How do bacteria make decisions? Part 6: It takes a village

The marvels of single celled organisms is that they are able to integrate all kinds of stimuli and make one grand decision that affects how they proceed. Bacteria do in one cell what we as humans do with billions. However, do bacteria contain the ability to think as a group or community?

The answer is absolutely. It is called quorum sensing. The pioneer for this research is Bonnie Bassler from Princeton University. Listening to her tell her story of the curiosity she felt when observing how and why a certain group of bacteria emitted light, or bio-luminescence is great. (Watch here). Through her investigation with a insignificant bacterium, Vibrio harveyi, she opened up a whole new field of microbiology.

Many bacteria synthesize signaling molecules that serve as messages to other bacteria saying, “I am here”. Since bacteria don’t have senses that we are familiar with like sight and hearing, these signaling molecules tell other bacteria who is around. When there aren’t a lot of bacteria sending out the signal, no big decisions are made. However, when enough bacteria are around to tell all other village members the approximate population, all village members act together to make a committed decision. In the case of V. harveyi it is the production of a light emitting molecule, but for other bacterial species it may be activation of pathogenicity. From the perspective of the bacterium, you don’t want to decide alone to make a big commitment like invading another organism. By taking a bacterial census through quorum sensing, these bacteria make a educated decision only when their population is high enough to make an impact. For some species, this critical number may be less than ten. However, in some cases, the population needs to be in the millions.

I think bacteria can teach us a very important lesson via quorum sensing: don’t go it alone. It takes a village.

Azospirillum brasilense electron micrograph

From vinegar, a potential cheap energy alternative: Bacterial nanowires Part 1

Energy. We all have it and we all need it on multiple levels. Within our body, energy is stored in a molecular currency that is conserved among all living organisms, adenosine triphosphate, ATP. Of course, you should know that as humans, we require oxygen to live. During our metabolism, hydrogen atoms are divided into their two opposite parts, the proton and electron. The electrons are shuttled through several enzyme complexes while the protons are pumped out of the mitochondrial matrix creating a much greater proton concentration outside than inside. This imbalance is what drives Nature’s smallest rotary motor, ATP synthase. But what about the electrons? Your body has no need for them, energetically speaking so something needs to accept them for the big show to continue. In our case, the acceptor is oxygen. Oxygen accepts the electrons, and the protons that come along to reconstitute the full hydrogen atom, to form water, H2O. A lot of organisms need oxygen for the same reason. However, just as many organisms have no such requirement while some others are afraid of oxygen.

This leads to the question of what accepts the electrons within organisms that don’t have oxygen present? Anaerobic (“no oxygen”) respiration can utilize many different molecules to accept electrons depending upon the genetic capacity of the organism in question. The more genes within a genome that encode enzymes that can coerce compounds to accept electrons, the more options an organism has in regards of what environment they can survive and thrive. If you have kept up with this blog, you know about a group of bacteria that have evolved a variety of strategies to survive in some of the most undesirable environments on (or in) Earth; Geobacter.

Geobacter have been identified in many anaerobic environments including, soil, sediments, wetlands, and even rice paddies. Geobacter are the predominant species in these environments where there is no oxygen and few other choices for electron acceptors. They are very efficient with their energy usage as well as creative in the ways in which they “relieve” themselves of unwanted electrons. In the absence of oxygen, Geobacter have two major methods of removing the reducing power of electrons. The method of choice used depends upon the type of compounds within their environment capable of accepting electrons; soluble or insoluble. Soluble, water dissolving, compounds include many common organic materials such as amino acids and carbohydrates. Uptake of these molecules is possible and necessary. However, not all soluble compounds are easily tolerated by Geobacter including heavy metals. How can Geobacter utilize these electron acceptors if they can’t bring them inside their cell membranes? The answer is by taking the electrons outside the cell through a labyrinth of electron shuttling proteins called cytochromes. Cytochromes, especially the predominant Geobacter type cytochrome c, use prosthetic cofactors like hemes or copper ions to ferry electrons out of the cell to waiting acceptors.

