From vinegar, a potential cheap energy alternative: Bacterial nanowires Part 2 with three animations


animated bacteria gif, bacteria gif, metabolism gif
Acetate entering the cell

I know you are wondering how vinegar fits into all of this. Acetate, or acetic acid, is what constitutes vinegar. It also is the basic two carbon currency in organic metabolism. It is the basis of acetyl-CoA, a molecule utilized in carbohydrate metabolism as well as fatty acid synthesis and degradation. It can be a major source of the precious hydrogen atoms to drive energy production in Geobacter.

animated bacteria gif, metabolism gif
Once entering the cytoplasm, acetate is converted to acetyl-phosphate via acetate kinase (black, right) and ATP. Then acetyl-phosphate is converted to acetyl-CoA via phosphate acetyltransferase (black, left) and coenzyme A.

Once acetate enters into the cell, it undergoes phosphorylation by acetate kinase (ACK) to form acetyl-phosphate. Phosphorylation is an important way to activate molecules so they can be utilized in metabolic pathways. Once formed, acetyl-phosphate is a substrate for phosphate acetyltransferase (PTA) which converts acetyl-phosphate to acetyl-CoA. Once formed, acetyl-CoA can enter to many different metabolic pathways.

Research studies have shown biostimulation (addition of some nutrient to stimulate growth of organisms) of uranium-contaminated sites with acetate can increase the reduction of uranium from a soluble form to an insoluble form that is no longer a threat for entrance into the water shed. Increased uranium reduction is the equivalent to increased electricity generation just by swapping the terminal electron acceptor from the electron transport system from uranium to electrode of a microbial fuel cell.

So there you have it, adding vinegar (acetate) can stimulate the generation of bioelectricity rather cheaply.

animated bacteria gif, geobacter gif, bacteria gif
Electrons (glowing ball) are transferred from MacA (maroon) via cellular respiration to PpcA (bright red) in the periplasm to the awaiting geopilus (green) for extracellular electron transfer to a waiting electron acceptor.

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

Biology quiz


Love it! My weakness for animals is overwhelming sometimes…

Adventures and Musings of an Arch Druidess

image

View original post

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.