeA-ssfA DNA fragment that contained the first two repeats of the smeA-ssfA BldC binding site, 5′-GCAATTCGGTCGAATTTC-3′ (Fig.  3b ). The DNA was constructed to generate pseudo-continuous packing of the DNA, which was indeed generated in the crystals (see Methods). The structure was solved by molecular replacement (MR) and refined to R work / R free values of 20.9%/27.8% to 3.09 Å resolution (Supplementary Table  3 ). The structure reveals a striking extended protein-nucleic acid filament with multiple BldC subunits arranged in the same head-tail manner as observed in the BldC- whiI opt structure (Figs.  5b,c and  6a ). The asymmetric BldC dimer contacts and DNA docking mode in this structure are identical to those observed in the BldC- whiI opt structure. Because the DNA is pseudocontinuous, the register of the DNA sequence in this structure was unclear. Indeed, due to the continuous stacking of the DNA, it was possible that the 9 bp sites bound by each BldC subunit are statistically disordered (half of the time containing one 9 bp sequence and the other half, the other 9 bp sequence). That is the stacking of the 18mer, end to end, creates two BldC repeats with consensus repeats, AATTCGGT C and GAATTTCG C , which conserves the CG bp recognized by Arg30 (underlined). To address the possibility that the DNA may be statistically disordered, X-ray intensity data were collected on a crystal grown with DNA containing a thymine to 5-iododeoxyuracil substitution (5′-GTAAXTCGGTCGAATTTC-3′, where X is 5-iododeoxyuracil). An electron density difference map revealed no strong electron density peaks for the iodine indicating that the DNA is statistically disordered.

Comparison of B-DNA to BldC bound DNA. a Comparison of the BldC- whiI opt and BldC- smeA-ssfA structures. BldC forms identical head-tail dimers in both structures. b The cooperative binding of multiple BldC subunits significantly distorts and shortens the DNA

While the DNA contacts in this structure are statistically disordered, the structure reveals how multiple BldC subunits can bind a promoter site with multiple cognate repeats to create an extended protein superstructure. This superstructure results in a continuous electropositive patch that tracks along the length of the DNA (Fig.  5c ). This regular superstructure would also explain the periodic hypersensitivity revealed in the DNase I protection experiments. The continuous coating of its DNA site by BldC binding also suggests one obvious mechanism of transcription repression via sterically restricting access of RNAP to the promoter. This mechanism would be at play despite the directionality of the BldC head-tail oligomer along the DNA. The binding of multiple BldC subunits along the DNA also leads to severe DNA distortion and shortening: the BldC subunits reduce the length of the DNA by a third when compared to canonical B-DNA (Fig.  6b ). Consequently, the DNA has an overall positive writhe.

Our combined data reveal that while BldC harbors a MerR-like wHTH motif, it binds DNA in a manner distinct from classical MerR family proteins 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 . Interestingly, recent structural studies on other non-MerR proteins have revealed wHTH domains with structural similarity to the MerR wHTH. For example, structural analyses of the master regulators of nitrogen metabolism in B. subtilis , TnrA and GlnR, revealed that both proteins have a MerR-like wHTH motif, however both TnrA and GlnR lack the coiled-coil domain of classical MerR proteins but instead contain N-terminal extensions and unstructured C-terminal regions 34 . Instead of using the canonical coiled-coil, TnrA and GlnR dimerize upon DNA binding through residues in their N-terminal regions and use their C-terminal regions to interact with glutamine synthetase (GS) 34 . In common with canonical MerR proteins, however, both TnrA and GlnR bind as homodimers to palindromic DNA sites. Structural homology searches also uncovered architectural DNA binding proteins that do not function in transcription, including RacA and Xis, which harbor wHTH structures similar to MerR proteins 35 , 36 , 37 .

