Bacterial Research

[Mechanist1]

Post interesting research or articles associated with bacteria.

Some view Bacteria as computers making computers. Some views cells as Robust Computational Systems. Populations of bacteria appear to collectively weigh and initiate different survival strategies and Expect The Unexpected. These critters appear to be smarter than you thought being able to ‘Learn’ And Plan Ahead with their own language.

And now we are seeing the ‘Dawning of a New Age’ in Bacteria Research

ScienceDaily (July 12, 2010) — Lowly bacteria are turning out to be much more complex than previously thought.

In the July 2010 issue of the journal Molecular Microbiology, Loyola University Health System researchers describe an example of bacterial complexity, called "protein acetylation," which once was thought to be rare in bacteria.

This discovery that protein acetylation is common in bacteria has led to the “dawning of a new age” in bacterial research, senior author Alan Wolfe, PhD. and colleagues wrote.

Protein acetylation is a molecular reaction inside the cell. It modifies and thus affects the function of proteins, including the molecular machinery responsible for turning genes on or off.

Bacteria make up one of the three domains of life. The other two domains are archaea (single-cell organisms distinct from bacteria) and eukaryotes (which include plants and animals). Bacteria evolved before eukaryotes, but they are not as primitive as once thought.

“Bacteria have long been considered simple relatives of eukaryotes,” Wolfe and colleagues wrote. “Obviously, this misperception must be modified.”

For example, protein acetylation historically had been considered mostly a eukaryotic phenomenon. But recent research indicates that acetylation also has a broad impact on bacterial physiology.

“There is a whole process going on that we have been blind to,” Wolfe said.

Wolfe’s laboratory works with intestinal bacteria called Escherichia coli, commonly called E. coli. While some strains of E. coli can cause serious food poisoning, most strains are harmless or even beneficial.

E. coli and its 4,000 genes have been extensively studied for decades. Consequently, researchers now have the ability to quickly determine what happens when a gene is deleted or made more active. “We’re explorers with lots of tools,” Wolfe said.

Studying protein acetylation will improve scientists’ basic understanding of how bacterial cells work. This in turn could lead to new drugs to, for example, kill or cripple harmful bacteria.

“We’re in the very early days of this research,” Wolfe said. "We’re riding the front of the wave, and that’s exhilarating. The graduate students in my lab are working practically around the clock, because they know how important this is."

Wolfe is a microbial geneticist and professor in the Department of Microbiology and Immunology at Loyola University Chicago Stritch School of Medicine. His co-authors are graduate students Linda Hu and Bruno Lima.

Wolfe’s lab is supported by the Stritch School of Medicine Research Funding Committee and by a four-year $2 million grant from the National Institutes of Health.

Enjoy.

[Mechanist1]

Do Ocean-Bottom Bacteria Make Their Own Power Grids?

Deep on the ocean floor, colonies of bacteria appear to have connected themselves via microscopic power grids that would be the envy of any small town. Much remains unknown about the process, but if confirmed the findings could revolutionize scientists' understanding of how the world's smallest ecosystems operate.

Oxygen-breathing bacteria that live on the ocean bottom have a problem. Those sitting atop the sediment have ready access to oxygen in the water but not to the precious mineral nutrients that lie out of reach a centimeter or so below the ground. Meanwhile, those microbes that live in the sediment can access the nutrients, but they lack oxygen. How do both groups survive?

Microbial ecologist Lars Peter Nielsen of Aarhus University in Denmark figured the surface and subsurface bacteria were somehow exchanging oxygen and nutrients with one another. To find out how, he and colleagues scooped up some mud from the bottom of the 20-meter-deep ocean in Aarhus Bay and other waters near the university and plopped it into a beaker in their lab.

Then the researchers did something they knew would make the bacteria unhappy: They started removing the oxygen from the water. If the bacteria were swapping materials, as Nielsen had suspected, those living below the surface of the mud would have gradually noticed that their oxygen supply was being cut off; they would have registered chemical changes in the sediment that could be detected by sensors. But instead, Nielsen and colleagues witnessed something far more rapid. Almost as soon as the researchers began removing the oxygen, the subsurface bacteria stopped consuming hydrogen sulfide in the mud. More important, this metabolic shutdown was a sign that the buried bacteria almost instantly realized something in the environment far above them had changed. The researchers also detected very rapid pH changes in the water in the beaker.

These responses occurred too quickly for any sort of chemical exchange or molecular process such as osmosis, says Nielsen. The most plausible option, his team reports in the 25 February issue of Nature, is that the bacteria are somehow communicating electrically by transmitting electrons back and forth. How exactly they do this is unclear, but Nielsen suspects the organisms may all be connected to each other via a microscopic electric grid, possibly made from tiny grains of metal, such as iron and manganese, in the sediment.

If the wiring idea turns out to be true, it essentially would turn the bacterial community into a cross-sediment power grid—one that would span some 20 kilometers if scaled up for humans. Instead of receiving oxygen from the surface and turning it into energy—something the researchers say is not possible given the thickness of the sediment depth observed—the buried bacteria would simply receive energy in the form of electrons from the grid. In response, the subsurface bacteria could survive while buried and send nutrients back up to their comrades on the surface via chemical migration.

Still, Nielsen says, much remains unknown about how such a grid would work. “What are the wires made of?” he asks. “How do they connect to cells and one another, and how are they built?”

Geobiologist Kenneth Nealson of the University of Southern California in Los Angeles agrees that new findings “fall into the category of ‘must have an explanation other than chemistry.’ The excitement now lies in coming up with the mechanism[s] responsible for electron movement.”

