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!