Interestingly, BldC appears similar to classical MerR proteins in that it makes few base specific contacts. Indeed, the structures of BmrR, MtaN, and CueR bound to DNA revealed that only one to two residues make base contacts per subunit 17 , 19 , 20 . This is consistent with MerR proteins employing indirect readout as part of their DNA binding mechanisms. Notably, unlike canonical MerR regulators, the MerR-like protein RacA was observed to make YpG contacts using an arginine that is equivalent to the BldC residue Arg30 36 . However, aside from this similarity, RacA and BldC utilize very different DNA binding mechanisms. In particular, the interaction of RacA with its GC-rich DNA site does not lead to global DNA bending but causes a significant widening of its entire minor groove. By contrast, BldC binding induces significant global bending in its bound DNA and a narrowing of the AT-rich minor grooves. Also, unlike RacA, which binds DNA as a symmetric dimer, BldC binds direct repeats in a head-tail manner. To our knowledge, BldC is the only MerR-like transcription regulator that binds direct repeats and employs only its wHTH domain for DNA contact and oligomerization. Bacterial transcription regulators that bind DNA direct repeats appear less common than those that bind palindromic DNA sites as symmetric dimers. Well characterized examples of bacterial regulators, other than BldC, that bind direct repeats include some members of the large family of two component response regulators (RR) 38 , 39 , 40 . RRs harbor N-terminal receiver domains flexibly attached to DNA-binding domains. More than 95% of characterized RRs utilize a HTH DNA-binding domain while the remaining 5% of RRs employ a LytTR domain for DNA binding. Structures have been obtained for both these types of DNA-binding domain, revealing that some RRs, such as PhoP, PmrA, and AgrA,  bind DNA direct repeats. Studies on the RR AcrA revealed that, like BldC, it can bind multiple tandem repeats 41 , however a structure is not yet available of the full length AcrA bound to cognate DNA elements.

Finally, bioinformatic analyses reveal that small, BldC-like proteins radiate throughout the domain of bacteria, being present in ~500 species, including actinomycete pathogens ( Mycobacterium tuberculosis and Corynebacterium diphtheriae ), commercially important actinomycetes ( Corynebacterium glutamicum ), and other Gram-positive (e.g ., Bacillus thuringiensis ) and Gram-negative bacteria (e.g., Sinorhizobium meliloti and Porphyromonas gingivalis ) (Supplementary Fig.  11a ). Sequence analysis shows strong conservation of key DNA-binding and head-tail oligomerization residues in BldC-like proteins in the actinomycetes. More distant members of the BldC family also contain hydrophobic residues in regions involved in head-tail dimer formation (Supplementary Fig.  11a ). However, key residues involved in BldC head-tail dimer formation are not conserved in classical MerR family proteins. In particular, Leu43, which interacts with Trp31ʹ and Phe21ʹ to form the key hydrophobic core of the BldC head-tail dimer, is replaced by a charged residue (glutamic or aspartic acid) in ZntR, CueR, MtaN, and BmrR, or by a polar residue (serine, tyrosine or histidine) in SoxR, MerR, and TipAL (Supplementary Fig.  11b ). Modeling indicates that such charged or polar residues would prohibit formation of a head-tail dimer as they would be placed proximal to hydrophobic side chains. These findings suggest that, unlike classical MerR proteins, the other BldC-like proteins identified bioinformatically are likely to have the same DNA binding mode observed for BldC itself, and that they can likewise form extended protein-nucleic acid superstructures. In that regard, it is interesting to note that some BldC-like orthologues in the database are annotated as possible resolvases/integrases, consistent with our finding that BldC shares strong structural similarity to Xis. These findings suggest formerly overlooked, possible evolutionary connections between MerR transcription regulators and integrases and DNA architectural proteins.

Cell culture, strains, plasmids, and oligonucleotides

Strains and plasmids used in this study are listed in Supplementary Table  4 . Oligonucleotides used are listed in Supplementary Table  4 unless given in the text. Streptomyces coelicolor strains were grown on mannitol soy flour (MS, also known as SFM) or R5 solid media 42 . Strains used for ChIP-chip analysis were grown in a 1:1 mixture of yeast extract-malt extract (YEME) and tryptic soy-broth (TSB) liquid media 42 at 30 °C.

