How do bacteria make decisions? Part 2

bacterial, motility, chemotaxis
The path bacterial cells swim tracked using motion tracking software

Yesterday, we looked at one of the first factors (or protein families specifically) that guide bacteria in their decisions. Which direction to travel is not the only decision needed to be made by bacteria (more coming soon). I wrote about methyl-accepting chemotaxis proteins (MCPs) briefly (more visuals to come). These proteins interact directly or indirectly by sensing changes caused by chemical compounds from the bacterium’s environment. Today I will briefly write about the next step towards decision making in a bacterial cell in regards to direction of travel. MCPs by themselves would be useless if they did not interact with some other cellular machinery. Lucky for bacteria, the MCPs are only the first of many specialized proteins for regulating direction of travel. If a chemical binds to an MCP outside the cell, how does the inside of the cell get the message? When chemicals bind to an MCP or stop binding to it, it slightly changes the structure of the MCP. It is thought association or dissociation of chemicals to MCPs causes a rotation like a slight turn of a door knob. Depending on if the MCPs are rotated or not changes the activity of another enzyme that interacts with MCPs, a protein called CheA (pronounced, ‘key A’). When CheA is active, it converts two other proteins into an active form, CheB and CheY. Confused yet? When CheY is in its active form, it interacts with the base of the flagellum and causes the flagellum to switch direction of rotation and causes the bacterium to change the direction it is moving. The take home message for the mechanism is this: when the MCPs are not interacting with chemicals (nutrients), CheA and CheY are active, and the flagellum switches rotation to make the cell go in a different direction. Hopefully for the cell, the new direction it is traveling will have more nutrients that will interact with the MCPs and block more changes in direction by CheA/CheY activity.

You might ask, if chemical compounds are always bound to the MCPs, what if the cell begins going to passed the best environment and needs to turn around? Good question. That is where the other protein activated by CheA comes in, CheB. What makes this system unique is the ability to adapt to current conditions (nutrient chemical levels) so the cell can respond to new information. A set of protein enzymes act upon part of the MCPs that can cause a change in how rotated (think door knob again) the MCP is. If the MCP is always interacting with a nutrient, a protein called CheR changes the MCP structure and causes rotation back towards the non-interacting form of the MCP. When CheA is active, it can activate CheB which reverses the changes caused by CheR. Ultimately, the whole system remains sensitive to new information over a wide range of nutrient concentrations (a 1000-fold range).

This whole system and its parts and regulation took several years for me to understand. I’m sure I did not do it justice, but hopefully you can get a small glimpse into the truth about “simple” bacteria.

In Part 3, I will discuss other decisions that bacteria make besides which direction to go in search of the promised land of milk and honey, or in this case, carbon and nitrogen sources.

A Gram-negative bacterial flagellum
A Gram-negative bacterial flagellum (Photo credit: Wikipedia)

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>

MyTH: Week 3 bacterial species is Caulobacter crescentus

This is a physical model of a bacterial flagel...
This is a physical model of a bacterial flagellum. It was imaged and modeled at Brandeis University in the DeRosier lab and printed at the University of Wisconsin – Madison. It was fabricated on a ZCorp Z406 printer from a VRML generated at Brandeis. (Photo credit: Wikipedia)
Caulobacter crescentus
Caulobacter crescentus (Photo credit: Microbe World)

It’s time again for the weekly My Tiny Highlight (MyTH). This week we will explore one of my favorites, Caulobacter crescentus. C. crescentus is a unique bacterium that has made it the focus of a lot of research due to its lifestyle and easy observable changes in cell shape. Part of the C. crescentus life cycle is spent freely swimming in its aquatic habitat using a single flagellum. These are called swimmer cells. At some point in development, the swimmer cell ejects the flagellum from itself and begins growing a stalk on the opposite cell pole as the flagellum. As the stalk continues growing, the cell produces a VERY stickly glue called holdfast at the tip of the stalk which is used to attach to a surface and is called a stalked cell. The cell undergoes division assymetrically; meaning, the two daughter cells produced are not identical (as is the case for most bacteria). One daughter becomes a swimmer cell due to new flagellum synthesis on one pole while the other remains stalked.

