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

E. coli Up Close and Personal: Scientific Rockstar and Public Enigma

This is an article created as guest post for Kitchen Table Science.

It seems nothing puts fear in the hearts of the masses like mentioning E. coli. Most think of the disease-causing germ that contaminates everything from spinach to beef. I agree the strain Escherichia coli O157:H7 and its cousins O26, O145, STEC O104:H4, and others, are a wretched bunch that give the whole species a bad reputation. What makes these strains so vile are the extra proteins encoded within their genome. For example, E. coli O157:H7 has a larger genome coding for 5561 proteins while the parent strain E. coli W codes for 4739 proteins. Thus is the life of a bacterium. The fact there are so many bacteria means they are usually in close proximity to each other. Physical contact between bacteria, not just those of the same species, allows for the transfer of genetic material between two cells (horizontal gene transfer); the closest thing to sexual reproduction you will find for prokaryotes. If the genes transferred to the recipient give it an advantage or new ability that helps it compete and thrive in its environment, they will remain in the genome. Otherwise, they will be discarded after genome compaction.

Most E. coli are completely harmless and, in fact, beneficial. If the general public knew more than what was broadcasted on the 24 hour news channels, they would see the tiny rockstar scientists have known about for some time now. Beginning in earnest in the 1950s, E. coli is easily cultured in laboratories and very cheaply. Its quick generation time (20 min. at optimum temperature) made it a great model organism to study in many fields of science and medicine. This organism is the work horse of biotechnology due to the relative ease of manipulating its genome or adding complete genetic circuits into the cell using plasmids.

Sidebar

Even after 50 years of intense research, E. coli still holds many unknowns out of the reach of our knowledge. Like all other sequenced genomes, there are a number of “hypothetical proteins” and “proteins of unknown function”. This means by our best abilities, we can locate parts of the genome that code for proteins, however, this doesn’t mean we are able to understand the function of a particular protein.

Image courtesy of Predrag Radivojac. Thanks, Pedra.

The above shows just how much work is left to understand the biological capabilities of Mother Nature. Short version: over 40 gene sequences in databases, but the number of which that we know what the function is holding steady around 500,000 and the number of solved protein structures is over 100,000. This is a growing gap between the known and unknown.

 Where would we be without E. coli?

One advantage of E. coli is their effect on our immune system. Some may find this counter-intuitive, but E. coli can lower the workload of our immune system when pathogens are present, especially in the intestine. When E. coli attach to the GI wall, it changes the acidity of the lining thus making infection from other bacteria less likely. Another benefit is in overall digestion. E. coli promotes better breakdown of food thus preventing accumulation of waste which is a major cause of bloating and constipation.

Many outside the scientific community may not be aware of how integral E. coli are to the advancement of many fields including medicine, pharmacology, biology, and even human physiology. Another reason to not believe the hype.

Repeat after me: There is no newly discovered hidden code in DNA.

It is a very sad and unfortunate occurrence when newly released research findings are hyped and overstated. This week the University of Washington Office of News & Information released a press release embarrassingly called “Scientists discover double meaning in genetic code“. Since then, the release has been picked up by websites across the globe. In that way, the press release did its job. Unfortunately, the statements within the release along with the title have done a world of harm. I can only hope it was unintended.

The release starts by stating scientists discovered a second code hiding within DNA.

This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

This ‘second code’ will not change anything scientists do regarding studying DNA. This ‘hidden second code’ has been known and studied for decades.

Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

Let me rewrite this paragraph to make it factual:

Since the genetic code was deciphered in the 1950s, scientists have continued to find additional layers of complexity in the regulation of how genes are transcribed to make proteins. The current study from UW scientists have added additional knowledge to this growing field.

This is the most unfortunate part:

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

This release was written by writers in a news department as a marketing piece, but when the scientist also grossly exaggerates the findings, it is very sad. Like Emily Willingham said in Forbes, “I can only hope that Stamatoyanopoulos didn’t really say that”. Scientists have not made any such assumption and have decades of evidence to the contrary.

