How do bacteria make decisions? Part 1.

PALM image, chemotaxis, azospirillum brasilense, <span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.1000137&rft.atitle=Self-Organization+of+the+Escherichia+coli+Chemotaxis+Network+Imaged+with+Super-Resolution+Light+Microscopy.&rft.jtitle=PLoS+Biology&rft.volume=7&rft.issue=6&rft.spage=e1000137&rft.date=2009&rfr_id=info%3Asid%2Fscienceseeker.org&rft.au=Greenfield+Derek&rft.aulast=Greenfield&rft.aufirst=Derek&rft.au=et+al+&rft.aulast=et+al&rft.aufirst=&rfs_dat=ss.included=1&rfe_dat=bpr3.included=1;bpr3.tags=Research+%2F+Scholarship">Greenfield D. & et al  (2009). Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy., <span style="font-style:italic;">PLoS Biology, 7</span> (6) e1000137. DOI: <a rel="author" href="http://dx.doi.org/10.1371%2Fjournal.pbio.1000137">10.1371/journal.pbio.1000137</a></span>
This beautiful figure shows where different chemotaxis proteins are found within an E. coli cell at stunning resolution. From Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, et al. (2009) Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. PLoS Biol 7(6): e1000137. doi:10.1371/journal.pbio.1000137

Yes. You read the title correctly. Decision making is not limited to animals like humans or birds. Bacteria also make decisions with intricate precision. Imagine being so tiny that you are literally moved by water molecules bumping into you. This is what bacteria encounter perpetually. Now, imagine having no eyes, no ears, no sense of touch, no taste or nose. How would you know what or who was around you? How would you find food now as compared to where you were a short time ago? This is where being able to sense important things like a food source is critical. Bacteria have this on their “mind” all the time. Depending on the size of a bacterium’s genome, these tiny organisms have the ability to sense hundreds to thousands of internal and external signals like carbon sources, nitrogen sources, and pH changes. If these bacteria are motile (able to move around), they can compare how conditions are for them now against how they were a few seconds ago. That’s right, bacteria have a memory albeit short. If conditions are better, they can continue to move in a forward direction. If conditions are worse compared to a few seconds earlier, they can change direction and continue searching for better conditions in their environment to generate energy. But, how do they decide?

I will focus on a lesser known bacterium as my example since I have the most knowledge about it. Azospirillum brasilense is found in the soil around the world and interacts with the roots of cereal plants like corn and wheat. A. brasilense is almost always (except when attached to plant roots) motile and searching for the best niche to provide energy for the cell. This bacterium can “make” its own usable form of nitrogen from nitrogen gas in the air through a process known as nitrogen fixation. This costs the cell a lot of energy so they are searching for nitrogen sources as well as the necessary carbon sources for life. The microscopic world can be cut throat. Having the ability to sense a greater variety of food compounds could mean the difference between being the predominant species in town or being on the fringe.

Back to the question about how these cells decide which direction to travel. One way is through a dedicated group of proteins that regulate how often the cell switches direction. This group of proteins control chemotaxis, the movement of a cell in response to chemicals within their environment. The number of chemotaxis genes varies depending on the complexity of metabolism for a bacterium. The champion at the moment is 129 from Pseudomonas syringae pv. oryzae str. 1_6. The proteins that actually sense the chemical signal are called methyl-accepting chemotaxis proteins (MCPs) or chemoreceptors. Azosprillum brasilense has 48 MCPs within its genome. This does not mean, however, that A. brasilense cells can only sense 48 different chemicals. Most, but not all, of these MCPs don’t interact with the chemicals themselves but sense the changes in the amount of energy the cell has within the environment they reside. If things are good, the MCPs are inactive. However, if energy levels are lower than they were a few seconds before, the MCPs become active and begin the signal to change direction. And these MCPs are VERY sensitive to changes. For example, if the A. brasilense cells are swimming in a liquid medium with 1,000 molecules of sugar, they will detect changes of addition or removal of a few sugar molecules in the medium. Now, move these cells immediately into a medium with 1,000,000,000,0000 sugar molecules and they still will be able to detect removal or addition of a few sugar molecules. This is called adaptation and allows the cells to remain sensitive no matter the concentrations of compounds they encounter.

In Part 2, we will talk about what happens next in the decision making process of bacteria.