This is where it gets interesting…

What if only insoluble electron acceptors are present? There’s an op for that! Operon that is. Actually, several operons that are active when sources of soluble electron acceptors are very low. Geobacter can synthesize extracellular appendages that can navigate over several cell lengths to find insoluble acceptor compounds including the predominant iron Fe3+ within the subsurface. These appendages called pili are found in many other bacteria. However, there is something a little more special about Geopili, they can conduct electricity. The protein subunits that compose the geopilus have a shorter peptide sequence than the one found in a majority of other pili systems. Also, a few of the cytochromes c proteins that shuttle electrons to the outer membrane of the cell can actual be deposited along the pilus to deliver electrons to waiting acceptors far away from the actual cell itself.

animated bacteria GIF, bacterial nanowire gif
A Geobacter cell protracts pili (black) out into its environment. As it does so, cytochrome c proteins (blue) are deposited upon the pilus for electron transfer to insoluble electron acceptors (brown).

Shocking: animated preview of explaining bacterial nanowires

animated biochemistry gif
A model of the protein structure of a Geobacter pilus with the N-terminal phenylalanine in spacefill and colored blue.

I am working on a post about how huge the discoveries that bacteria can conduct electricity can potentially be. This is a simple animation showing a model of a Geopilus with the phenylalanine residues at the amino terminus of each subunit in spacefill and colored blue. It is suggested the electrons leaving the bacterial cell travel along these pili via aromatic amino acids, especially the phenylalanines.

Animated GIFs: cyclic-di-GMP binding to PilZ protein and a riboswitch

animated biochemistry gif
NMR structure of a PilZ protein from Pseudomonas aeruginosa binding to cyclic-di-GMP. Residues needed to bind c-di-GMP will appear, shown in orange. Lastly, a surface rendering of the complex.
animated GIF, cyclic-di-GMP dimer 20 conformations
The cyclic-di-GMP dimer from the previous figure in the 20 different conformations when bound to PA4608.

 

a riboswitch that regulates gene expression. This particular riboswitch binds very tightly to cyclic-di-GMP

 

 

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 6 focus: Anaeromyxobacter spp.

This week I will write about bacteria that I dare say any of my readers know about, Anaeromyxobacter. Time again for My Tiny Highlight (MyTH). These bacteria were only recently discovered, first in Michigan but later in other sites. They are a peculiar member of a familiar group of bacteria, Myxococcus. Unlike the name suggests, Anaeromyxobacter can grow in the presence of oxygen, but they prefer anaerobic environments. They are found deep in the subsurface and can metabolize hazardous material for energy production similar to other deltaproteobacteria like Geobacter. Compounds in the environment that contain chlorine atoms are usually not a good thing. Luckily, Anaeromyxobacter can utilize these compounds to produce energy. Needless to say, Anaeromyxobacter are very versatile metabolically speaking since they can respire on 2-chlorophenol (or other halophenols), Uranium, iron, manganese, oxygen, nitrite, nitrate, nitrous oxide, and fumarate, to name a few. As far as metabolism goes, these bacteria are about as robust as they come. I personally have studied the genomes available for this genera of bacteria for a postdoc proposal. I can tell you, these guys are remarkable on many fronts.

First, Anaeromyxobacter have over half as many c-type cytochromes as the model Shewanella, 69 to 40. Cytochromes are the workhorses of metabolism that guide electrons towards the final electron acceptor like oxygen, iron, or uranium. Cytochromes accomplish this by shuttling electrons on heme groups. It is not uncommon for cytochromes to have multiple heme groups. Remarkably, Anaeromyxobacter has one cytochrome that has an astounding 40 heme groups. Shewanella cytochromes have  up to 10 hemes, to my knowledge.

What caught my eye was the number of PilZ domain proteins encoded within Anaeromyxobacter genomes. Four Anaeromyxobacter genomes have been sequenced: A. dehalogenans 2CP-C, 2CP-1, and FW105-9 as well as Anaeromyxobacter spp. K. Peeking into the genomes, all four are dead last in the number of enzymes that breakdown the bacterial second messenger molecule cyclic-di-GMP out of 1822 genomes that have at least 1 (they have 1 each). All four genomes are middle of the pack for the number of genes encoding enzymes to synthesis c-di-GMP with 10 (rank 989 out of 2032). Are you ready for this? Two of the four genomes contain 21 PilZ domain proteins (the binding domain of c-di-GMP). This is fourth among 1321 genomes which contain at least 1  PilZ protein; fourth most! The other two genomes are not that shabby at 18 and 13 PilZs each (rank 14 and 22 out of 1321 genomes, respectively).  Take a look at Table 1 to compare these numbers to the genomes of two model subsurface organisms from Geobacter and Shewanella.

