Bacterial Chemotaxis and Human Memory: Pete and Repeat

Many do not place ‘bacteria’ and ‘memory’ in the same sentence. Normal human perception does not connect the two concepts. However, Mother Nature seems to have a more profound perception. The past 50 years or so of scientific investigation has shown how our uniqueness as humans is actually commonplace across all forms of life on Earth. Case in point, how closely associated molecular memory is between bacteria and human.

Bacteria use adaptation to signals as memory

Swimming bacteria do not move randomly in their environment. This behavior would be futile and counterproductive. Instead, bacteria are constantly monitoring their environment in search of food and poisons. Moving towards the former and away from the latter. This observation was first published in the late 19th century. Bacteria, like the famous and infamous E. coli, use molecular antennae to receive these important ‘signals’ as the basis in the decision of which direction to swim. What if the bacteria find a great place to reside with lots of food but still need to receive signals to ensure they remain there? The antennae have sections that can be modified easily and reversibly. These modifications, in the form of methylation, alter the sensitivity of the antenna protein to subsequent signals. Methylation allows these antennae not to receive the number of absolute signals but relative signals. In other words, the antenna protein through fine-tuned methylation detects changes in the number of signals now versus some time in the past. This is the basis of molecular memory.

These antennae are proteins called methyl-accepting chemotaxis proteins, or MCPs. MCPs accept methyl groups from the essential cofactor S-adenosylmethionine (aka SAM or AdoMet). AdoMet is essential to both prokaryotes and eukaryotes like humans. The methyl groups are added by a protein called CheR (pronounced ‘key R’) which transfers the methyl from AdoMet to very specific amino acid side groups of glutamate. The process, called O-methylation adds the methyl group to the single-bonded oxygen on the carboxyl.

O-methylation reaction
O-methylation reaction. Courtesy of www.brenda-enzymes.org.

The length of a bacterium’s molecular memory is very short in comparison to how we perceive memory at only a few seconds. But, to bacteria it is long enough to successfully navigate the environment with similar precision when concentrations of food or poison vary (up to several orders of magnitude, or ~1000x).

Does the basis of molecular memory in humans mimic bacteria?

Eukaryotes, including humans, use a very similar mechanism in signal transduction to bacteria. Phosphorylation (transferring a phosphate group from ATP or GTP to a protein amino acid) is the basis of all signal transduction and cell regulation. Bacteria use histidine kinases and response regulators, as do plants to some degree. However, the majority of regulation through signal transduction in eukaryotes is through two types of proteins, RAS proteins and the heterotrimeric G-proteins. G-proteins interact with membrane receptors that regulate their activity. What determines which surface receptors G-proteins interact with? Isoprenylcysteine methyltransferase, or ICMT, is one of two methyltransferases that regulate signal transduction activity. ICMT is a membrane protein that uses AdoMet to add methyl groups to isoprenylcysteine, a post-translationally modified cysteine residue on both heterotrimeric and RAS-related G proteins. Methylation regulates which receptors the G-proteins interact with, thus playing a major role in connecting the initial signal to downstream regulatory pathways. The carboxyl methylation essentially modulates G-protein signalling globally.

G-protein carboxyl methylation is regulated by GPCR signaling and, as seen above, GPCR signaling is regulated by G-protein carboxyl methylation. This feedback/feed forward loop could be seen as a form of molecular memory stored in methylation patterns. Within the brain, ICMT activity is almost exclusively found in the region controlling coordination of movement. Thus, methylation could be used to modulate certain neuronal signaling pathways which result in learned patterns of sensory-motor skills.

The only other major methyltransferase is from a protein known as PPMT. PPMT interacts with a major enzyme in signal termination, the protein phosphatase PP2A. PPMT adds methyl groups to the backbone carboxyl of a specific leucine in PP2A. This carboxyl methylation helps determine which B subunit PP2A interacts with and where in the cell PP2A can be found. PPMT structurally resembles CheR in bacterial memory. Moreover, the enzyme that removes the methyl group from PP2A, PME, structurally resembles the bacterial enzyme that removes methyls from MCPs, CheB.

PP2A is one of the major regulators of pathway coordination to maintain synaptic plasticity in the brain. Interestingly, methylation defects and PP2A-PME complexes are suggested to play a role in the cause of Alzheimer’s Disease and memory loss. Methylation defects leading to defective phosphatase activity of PP2A leads to accumulation of a phosphorylated subunit of the structural protein microtubule. In this phosphorylated form, the filaments used to keep axons structurally sound collapse and lead to loss of normal synapses. Therefore, molecular memory in the form of methylation plays a vital role in promoting normal brain activity and its disruption can ultimately lead to dementia. 