The study shows that changes in the DNA sequence can have two-fold consequences upon the protein made from it. It can change the amino acid sequence of the protein and change which proteins bind that help transcribe the DNA into the RNA used to create the protein. This is not new. The finding that made this study worth of the prestige of publishing into Science is the frequency of the DNA code that is used to determine which proteins bind to the DNA to create the right form of the protein. These proteins, known as transcription factors, have been known for decades and bind to a number of DNA sequences to ensure the cell creates the exact protein needed.

As is common in press releases, the last part of the piece tries to explain DNA and the language of genes. In this aspect, the release does an even worse job:

The genetic code uses a 64-letter alphabet called codons.

The genetic code uses 64 different combinations of nucleotide sets of three, called codons; most of which code for one of the twenty amino acids needed to make a protein.

I could keep going, but I’m exhausted by trying to set the record straight.

Life in Motion: More realistic look using protein conformations

animated gif, animated bacteria gif, animated biochemistry gif
Outer membrane proteins (at top): OmpX and OmpG. Periplasmic proteins from left to right: Cytochrome c7, arsenate reductase, PpcA. Inner membrane is the methane monooxygenase with a methane monooxygenase regulatory factor beneath in the cytoplasm.

When I took biology in school, all the figures were boring and frozen. It wasn’t until I took biochemistry that I realized life isn’t stagnant. Everything within a living cell is constantly in motion. So, why not depict a figure showing that? The figure above is compiled of NMR structures of various proteins with each frame of the gif being a different confirmation or vibration from the available PDB file. Hope you enjoy!

MyTH: Week 4 bacteria highlight: Geobacter spp.

Welcome to Week 4 of My Tiny Highlight (MyTH) series. This week I will focus on not a species. Instead, I will focus on a genera; Geobacter. Like the previous highlights, Geobacter are proteobacteria that has become relevant only more recently. Geobacter were first discovered and isolated in the late 1980s by UMass professor Derek Lovley. In a short amount of time, Geobacter has become a model organism in highly active research areas. These include bioremediation and microbial fuel cells. Several different Geobacter spp. are routinely found in soil and sediment samples from contaminated sites. For many bacteria, oxygen is not required to survive. During the course of evolution, many bacteria, including Geobacter, can undergo anaerobic respiration, or create energy without the need for oxygen. The first Geobacter genome was published in 2003 to much fanfare in the journal Science. One reason for this was the discovery that Geobacter are motile, having several chemotaxis proteins. Also found was an unprecedented number of cytochrome (111!) genes which are usually used for electron transfer via attached heme groups to the protein. The number of bound hemes vary between 1 and 27. Very impressive. In order to survive, these bacteria can use a host of molecules as an “electron sink” so their metabolism can continue. Geobacter have two main strategies for this; if the “sink” is soluble, they can utilize a host of cytochrome c proteins on their outer membrane exposed to their environment. If these “sinks” are insoluble like metals for example, they can essentially extend appendages from their membrane to the “sink”.

This is where it gets interesting…

These appendages called pili have extracellular cytochrome c proteins along their length. So, electrons are transported from inside the cell through the pili and cytochromes to the available electron sink. Essentially, they are able to conduct electricity as a means of respiration. Here are two animations showing the differences:

 

extracellular electron transfer, geobacter
Electrons: yellow
iron: black
MacA protein: dark green
PpcA: blue
OmcB: black
other outer membrane cytochromes: orange and light green
bacterial nanowire, bacteria, chemotaxis, microbiology, geobacter
A bacterial nanowire. Electrons (yellow) are passed through pili (purple) to OmcS (cyan) for reduction of iron (black).

 

Animated GIF: Extracellular electron transfer to soluble iron. Example of Geobacter respiration

extracellular electron transfer, geobacter
Electrons: yellow
iron: black
MacA protein: dark green
PpcA: blue
OmcB: black
other outer membrane cytochromes: orange and light green

When Geobacter are in an environment where soluble iron is present, this can serve as the terminal electron acceptor in metabolism through an elaborate electron highway.

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)