<span title=”ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.1000137&rft.atitle=Self-Organization+of+the+Escherichia+coli+Chemotaxis+Network+Imaged+with+Super-Resolution+Light+Microscopy.&rft.jtitle=PLoS+Biology&rft.volume=7&rft.issue=6&rft.spage=e1000137&rft.date=2009&rfr_id=info%3Asid%2Fscienceseeker.org&rft.au=Greenfield+Derek&rft.aulast=Greenfield&rft.aufirst=Derek&rft.au=et+al+&rft.aulast=et+al&rft.aufirst=&rfs_dat=ss.included=1&rfe_dat=bpr3.included=1;bpr3.tags=Research+%2F+Scholarship”>Greenfield D. & et al  (2009). Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy., <span style=”font-style:italic;”>PLoS Biology, 7</span> (6) e1000137. DOI: <a rel=”author” href=”http://dx.doi.org/10.1371%2Fjournal.pbio.1000137″>10.1371/journal.pbio.1000137</a></span>

What is in a genome?

English language svg version of Image:Plasmid ...
English language svg version of Image:Plasmid (numbers).svg Description : This image shows a line drawing of a bacterium with its chromosomal DNA and several plasmids within it. The bacterium is drawn as a large oval. Within the bacterium, small to medium size circles illustrate the plasmids, and one long thin closed line that intersects itself repeatedly illustrates the chromosomal DNA. (Photo credit: Wikipedia)

I first have to apologize. The mission of this blog is to inform those who are curious about science and nature. My ADD gets the best of me sometimes and I digress towards more policy and advocation.

So…what is in a genome? A broad question with lots of answers. Let’s start with the ‘simple’ example of a genome; bacteria. Unlike humans, and other animals, bacteria have only one true chromosome which is circular. Many bacteria, however, have extra DNA not on the chromosome. This extra DNA is also circular and usually called a plasmid. Many bacteria have several plasmids, and some even have very large plasmids called cosmids.

There is not a lot of room within a bacterial cell, so there is not a lot of ‘junk’ DNA in its chromosome. If an average gene is 1000 base pairs (bp), then a 7 Mbp (7,000,000 bp) genome usually has about 6500 genes. This means bacteria pack a big punch in a small size cellular blueprint. Other than genes, bacteria contain DNA elements that help regulate what and when genes are actively transcribed into RNA to produce functional proteins. Promoters are areas of DNA upstream of genes that are attractive places for some proteins to interact with. Some proteins activate gene transcription while other repress transcription. This ensures only the proteins needed by the cell are being produced since making and degrading unneeded proteins costs energy.

What about plants and animals?

I’ll leave plants out since I’m not knowledgeable enough to write about them. Animals have very elaborate genomes. The number of chromosomes vary for each organism and are not circular. For simplicity, I will discuss humans. Humans have pairs of each chromosome that are identical except for the pair that determine a persons sex. Even identical chromosomes are essentially different in the characteristics of individual genes (see dominant and recessive alleles). Strands of DNA are wrapped around proteins known as histones which interact to compact the size of the chromosome.

The major chromatin structures.
The major chromatin structures. (Photo credit: Wikipedia)

Human genes have MANY ways of being regulated. The histones themselves can undergo modification by enzymes that affects how compact they are and how attractive they are to proteins regulating gene transcription. Like bacteria, human gene transcription can be regulated by promoters. However, unlike bacteria, these genes will not totally be used to make a protein. Human genes are composed of introns, regions not translated into a protein, and exons, regions that are translated into protein. Human messenger RNA is processed after transcription which removes intron sequences leaving only exons that will be shuttled out of the nucleus for protein synthesis. To make this more complicated, during processing, many genes can undergo something called alternative splicing. This means as mRNA is being processed, even some exons can be removed resulting in different versions of a protein! 

Other elements can regulate gene transcription besides promoters. Animals have DNA elements called enhancers and insulators that may or may not be located close to actual genes. Enhancers and insulators can intricately interact to regulate gene expression.

Français : Organisation de l'ADN en chromosome...
Français : Organisation de l’ADN en chromosome National Human Genome Research (USA) (Photo credit: Wikipedia)

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I will leave it at this. I hope you enjoyed my little ramble about genomes. Let me know what you think…please…