 |
|
Bioclocks work by controlling chromosome coiling
November 26, 2007There is a new twist on the question of how biological clocks work.
In recent years, scientists have discovered that biological clocks help organize a dizzying array of biochemical processes in the body. Despite a number of hypotheses, exactly how the microscopic pacemakers in every cell in the body exert such a widespread influence has remained a mystery.
Now, a new study provides direct evidence that biological clocks can influence the activity of a large number of different genes in an ingenious fashion, simply by causing chromosomes to coil more tightly during the day and to relax at night.
"The idea that the whole genome is oscillating is really cool," enthuses Vanderbilt Professor of Biological Sciences Carl Johnson, who headed the research that was published online Nov. 13 in the Proceedings of the National Academy of Sciences. "The fact that oscillations can act as a regulatory mechanism is telling us something important about how DNA works: It is something DNA jockeys really need to think about."
Johnson's team, which consisted of Senior Lecturer Mark A Woelfle, Assistant Research Professor Yao Xu and graduate student Ximing Qin, performed the study with cyanobacteria (blue-green algae), the simplest organism known to possess a biological clock. The chromosomes in cyanobacteria are organized in circular molecules of DNA. In their relaxed state, they form a single loop. But, within the cell, they are usually "supercoiled" into a series of small helical loops. There are even two families of special enzymes, called gyrases and topoisomerases, whose function is coiling and uncoiling DNA.
The researchers focused on small, non-essential pieces of DNA in the cyanobacteria called plasmids that occur naturally in the cyanobacteria. Because a plasmid should behave in the same fashion as the larger and more unwieldy chromosome, the scientists consider it to be a good proxy of the behavior of the chromosome itself.
When the plasmid is relaxed, it is open and uncoiled and, when it is supercoiled, it is twisted into a smaller, more condensed state. So, the researchers used a standard method, called gel electrophoresis, to measure the extent of a plasmid's supercoiling during different points in the day/night cycle.
The researchers found a distinct day/night cycle: The plasmid is smaller and more tightly wound during periods of light than they are during periods of darkness. They also found that this rhythmic condensation disappears when the cyanobacteria are kept in constant darkness.
"This is one of the first pieces of evidence that the biological clock exerts its effect on DNA structure through the coiling of the chromosome and that this, in turn, allows it to regulate all the genes in the organism," says Woelfle.
Some cyanobacteria use their biological clocks to control two basic processes. During the day, they use photosynthesis to turn sunlight into chemical energy. During the night, they remove nitrogen from the atmosphere and incorporate it into a chemical compound that they can use to make proteins.
According to the Johnson lab's "oscilloid model," the genes that are involved in photosynthesis should be located in regions of the chromosome that are "turned on" by the tighter coiling in the DNA during the day and "turned off" during the night when the DNA is more relaxed. By the same token, the genes that are involved in nitrogen fixation should be located in regions of the chromosome that are "turned off" during the day when the DNA is tightly coiled and "turned on" during the night when it is more relaxed.
The researchers see no reason why the bioclocks in higher organisms, including humans, do not operate in a similar fashion. "This could be a universal theme that we are just starting to decipher," says Woelfle.
The DNA in higher organisms is much larger than that in cyanobacteria and it is linear, not circular. Stretched end-to-end, the genome in a mammalian cell is about six feet long. In order to fit into a microscopic cell, the DNA must be tightly packed into a series of small coils, something like microscopic Slinkies.
Previous studies have shown that in higher organisms between 5 to 10 percent of genes in the genome are controlled by the bioclock, compared to 100 percent of genes in the cyanobacteria. In the case of the higher organisms, the bioclock's control is likely to be local rather than the global situation in cyanobacteria.
With a circular chromosome (as in cyanobacteria), twisting it at any point affects the entire molecule. When you twist a linear chromosome at a certain point, however, the effect only extends for a limited distance in either direction because the ends are not connected. That fits neatly with the idea that the bioclock's influence on linear chromosomes is limited to certain specific regions, regions where the specific genes that it regulates are located.
Vanderbilt University
"The idea that the whole genome is oscillating is really cool," enthuses Vanderbilt Professor of Biological Sciences Carl Johnson, who headed the research that was published online Nov. 13 in the Proceedings of the National Academy of Sciences. "The fact that oscillations can act as a regulatory mechanism is telling us something important about how DNA works: It is something DNA jockeys really need to think about."
Johnson's team, which consisted of Senior Lecturer Mark A Woelfle, Assistant Research Professor Yao Xu and graduate student Ximing Qin, performed the study with cyanobacteria (blue-green algae), the simplest organism known to possess a biological clock. The chromosomes in cyanobacteria are organized in circular molecules of DNA. In their relaxed state, they form a single loop. But, within the cell, they are usually "supercoiled" into a series of small helical loops. There are even two families of special enzymes, called gyrases and topoisomerases, whose function is coiling and uncoiling DNA.
The researchers focused on small, non-essential pieces of DNA in the cyanobacteria called plasmids that occur naturally in the cyanobacteria. Because a plasmid should behave in the same fashion as the larger and more unwieldy chromosome, the scientists consider it to be a good proxy of the behavior of the chromosome itself.