Chromatin immunoprecipitation-microarray studies

To carry out the ChIP-chip experiments, S. coelicolor M600 was grown in duplicate for 15 h in YEME/TSB liquid medium and a single culture of the congenic bldC null mutant strain J2166 was grown in the same way as the control. Formaldehyde was added to cultures at a final concentration of 1% (v/v) and incubation was continued for 30 min. Glycine was then added to a final concentration of 125 mM to stop the cross-linking. Cultures were left at room temperature (RT) for 5 min before the mycelium was harvested and washed twice in PBS buffer pH 7.4. Each mycelial pellet was resuspended in 0.5 ml lysis buffer (10 mM Tris HCl pH 8.0, 50 mM NaCl) containing 15 mg/ml lysozyme and protease inhibitor (Roche Applied Science) and incubated at 25 °C for 1 h. Subsequently, 0.5 ml IP buffer (100 mM Tris HCl pH 8, 250 mM NaCl, 0.5% Triton-X-100, 0.1% SDS) containing protease inhibitor was added and samples were chilled on ice. Samples were sonicated for 7 cycles of 15 s each at 10 microns to shear the chromosomal DNA into fragments ranging from 300–1000 bp in size. Samples were centrifuged twice at 34,000 ×  g at 4 °C for 15 min to clear the cell extract, after which 10 µl of cell extract was set aside for total DNA extraction. The remainder (900 µl) was incubated with 45 µl protein A-sepharose (Sigma) for 1 h on a rotating wheel to clear from non-specifically binding proteins. Samples were then centrifuged for 15 min at 4 °C and 34,000 ×  g to remove the beads. Supernatants were incubated with 75 μl crude anti-BldC antiserum (76 mg/ml; custom made [16]) overnight at 4 °C with rotation. Subsequently, 90 µl protein A-sepharose was added to precipitate BldC and incubation was continued for 4 h. Samples were centrifuged for 5 min and the pellets were washed twice with 0.5x IP buffer, then twice with 1x IP buffer. Each pellet was incubated overnight at 65 °C in 150 µl IP elution buffer (50 mM Tris HCl pH 7.6, 10 mM EDTA, 1% SDS) to reverse cross-links, and 10 µl of the total cell extract control was treated in the same way. Samples were centrifuged at 34,000 × g for 5 min to remove the beads. Each pellet was re-extracted with 50 µl TE buffer (10 mM Tris HCl pH 7.4, 1 mM EDTA) and the resulting supernatant was combined with the primary supernatant and incubated with 0.2 mg/ml Proteinase K (Roche) for 2 h at 55 °C. The resulting samples were extracted with phenol-chloroform and further purified using QiaQuick columns (Qiagen). DNA was eluted in 50 µl EB buffer and quantified using a NanoDrop spectrophotometer (Thermo Scientific).

DNA labeling and hybridization to DNA microarrays were carried out by using a Bio-Prime kit (Invitrogen). Briefly, for these experiments 800 ng of the total and immuno-precipitated DNA was labeled with Cy5-dCTP and Cy3-dCTP, respectively. Using an Agilent Technologies hybridization oven, the labeled DNA was hybridized to high-density DNA microarrays representing the genome of S. coelicolor , which were designed and manufactured by Oxford Gene Technology (OGT). Following washing, the arrays were read using an Agilent Technologies scanner and the Cy5 and Cy3 signals were quantified using Agilent’s Feature Extraction software.

From the data files received from OGT, columns relevant for further analysis were extracted using a bespoke Perl script. This resulted in three files (two for the WT replicates and one for the control) containing the following columns: name of the probe; start of the probe on the S. coelicolor genome; end of the probe on the S. coelicolor genome; median green (Cy3) signal intensity; median red (Cy5) signal intensity; the probe sequence. Each of the three files obtained above was read into R and the Cy3 and the Cy5 signals were transformed to their log2 values and normalized using the normalizeQuantiles function of the Bioconductor package limma. Log ratios of the Cy3–Cy5 signals were then calculated and normalized to the average signal intensity using the loess function of R. The three sets of normalized log ratios obtained were put in a single data frame in R. After making the design and contrasts matrices appropriate for the data, the limma functions lmFit, contrasts.fit and eBayes were applied in sequence. Finally, the function toptable was used to generate a table of probes listing enrichment ratios of the WT relative to the bldC mutant control, ordered by P -values (determined by empirical Bayes moderated t -statistic test) adjusted using the method of Benjamini and Hochberg 43 . Signals around probes with P -values less than or equal to 0.05 were then plotted and inspected manually to determine whether they were part of a signal peak or not.

Purification of BldC

Plasmid pIJ6838, a pET15b (Novagen) derivative expressing his-tagged full-length BldC, was introduced into E. coli BL21(DE3) and grown in Luria-Bertani liquid medium. Following IPTG induction for 3 h at 30 °C in the presence of 0.3 mM IPTG, a microfluidizer was used to disrupt cells. The lysate (in Buffer A: 25 mM Tris HCl pH 7.5, 300 mM NaCl, 5% glycerol) was loaded onto a nickel-nitrilotriacetic acid (Ni-NTA) column. The his-tagged BldC was eluted using increasing concentrations of imidazole in Buffer A. For protein used for crystallization trials, an additional SEC purification step was included. The protein was >95% pure after this step.