Chicken, meet egg. Egg, meet chicken.

So, from bacteria to human, carboxyl methylation is necessary for memory. Did these pathways evolve individually in parallel, or did the memory we have today originate in the predominant lifeforms found within us?

 

Suggested Reading

Li and Stock. (2009) Biol. Chem. 390: 1067-1096. DOI 10.1515/BC.2009.133

Animated GIF: Bacteria swimming

animated GIF bacteria, animated GIF, microbiology
Azospirillum brasilense cells swimming in an oxygen gradient. Magnified 40X

I’ve spoke a lot lately about bacterial chemotaxis. I wanted to give you a taste of the real deal. These cells are happily navigating the medium with many swimming in circles, a phenotype of Azospirillum brasilense cells prior to cell aggregation (grouped cells).

 

Citations:

Qi, X. et al. Swimming motility plays a key role in the stochastic dynamics of cell clumping. (2013) Physical Biology 10: 026005. Link

Bible, AN., Russell, MH., Alexandre, G. The Azospirillum brasilense Che1 chemotaxis pathway controls swimming velocity, which affects transient cell-to-cell clumping. (2012) Journal of Bacteriology 194: 3343. Link

MyTH: Week 5 focus is Pseudomonas aeruginosa

Time again for My Tiny Highlight (MyTH) of a particular bacterium. This week is the infamous Pseudomonas aeruginosa. This trooper can be found almost anywhere on earth due to its ability to use all kinds of material as food including diesel and jet fuel. Most of us know it as a common infection you get while in the hospital because it is so darn hard to kill. If you know someone that suffers from cystic fibrosis, this bacterium can be fatal as it is commonly found in the lungs of these patients causing pneumonia. I personally learned about this bacterium in school when talking about hot tubs due to its resistance to disinfectants.

P. aeruginosa is one of the most famous microbes for forming biofilms. A biofilm is a group of cells that attach to each other and to some surface usually by secretion of sticky sugars from the cells. A common sticky sugar, or exopolysaccharide (EPS), excreted by P. aeruginosa is alginate, an uncommon sugar for bacteria since it is most commonly found associated with brown algae. Its existence in Pseudomonas has led to significant knowledge about the synthesis of alginate (alginate biosynthesis; another ring in the bacterial circus). This knowledge is leading to novel medical applications for alginate.

P. aeruginosa is also known for its role in a multicellular behavior which seems strange for a single-celled organism but is becoming more and more common. Quorum sensing was first described over 40 years ago. I beg you to check out Bonnie Bassler‘s TED talk about this. QS is how single cell bacteria are able to send signals into the environment to communicate with members of their own species and with other types of bacteria as a way to assess their population.

Another feature of P. aeruginosa is their modes of transportation, i.e. motility. P. aeruginosa has two major modes of getting around their environment, swimming motility with flagella or “twitching motility” on a surface using Type IV pili. We have discussed flagellar motility before (Chemotaxis). Type IV pili (TFP) is different. Pili are somewhat similar to flagella because they protrude out of the cell and are used to move around. Unlike flagella, pili don’t rotate but rather extend out before retracting back to the cell pulling the cell in the direction of the pili tip. The coordination of pili extension and retraction is guided by a chemotaxis-like pathway. Many bacteria have evolved to use chemotaxis proteins that have adapted to new roles within the cell.

I will end this MyTH with a special shout out to one of my favorite researchers, Carrie Harwood. Caroline Harwood is a professor at the University of Washington in Seattle. Carrie’s daughter suffers from cystic fibrosis and this led to Carrie’s curiosity in P. aeruginosa. She is a pioneer and a role model for many female scientists including Becky Parales. For her tireless career, Carrie was inducted into the National Academy of Science a few years back. A recognition well deserved.

Pseudomonas aeruginosa scientist Carrie Harwood. One of the nicest people in Science!
Pseudomonas aeruginosa scientist Carrie Harwood. One of the nicest people in Science!

Another animated GIF: growing iron oxide on Geobacter pili: bacterial nanowires

bacterial nanowire, bacteria, chemotaxis, microbiology, geobacter
A bacterial nanowire. Electrons (yellow) are passed through pili (purple) to OmcS (cyan) for reduction of iron (black).

Bacteria Chemotaxis Explained with Animated GIFs. Bacterial Behavior in Motion

bacteria, chemotaxis, random bias
With no attractant or repellant, bacteria have a “random bias”. This means they switch direction randomly.
bacteria, chemotaxis, attractant response
When bacteria are in an attractant gradient (colored orange), they switch direction less often when attractant concentration is higher.
bacteria, chemotaxis, repellant response
However, when a repellant is present (colored red), bacteria switch direction more often in high repellant concentrations.

 

 

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>