When the plasmid is relaxed, it is open and uncoiled and, when it is supercoiled, it is twisted into a smaller, more condensed state. So, the researchers used a standard method, called gel electrophoresis, to measure the extent of a plasmid's supercoiling during different points in the day/night cycle.
The researchers found a distinct day/night cycle: The plasmid is smaller and more tightly wound during periods of light than they are during periods of darkness. They also found that this rhythmic condensation disappears when the cyanobacteria are kept in constant darkness.
"This is one of the first pieces of evidence that the biological clock exerts its effect on DNA structure through the coiling of the chromosome and that this, in turn, allows it to regulate all the genes in the organism," says Woelfle.
Some cyanobacteria use their biological clocks to control two basic processes. During the day, they use photosynthesis to turn sunlight into chemical energy. During the night, they remove nitrogen from the atmosphere and incorporate it into a chemical compound that they can use to make proteins.
According to the Johnson lab's "oscilloid model," the genes that are involved in photosynthesis should be located in regions of the chromosome that are "turned on" by the tighter coiling in the DNA during the day and "turned off" during the night when the DNA is more relaxed. By the same token, the genes that are involved in nitrogen fixation should be located in regions of the chromosome that are "turned off" during the day when the DNA is tightly coiled and "turned on" during the night when it is more relaxed.
The researchers see no reason why the bioclocks in higher organisms, including humans, do not operate in a similar fashion. "This could be a universal theme that we are just starting to decipher," says Woelfle.
The DNA in higher organisms is much larger than that in cyanobacteria and it is linear, not circular. Stretched end-to-end, the genome in a mammalian cell is about six feet long. In order to fit into a microscopic cell, the DNA must be tightly packed into a series of small coils, something like microscopic Slinkies.
Previous studies have shown that in higher organisms between 5 to 10 percent of genes in the genome are controlled by the bioclock, compared to 100 percent of genes in the cyanobacteria. In the case of the higher organisms, the bioclock's control is likely to be local rather than the global situation in cyanobacteria.
With a circular chromosome (as in cyanobacteria), twisting it at any point affects the entire molecule. When you twist a linear chromosome at a certain point, however, the effect only extends for a limited distance in either direction because the ends are not connected. That fits neatly with the idea that the bioclock's influence on linear chromosomes is limited to certain specific regions, regions where the specific genes that it regulates are located.
Vanderbilt University
Cyanobacteria Current Events and Cyanobacteria News RSSKiller algae a key player in mass extinctions
Supervolcanoes and cosmic impacts get all the terrible glory for causing mass extinctions, but a new theory suggests lowly algae may be the killer behind the world's great species annihilations.
Caltech researchers reveal unexpected sources of nitrogen fixation
Researchers at the California Institute of Technology (Caltech) have identified an unexpected metabolic ability within a symbiotic community of microorganisms that may help solve a lingering mystery about the world's nitrogen-cycling budget.
A new day dawned fast
In 1980, Luis Alvarez and his collaborators stunned the world with their discovery that an asteroid impact 65 million years ago probably killed off the dinosaurs and much of the the world's living organisms. But ever since, there has been an ongoing debate about how long it took for life to return to the devastated planet and for ecosystems to bounce back.
Laser technique has implications for detecting microbial life forms in Martian ice
An innovative technique called L.I.F.E. imaging used successfully to detect bacteria in frozen Antarctic lakes could have exciting implications for demonstrating signs of life in the polar regions of Mars.
WUSTL research finds individual cells isolated from the biological clock can keep daily time, but are unreliable
Alexis Webb enters a small room at Washington University in St. Louis with walls, floor and ceiling painted dark green, shuts the door, turns off the lights and bends over a microscope in a black box draped with black cloth. Through the microscope, she can see a single nerve cell on a glass cover slip glowing dimly.
Novel bacterial strains clear algal toxins from drinking water
Novel bacterial strains capable of neutralizing toxins produced by blue-green algae have been identified by researchers at Robert Gordon's University, Aberdeen.
Nitrogen fixation and phytoplankton blooms in the southwest Indian Ocean
Observations made by Southampton scientists help understand the massive blooms of microscopic marine algae - phytoplankton - in the seas around Madagascar and its effect on the biogeochemistry of the southwest Indian Ocean.
New images of marine microbe illuminate carbon and nitrogen fixation
Trichodesmium is unusual among marine microbes because it both "breathes" carbon dioxide like plants, while also taking nitrogen gas from the air and "fixing" it into a fertilizer of the seas.
Deep-sea rocks point to early oxygen on Earth
Red jasper cored from layers 3.46 billion years old suggests that not only did the oceans contain abundant oxygen then, but that the atmosphere was as oxygen rich as it is today, according to geologists.
Discovering the secret code behind photosynthesis
Scientists from Queen Mary, University of London have discovered that an ancient system of communication found in primitive bacteria, may also explain how plants and algae control the process of photosynthesis.