In vitro DNA binding assays

DNase I footprinting experiments were carried out similar to previous studies 44 and according to the method supplied with the Sure Track footprinting kit (GE Healthcare). Specifically, DNA fragments were prepared by PCR using the oligonucleotides pairs 6029_F1 and 6029_R1 and 1415_F2 and 1415_R2 to generate DNA probes spanning the BldC-binding sites in the whiI and smeA-ssfA promoters, respectively. Oligonucleotides were first end-labeled with T4 polynucleotide kinase (GE Healthcare) and [γ- 32 P]-ATP as described by the manufacturer. Binding reactions were performed in a total volume of 40 μl containing 10 mM Tris HCl pH 7.8, 150 mM NaCl, 2 mM dithiothreitol, 1 µg poly(dI-dC) (Roche), and 10% (v/v) glycerol in the presence of approximately 110,000 cpm of the DNA probe. Following DNase I treatment and purification, products were separated on denaturing 6% (w/v) polyacrylamide gels and visualized using a FLA-7000 phosphorimager (Fujifilm).

Hydroxyl radical footprinting was performed using a protocol similar to that described previously 45 . Specifically, the binding reactions and probes were identical to those used for the DNase I footprinting experiments, but in a total volume of 25 μl and in the absence of glycerol. After 20 min at RT, Fe(NH 4 ) 2 (SO 4 ) 2 , and EDTA were added to final concentrations of 10 µM and 20 µM, respectively, followed by the addition of sodium ascorbate to 1 µM and H 2 O 2 to 0.015% (v/v). Reactions were incubated for a further 1–4 min at RT before quenching the reaction with 9 μl stop solution (27.77 mM thiourea, 27.77 mM EDTA, 1 M Na acetate, containing 25 μg yeast tRNA). Samples were precipitated with three volumes of ethanol, re-dissolved in stop solution, phenol–chloroform extracted and analyzed in the same way as the DNase I footprints.

Electrophoretic mobility shift assays (EMSAs) were carried out using a DNA probe containing the BldC-binding site from the smeA-sffA promoter, radiolabelled on the forward strand. The probe was generated by PCR using the oligonucleotides 1415_F2 and 1415_R2. For EMSA experiments, increasing concentrations of BldC protein was added from 0.004 μM to 1.2 μM. The reaction samples were incubated for 20 min at RT and then run on 5% polyacrylamide gels.

Crystallization and determination of BldC-DNA structures

The his-tag was removed from BldC prior to crystallization trials using a thrombin capture cleavage kit (Qiagen). Crystals of BldC bound to an optimized version of the whiI DNA site were obtained by hanging drop vapor diffusion. The DNA (termed whiI opt) contained TT and AA overhangs (top strand: 5′- TT CAATTCGGACAATTCGGACA-3′). For crystallization, BldC was concentrated to 0.5 mM before mixing with 0.5 mM double stranded whiI opt DNA and this complex then combined 1:1 with a crystallization solution consisting of 30% MPD, 0.1 M sodium acetate pH 5.0, and 25% PEG 1500, and placed over a 1 ml well containing the crystallization solution. Crystals were obtained at RT and took several weeks to grow to maximum size. To obtain phase information, a double mutant, BldC(L43M-L58M) was constructed and used to produce selenomethionine protein and isomorphous crystals grown with whiI opt DNA. The crystals diffracted to 5 Å, however, the diffraction limit was extended by dragging a crystal to the edge of the drop with a loop and allowing it to dehydrate before placing it in the cryo-stream. This permitted data collection beyond 3.5 Å resolution. The crystals take the hexagonal space group, P6 1 22. SAD X-ray intensity data were collected for a selenomethionine BldC(L43M-58M)- whiI opt crystal to 3.28 Å resolution at the selenium peak at the advanced light source (ALS) beamline 8.3.1. The data were processed in MOSFLM and scaled using SCALA. Autosol was used to determine heavy atom positions and perform density modification 46 . Due to the high solvent content (65%) density modification produced an experimental map of excellent quality, which was used to manually build the model. There are two BldC subunits and one DNA duplex in the crystallographic asymmetric unit (ASU). Once constructed, the model was subjected to multiple rounds of refinement using Phenix 46 , rebuilding using O 47 and validation with MolProbity 48 , resulting in final R work / R free values of 22.3%/26.8% to 3.28 Å resolution (Supplementary Table  3 ). The analysis of the DNA structure was carried out using w3DNA 49 .