Thinking about split personality, how can one cell contain both a flagellum and a stalk simultaneously; both being functional? This is the focus of years of research. One answer refers to my favorite molecule discussed in earlier MyTH posts, the bacterial second messenger cyclic-di-GMP. Cyclic-di-GMP is constantly being made and degraded in C. crescentus. However, the production and degradation are sequestered to opposite poles of the cell via precise protein localization. The enzyme needed to produce c-di-GMP is at the stalked pole while the enzyme to degrade c-di-GMP is at the swimmer pole. Although there are no physical compartments within this bacterial cell, the concentration of c-di-GMP is not uniform throughout. The proteins that interact with c-di-GMP are predominantly at the stalked pole and allow for the stalk to elongate and leave the flagellated pole alone. Brilliant!

caulo

 

 

C. crescentus is also of importance for its ability to clean up contaminated surface and subsurface groundwater because it is resistant to the effects of heavy metal exposure. Also, examination of the genome was used to determine the ancestry of C. crescentus. It contains gene clusters similar to Pseudomonas species and others that are predominantly found in the soil. This fact along with the presence of genes necessary to breakdown plant-derived carbon molecules suggests C. crescentus originated on land (or under it) before winding up in its present day niche.

English: Graphical representation of Caulobacter crescentus (Photo credit: Wikipedia)

Micro! Polo!: Discovering the beneficial bacteria needed to clean our messes

Micro polo

Bacteria do not have taste buds or eyes. However, they have very fine-tuned senses that relay information about the status inside as well as in their environment. To compete and survive in virtually all environments on the planet, bacteria have evolved to sense and utilize many chemical compounds (most of which are still unknown) for energy and existence no matter how we as humans feel about these compounds. Even toxic compounds are easily metabolized by some bacteria. Whether it is hydrocarbons like petroleum or groundwater contaminated with dry cleaning chemicals, bacteria have evolved pathways to utilize these compounds.

Imagine restoring highly contaminated land for public use without expensive machinery or excessive human exposure. Current research within DOE is working towards this goal through bioremediation, utilizing bacteria with ability to render radioactive or otherwise hazardous material harmless. Even though most microbes presently performing this task are unknown, meta-sequencing projects are turning up a common set of genes (and proteins) necessary for this process.

Let’s briefly take a look at some of these toxic compounds.

TCE to DCE

Here we have (from left to right) perchloroethene, trichloroethene, and dichloroethene. PCE is a common chemical used in dry cleaning and easily contaminates groundwater. It’s removal is expensive and time-consuming, not to mention dangerous given its toxicity. However, a small number (so far) of bacteria can actually use these chemicals during metabolism when oxygen is absent from the environment (deep underground, for example). DCE is still considered a contaminant, so, how do we get rid of it? A group of bacteria discovered not long ago actually have the complete set of genes to breakdown perchloroethene to ethylene, Dehalococcoides. These bacteria have small genomes relative to the average bacterium but contain a set of genes that will render these contaminants essentially harmless.

vinyl chloride and ethylene

Vinyl chloride, the next step in PCE degradation can be further reduced to ethylene by an enzyme called vinyl chloride reductase (Vcr). To date, only Dehalococcoides are found to contain Vcr genes.

Next, I will talk about other common contaminants and the wonderful bacteria that can clean them up.

“Write what you know about” – Mark Twain

Good advice from a great communicator. From now on, the majority of posts will relate in some way to bacteria, especially microbial genomics. Most of the remainder of posts will be related to science communication and education.

Why bother spreading the love for the little creatures? I believe this quote from microbialgenomics.energy.gov sums it up:

By some estimates, microbes make up about 60% of the earth’s biomass, yet less than 1% of microbial species have been identified. Because most do not cause disease in humans, animals, or plants and are difficult to culture, they have received little attention. Identifying and harnessing their unique capabilities will offer us new solutions to longstanding challenges in environmental and waste cleanup, energy production and use, medicine, industrial processes, agriculture, and other areas. Scientists also are starting to appreciate the role played by microbes in global climate processes, and we can expect insights about both the biological underpinnings of climate change and the contributions of microbes to earth’s biosphere. Their capabilities soon will be added to the list of traditional commercial uses for microbes in the brewing, baking, dairy, and other industries.

There is so much we don’t know about microbes. However, we are beginning to understand their enormous adaptability. Whether it is 30,000 feet above the ground or two miles beneath it, bacteria can inevitably survive. I will now focus on getting the word out about the little guys who can’t speak for themselves.

Microbes can be used in soil cleanup
Microbes can be used in soil cleanup (Photo credit: Wikipedia)