More Cyanobacteria Current Events and Cyanobacteria News Articles
 |
Cyanobacteria by Samit Ray (Author) The book entitled "Cyanobacteria" is an outcome of the author's twenty years experience in Algology . There is no such textbook or a reference book exclusively on this topic. Cyanobacteria is a group of organisms which have enormous evolutionary, ecological, economic and environmental significance specially with regard to human benefit. Naturally, it is very important to have a clear and in-depth knowledge about the various aspects of cyanobacterial origin, evolution, variations in morphology, ultrastructure, biochemistry, genetics, factors relating to cellular differentiation, enzyme synthesis, response to environmental variations (e.g., chromatic adaptation), ecological strategies of survival, production of toxins and benefits derived from these organisms for human benefit. |
 |
The Cyanobacteria: Molecular Biology, Genomics and Evolution by Antonia Herrero (Editor), Enrique Flores (Editor) |
 |
Kent 4oz Poly Ox Cyanobacteria & Organic Material Oxidizer by Kent Marine Poly Ox is an organic material oxidizer. It does not contain any algaecide. It assists in preventing growth of various cyanobacteria (commonly called red or blue-green slime algae) by simply removing their food source. It will oxidize leftover food, and dissolved and suspended organic matter. This will increase the water quality and provide a better environment for your fish and invertebrates! |
 |
CRC Handbook of Symbiotic Cyanobacteria by Amar Nath Rai (Author) In one convenient source, this ready reference brings together for the first time, all the information available on various cyanobacterial symbioses/symbiotic cyanobacteria. Comprehensive data on structure, physiology, biochemistry and molecular biology of the cyanobiont in various cyanobacterial symbioses is included. Aplied aspects such as use of Azolla in rice cultivation and artificial symbioses are addressed, along with a chapter dedicated to methodology. This informative new text is useful to researchers, teachers, and students. |
 |
NOW Foods Blue Green Algae 500 mg 180 VCaps by NOW Foods Blue-Green Algae (Aphanizomenon flos-aquae) is a unique superfood harvested from the pristine Upper Klamath Lake in the Oregon Cascades. This nutrient-dense, freeze-dried, whole food concentrate contains full spectrum of easily digestible minerals. |
 |
Harmful Cyanobacteria (Aquatic Ecology Series) by Jef Huisman (Editor), Hans C.P. Matthijs (Editor), Petra M. Visser (Editor) Several cyanobacterial species can produce powerful toxins that provide a serious threat for water quality, other aquatic organisms, and human health. These harmful cyanobacteria are especially prominent in freshwater ecosystems, and are a major concern for water managers. From a scientific perspective, there are many recent advances in this research area: |
 |
The Regulatory Potential of Marine Cyanobacteria by Ilka Maria Axmann (Author) |
 |
Boyd Chemi-clean 3 Grams by Boyd Enterprises Cynobacteria is usually encouraged with the presence of nitrate and ammonia, which are both fixed forms of nitrogen. Chemi-clean helps clean and remove this problem algae through its own unique process. Most other red slime removers use purely antibiotics, namely erythromycin to take care of the algae. The use of such substances with in your aquarium can have disastrous effects upon your nitrifying bacteria and cause your tank to crash, killing the inhabitants of your aquarium.The use of chemi-clean not only as a problem solver, when red slime is present, but as a regular maintenance procedure will help keep your water crystal clear and your tank free of unwanted cynobacteria.For best results, turn off UV sterilizer or Ozonizer and Protein Skimmer. Remove Chemi-Pure or Carbon Filtration... |
 |
Handbook on Cyanobacteria: Biochemistry, Biotechnology and Applications (Bacteriology Research Developments) by Percy M. Gault (Editor), Harris J. Marler (Editor) Cyanobacteria, also known as blue-green algae, blue-green bacteria or cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. They are a significant component of the marine nitrogen cycle and an important primary producer in many areas of the ocean, but are also found in habitats other than the marine environment; in particular, cyanobacteria are known to occur in both freshwater and hypersaline inland lakes. They are found in almost every conceivable environment, from oceans to fresh water to bare rock to soil. Cyanobacteria are the only group of organisms that are able to reduce nitrogen and carbon in aerobic conditions, a fact that may be responsible for their evolutionary and ecological success. Certain cyanobacteria also produce cyanotoxins. This new book... |
|
The Molecular Biology of Cyanobacteria (Advances in Photosynthesis and Respiration) by D.A. Bryant (Editor) The Molecular Biology of Cyanobacteria summarizes more than a decade of progress in analyzing the taxonomy, biochemistry, physiology, cellular differentiation and developmental biology of cyanobacteria by modern molecular methods, especially molecular genetics. During this period cyanobacterial molecular biologists have been `studying those things that cyanobacteria do well', and they have made cyanobacteria the organisms of choice for detailed molecular analyses of oxygenic photosynthesis. Part 1 contains chapters describing the molecular evolution and taxonomy of the cyanobacteria, as well as chapters describing cyanelles and the origins of algal and higher plant chloroplasts. Also included are chapters describing the picoplanktonic, oceanic cyanobacteria and prochlorophytes,... |
| © 2009 BrightSurf.com |