Wonder just how long this has been going on right under our noses :-?

[Mechanist1]

Introns go waaaay back:

Bacteria from Hot Springs Reveal Clues to Evolution of Early Life and to Unlock Biofuels’ Potential

ScienceDaily (June 8, 2010) — Bacteria that lives in hot springs in Japan may help solve one of the mysteries of the early evolution of complex organisms, according to a study publishing next week in PLoS Biology. It may also be the key to 21st century biofuel production.

Biochemists Alan Lambowitz and Georg Mohr began investigating Thermosynechococcus elongatus, a cyanobacterium that can survive at temperatures up to 150 degrees Fahrenheit, after they noticed an unusually high percentage of the bacteria's genetic sequence was composed of elements known as group II introns.

“Introns are mysterious elements in evolution,” says Lambowitz, a professor of molecular biology and director of the Institute of Molecular and Cellular Biology. "Until the 1970s it was believed that genes in all organisms would be continuous and that they would make a continuous RNA, which would then get translated into a continuous protein. It was found, however, that most genes of the eukaryotes, the higher organisms including humans, aren’t like that at all. Most of the genes in higher organism are discontinuous. They consist of DNA coding regions that are separated by areas known as introns.

“Genomes become loaded down with these introns, which are thought to have evolved from genomic parasites that existed for their own benefit and could spread without killing the host organism,” says Lambowitz. “It remains a major question in evolution as to why these introns exist, and how they came to compose such a large part of the human genome.”

In order to better understand the early history of introns, Lambowitz and Mohr have focused their investigation on bacteria because they’re believed to be the original evolutionary wellspring of the introns. They’re looking at T. elongatus in particular because it’s the only known bacteria in which introns have proliferated in a manner similar to that in higher organisms, such as humans.

“We can’t go back a billion years in a time machine to see how introns proliferated in the early eukaryotes,” says Mohr, a research scientist in Lambowitz’s lab. “What we can do is investigate the mechanisms that have allowed introns to proliferate in this organism, and try to infer how they evolved in eukaryotes, like humans, in which as much as 40 percent of the genome is made up of introns.”

Among the mechanisms they’ve identified, perhaps the most surprising has been that heat plays a significant role in allowing introns to proliferate in T. elongatus. High temperatures, like those found in the hot springs in which the bacteria live, can unwind the DNA strands in the genome and make it easier for the introns to insert themselves.

This evidence of “DNA melting,” says Lambowitz, is particularly suggestive when trying to imagine how introns proliferated in early eukaryotes, because the earth was hotter a billion or so years ago, when the early eukaryotes emerged. The genomes of the early eukaryotes may have begun with only a few introns, but over time, thanks in part to the high temperatures, the introns could have proliferated rapidly.

Lambowitz and Mohr’s investigation of introns in T. elongatus may also, unexpectedly, prove an enormous boon to researchers who are trying to use other high-temperature (“thermophilic”) bacteria to improve the efficiency of biofuels.

“There’s one bacterial species in particular,” says Lambowitz, “which lives at high temperature and is very good at converting cellulose to ethanol, but has been intractable to genetic manipulation. The Department of Energy has a considerable amount of money invested in it, and they need to improve the strains but haven’t been able to do it. When we discovered these thermophilic introns, which work better at high temperatures, we were able to adapt them pretty rapidly for gene targeting.”

The technology for using group II introns in gene targeting, known as targetron technology, was pioneered by Lambowitz and his coworkers. Lambowitz and Mohr are already working with scientists at Oak Ridge National Laboratory to see if they can successfully genetically engineer thermophilic bacteria for increased biofuel production. They also foresee applying what they’ve discovered about T. elongatus introns and temperature to a whole range of biotech and biomedical applications that involve organisms and enzymes that function best at high temperatures. However, they are still planning to delve further into the more profound, basic scientific questions that drew them to the subject in the first place.

Funding: This work was supported by National Institutes of Health grants GM037949 and GM037951 and Welch Foundation grant F-1607.

[Mechanist1]

Even microbes have immune systems analogous to ours. More about that:
CRISPR Critters: Scientists Identify Key Enzyme in Microbial Immune System

ScienceDaily (Sep. 14, 2010) — Imagine a war in which you are vastly outnumbered by an enemy that is utterly relentless -- attacking you is all it does. The intro to another Terminator movie? No, just another day for microbes such as bacteria and archaea, which face a never-ending onslaught from viruses and invading strands of nucleic acid known as plasmids. To survive this onslaught, microbes deploy a variety of defense mechanisms, including an adaptive-type nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats.

http://www.sciencedaily.com/images/2010/09/100909155650.jpg

The crystal structure of the Csy4 enzyme (blue) bound to a crRNA molecule (orange). The crRNA contains nucletotide sequences that match those of foreign DNA from a virus or plasmid, enabling it to target and silence the invaders. (Credit: Image courtesy of the Doudna group)

[kollectiv]

Hey, just because bacteria are mainly single-celled, doesn’t mean they are simple: the level of organization in biofilms is really quite amazing, for example, with altruistic behaviour being shown by members of the community, and complex webs of nutrition being set up. In fact, the way we study bacteria is pretty much the equivalent of taking a baby, cloning it repeatedly in a sterile environment with no sensory input - and think that the behaviour of the clones represents the species at large.

Bacteria are very much community organisms, which have very good capacity for taking on new traits via picking up DNA in their environment, and an as yet under-appreciated facility for communicating with their own species, other species, and even with eukaryotes.

Not as smart as viruses, mind…B-)