The BldC- whiI opt structure revealed that each BldC subunit binds a 9 bp DNA site arranged as direct repeats. Hence, to obtain a BldC- smeA-ssfA promoter DNA complex, WT BldC was mixed with a DNA site that contained the first two BldC binding sites from the smeA-ssfA promoter anticipating that pseudocontinuous DNA packing would generate the smeA-ssfA site. Crystals of the complex were obtained by mixing 0.5 mM BldC (subunit) with 0.5 mM smeA-ssfA DNA and concentrating the mixture 3-fold using a 30 kDa microcon concentrator. The concentrated mixture was crystallized by mixing it 1:1 with 35% PEG 400, 0.1 M CaCl 2 , 0.1 M Hepes 7.5. Crystals were produced at RT and grew to maximum size within a week. The crystals take the tetragonal space group, P4 1 22. X-ray intensity data were collected at ALS beamline 8.3.1 and processed with MOSLM and scaled with SCALA. The structure was solved by molecular replacement (MR) using the previously determined P6 1 22 structure with the DNA truncated to 18 bp as a search model 50 . As the structure contained multiple copies of BldC and DNA, the structure was solved in a stepwise procedure. First, an initial solution consisting of two BldC subunits bound to a 18mer DNA site was obtained using MolRep. This solution was then used as a static model to find an additional 2 BldC-18mer complex. This strategy was followed until 10 BldC subunits and five 18mers were included in the model. This model was subjected to rigid body refinement followed by positional refinement in Phenix 46 . After this initial refinement, the R work was 39% and the F o − F c difference map revealed electron density for an additional BldC subunit and 9 bp of DNA, which were then added to the model. Thus, the asymmetric unit contains 11 BldC promoters bound to eleven 9 bp sites. Because the DNA was pseudocontinuous, the register of the DNA sequence was unclear. Indeed, because of the continuous stacking of the DNA, it was possible that the 9 bp sites bound by each BldC subunit are statistically disordered (half the time containing one 9 bp and the other half, the other 9 bp sequence). To address this possibility, X-ray intensity data were collected on a crystal grown with DNA containing a thymine to 5-iododeoxyuracil substitution (5′-GTAAXTCGGTCGAATTTC-3′, where X = 5-iododeoxyuridine). A difference map ( F wt − F iodo ) revealed no clear peaks indicating that the DNA is statistically disordered. For simplicity, each 9 bp sequence was constructed as 5′-AATTCGGAC-3′. After multiple cycles of refinement, rebuilding in O and validation in MolProbity 48 , the R work / R free values converged to 20.9%/27.8%, respectively. Data collection and refinement statistics are listed in Supplementary Table  3 .

Fluorescence polarization-based DNA binding experiments

Fluorescence polarization (FP) experiments were performed using a PanVera Beacon 2000 FP system at 25 °C. 5′-Fluroesceinated oligonucleotides were used for DNA binding experiments with WT BldC and BldC mutants. For each FP experiment, WT BldC or BldC mutant protein were titrated into 0.995 mL of reaction buffer (25 mM Tris, pH 7.5, 150 mM NaCl) containing 1 nM fluoresceinated oligonucleotide. Fluoresceinated oligonucleotides used in the experiments include the whiI opt (top strand: 5′-F-TTCAATTCGGACAATTCGGACA-3′ where 5′-F denotes the 5′ fluorescein label), 36mer optimized site (top strand: 5′-F-ATTCGGACAATTCGGACAATTCGGACAATTCGGACA-3′) and the smeA-ssfA promoter site (top strand: 5′-F-TAATTCGGTCGAATTTCCCCCATTTGCACCTTTTATCGTA-3′). The sequences of the three mutant whiI opt sites used for experiments shown in Supplementary Fig. 7 are: 5′-F-TTCGGCCCGGACGGCCCGGACA-3′ (top strand), 5′-F-TTCAATTCGCACAATTCGCACA-3′ (top strand), and 5′-F-TTCAATTCGTACAATTCGTACA-3′ top strand). The binding studies on BldC ( ±  the his-tag), selenomethionine BldC(L43M-L58M), and BldC mutants with the F- whiI opt DNA showed that the his-tag had no effect on DNA binding nor did the L43M-L58M mutations and selenomethionine substitution. FP experiments examining binding of the 36mer and smeA-ssfA sites were conducted with WT BldC and all data were fit using Kaleigraph.