Table 1: Annotated enzymes and receptor proteins for the bacterial second messenger cyclic-di-GMP in representative dissimilatory iron-reducing bacteria.

 Bacteria                                 DGCs                   PDEs                          PilZs

A. dehalogenans                     

2CP-C                          10 (989/2032)*    1 (1822/1822)             18 (14/1321)

2CP-1                          10 (989/2032)      1 (1822/1822)             21 (4/1321)

Fw105-9                     10 (989/2032)      1 (1822/1822)             13 (22/1321)

Anaeromyxobacter

K                                10 (989/2032)      1 (1822/1822)             21 (4/1321)

 G. lovleyi             43 (105/2032)      17 (1240/1822)            9 (53/1321)

S. oneidensis      51 (53/2032)         30 (43/1822)            4 (959/1321)

  • indicates (genome rank/ total number of genomes containing at least one representative of the domain)

Based on annotations from MiST2 and Pfam proteome databases (http://mistdb.com/ and http://pfam.sanger.ac.uk/proteome/browse)

To me, this signifies that Anaeromyxobacter really rely heavily on sensing c-di-GMP to regulate their metabolism and lifestyle. This is especially true when you consider where in the genome the PilZ genes are found. For example, A. dehalogenans 2CP-C encodes 18 PilZ proteins. Several of the genes for these are in gene neighborhoods with nitrogen metabolism genes suggesting a genetic link between c-di-GMP sensing and nitrogen metabolism. I wish I could have studied these links between c-di-GMP signaling and metabolism in some capacity other than bioinformatically. However, those discoveries will have to go to the next chump in higher education.

animated cyclic-di-GMP gif, second messenger gif
110 different confirmations of cyclic-di-GMP

Why should we care about bacteria? For one thing, they are smarter than us

animated bacteria GIF, electron transport chain gif
The human electron transport chain with ATP synthase
animated bacteria GIF, electron transport chain gif
Some of the protein members of bacterial electron transport chains

We think we are pretty smart as humans. It wasn’t until recently that dolphins were considered non-human “people” by scientists due to their intelligence. But, I guess it all depends on your perspective…

A lot of federal research funding promotes the study of known, and unknown, bacteria. Some watch dog groups may ask why should we as humans care about bacteria? This is my argument.

As humans, can we live 30,000 feet above ground? Can we live 4km (~2 mi.) below ground? Can we “eat” rocks? Can we survive extended periods of time without food? The answer to these questions are, “No.” However, if the questions are focused on bacteria, then the answer is an astounding, “Yes!” Are these abilities to survive in extreme environments significant to us as humans? The answer is beyond our imagination at this point. Metabolically speaking, bacteria are orders of magnitude more complex than humans who have to rely on energy production within their mitochondria, which are living fossils of a former bacterium (endosymbiont). Over the past couple billion years, bacteria have found creative ways to keep an advantage over their neighbors through, for example, utilizing new materials for energy or producing antibiotics. These examples come from the negligible percentage of known bacteria which stands at less than 1%. This is why research funding is vital and necessary.

In our changing climate, nations are looking for alternatives to replace fossil fuels like petroleum and natural gas to ensure the quality of later generations. Bacteria are Nature’s tiny chemical factories that have learned to use almost all natural, and some artificial, substances to generate cellular energy. One major factor when looking for alternative energy sources is sustainability. Bacteria are self-sustained when given the necessities for life which can be as little as sunlight and carbon dioxide while producing helpful byproducts than be utilized as alternative energy sources by the public. Such examples include ethanol, butanol, or hydrogen.  A major focus of funding is to enhance bacteria or their metabolic pathways to develop proficient generators of biofuels.

From the Industrial Revolution all the way through the Cold War, we have certainly made a mess of things in our environment. Some land is unfit for public use due to toxic or otherwise hazardous materials. Luckily for us, research has found an amazing discovery among the bacterial world. A subset of bacteria can and do harness the ability to utilize materials for energy production that we as humans if exposed to these compounds would become ill or die. The hazardous material seeping into the subsurface has altered the bacterial communities found within. Some of the ecological micro-communities rely upon each member to utilize a different byproduct of other community members in order for the community to exist. Several bacterial genera have been shown to remove toxic material like uranium or chromium from vital water tables we as humans rely upon for drinking water.

The metabolic versatility of bacteria is one of our tickets to a better world, but in order to utilize these little miracle generators, continued research is necessary.