Stoichiometry determination experiments

To determine the binding stoichiometry of BldC to the whiI opt, 36mer opt, and smeA-ssfA site, the buffer and conditions were identical to those used in the FP binding affinity determination experiments except that the concentration of the DNA site was increased to 10-fold above the K d (by using a solution containing 1 nM F-DNA and an amount of unlabeled DNA necessary to achieve a concentration 10-fold above K d ) thereby ensuring stoichiometric binding. For each oligonucleotide, BldC was titrated into the binding solution and the graph of the resulting data shows a linear increase in the observed mP until saturation with DNA, after which the mP values showed no further increase. The inflection point reflects the binding stoichiometry for each DNA site (obtained from the concentration values).

Size exclusion chromatography

SEC was used to probe the molecular weight of BldC using a using a HiLoad 26/600 Superdex 75 prep grade column. Experiments were performed in a buffer containing 200 mM NaCl, 5% glycerol, 20 mM Tris HCl pH 7.5 and 1 mM β-mercaptoethanol (BME). For SEC analysis BldC was included in the buffer at a concentration of 10 μM.

CD spectroscopy

Far-UV CD spectra of WT and mutant BldC proteins were recorded on an AVIV 435 CD Spectrophotometer in a 1 mm sample cell. Measurements were taken from 200 to 260 nm with a wavelength step of 1.0 nm and a 1 s averaging time. Each spectrum is the average of 5 scans. Protein concentrations ranged from 0.3 to 1.5 mg/ml (the final spectra were normalized for concentration) and the buffer composition was 20 mM NaH 2 PO 4 (pH 7.5), 300 mM NaF, 5% glycerol, and 0.5 mM Tris(2-carboxyethyl)phosphine (TCEP).

Data availability

ChIP-chip data supporting the findings of the study have been deposited at the ArrayExpress database under accession number E-GEOD-28908 [ https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28908/ ]. Structure factor amplitudes and coordinates for the BldC- whiI opt and BldC- smeA-ssfA structures have been deposited in the RCSB Protein Data Bank under the accession codes 6AMK and 6AMA . All other relevant data supporting the findings of the study are available from the corresponding authors upon reasonable request.

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Acknowledgements

We are grateful to the Oxford Gene Technology for expert handling of the ChIP samples, and Ray Dixon, Nick Tucker and Tony Maxwell for helpful discussion. This work was funded by BBSRC grant BB/H006125/1 (to M.J.B.), by the BBSRC Institute Strategic Programme Grant BB/J004561/1 to the John Innes Centre, and by the National Institutes of Health grant GM115547 (to M.A.S.). We would like to acknowledge the Advanced Light Source beamline 8.3.1 for data collection with a special thanks to Jane Tanamachi. The Berkeley Center for Structural Biology is supported in part by the National Institutes of Health, the National Institute of General Medical Sciences, and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Beamline 8.3.1 at the ALS is operated by the University of California Office of the President, Multicampus Research Programs, and Initiatives grant MR-15-328599 and the Program for Breakthrough Biomedical Research, which is partially funded by the Sandler Foundation.

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These authors contributed equally: Maria A. Schumacher, Chris D. den Hengst

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Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA

Maria A. Schumacher, Wenjie Zeng, Brady Travis & Richard G. Brennan

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK

Chris D. den Hengst, Matthew J. Bush, T. B. K. Le, Ngat T. Tran, Govind Chandra & Mark J. Buttner

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Contributions

M.A.S., C.D.d.H., R.G.B. and M.J.But. designed the research. M.A.S., R.G.B., M.J.Bus. and M.J.But. wrote the manuscript. C.D.d.H., M.J.Bus., T.B.K.L. and N.T.T. performed the ChIP-chip, footprinting, EMSA, and operator optimization experiments. G.C. analyzed the raw ChIP-chip data. W.Z. purified proteins for crystallization and performed SEC. B.T. carried out CD analyses. M.A.S. performed the crystallization and structure determinations and FP binding assays.

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Correspondence to Maria A. Schumacher , Richard G. Brennan or Mark J. Buttner .

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Schumacher, M.A., den Hengst, C.D., Bush, M.J. et al. The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development. Nat Commun 9 , 1139 (2018). https://doi.org/10.1038/s41467-018-03576-3

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Published : 19 March 2018

DOI : https://doi.org/10.1038/s41467-018-03576-3

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