Microbial nanowires, OmcZ filaments and Borgs:

 

Picture drawn by DALL-E to the prompt "Microbial nanowires and OmcZ filaments on Bacteria"

What are nanowires?

Microbial nanowires are specialized structures produced by certain types of bacteria, most notably a species known as Geobacter sulfurreducens. These nanowires are essentially tiny conductive filaments, capable of transmitting electrical currents. They play a significant role in the bacteria's metabolism and environmental interactions.

Geobacter sulfurreducens and other similar bacteria are anaerobic, which means they do not require oxygen to live and grow. These bacteria are often found in environments such as soil and sediments where oxygen may be limited or absent.

To survive in these conditions, they utilize a process called extracellular electron transfer (EET), where they transfer electrons to external acceptors when oxygen is not available. This process is critical for these bacteria to dispose of excess electrons generated during their metabolic processes.

The microbial nanowires are a key part of this EET process. They essentially act as biological "wires", conducting electrons from the interior of the bacterial cell to external electron acceptors, which could be minerals in the soil or even electrodes in a microbial fuel cell.

Scientists are particularly interested in these microbial nanowires because of their potential applications. For example, they could be used in bioelectrochemical systems such as microbial fuel cells, where bacteria generate electricity by breaking down organic matter. They also hold potential for bioremediation, where bacteria could be used to clean up polluted environments by breaking down harmful substances.

Microbes also could use nanowires to temporarily store electrons on metals. Building up an electron concentration on a metal anode would create a battery of sorts that the cells could later use to fuel metabolic activity. While these potential implications provide a reasonable hypothesis towards the role of the bacterial nanowire in a biological system, more research is needed to fully understand the extent of how cellular species benefit from nanowire use.

Two papers below describe novel features of nanowires.

 OmcZ is the only cytochrome known to form  that facilitate long-range (>10 μm) extracellular electron transfer between cells.

Wang et al. eLife 2022;11:e81551. DOI: https://doi.org/10.7554/eLife.81551 "Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times"

1. This paper reports the cryo-EM structure of the octaheme cytochrome OmcZ from Geobacter sulfurreducens. OmcZ forms extracellular conductive filaments that facilitate long-range electron transport.

2. The structure reveals that OmcZ has a unique protein fold and heme arrangement compared to two other cytochrome nanowires (OmcS and OmcE) from Geobacter whose structures were previously solved.

3. In contrast to the linear heme chains in OmcS/E, OmcZ has a branched arrangement with heme pairs oriented at distinct angles. One heme diverges from the chain and is highly solvent exposed.

4. OmcZ lacks the inter-subunit heme coordination seen in OmcS/E and has no glycosylation. These differences indicate OmcZ is a new type of cytochrome nanowire that evolved separately.

5. The solvent exposed heme in OmcZ may allow it to form more conductive networks on surfaces compared to OmcS/E. This fits with prior measurements showing OmcZ has higher conductivity.

 Areas for Further Research:

1. Determining the molecular basis for OmcZ's greater apparent conductivity using computational modeling of its heme chain electronic properties. How does solvent exposure affect hopping rate?

2. Structural studies of OmcZ homologs like those found in methane-oxidizing archaea. Do they share the distinct heme arrangement and exposed heme site?

3. Testing conductive properties of OmcZ networks on electrodes using AFM or other nanoscale techniques. Do the exposed hemes enhance contact with surfaces?

4. Exploring whether OmcZ's branched heme motif is found in other multi-heme cytochromes. This could reveal new conductive filament families evolutionarily distinct from OmcS/E.

5. Investigating the role of OmcZ in Geobacter biofilm formation. Does the exposed heme help wire cells together into more conductive networks compared to OmcS/E filaments?

 Marie C. Schoelmerich et al  2023 BioRxiv https://doi.org/10.1101/2023.08.01.549754  "Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires"

1. The paper validates and expands on previous findings that Borgs are a distinct class of huge (up to 1.1 Mbp) extrachromosomal genetic elements in anaerobic methane-oxidizing archaea called Methanoperedens. Using long-read nanopore sequencing, the authors confirm the linear structure and inverted terminal repeats of several published Borg genomes first assembled from short reads.

2. Analysis of 17 complete and near-complete Borg genomes reveals 40 conserved single-copy marker genes present in all Borgs that define a largely syntenous genomic backbone. These marker genes enabled identification of 3 new Borgs from metagenomic data, indicating their utility for Borg discovery.

3. Phylogenetic analysis of the 40 marker genes divides the Borgs into 2 major clades and provides evidence for vertical inheritance from a common ancestral type followed by diversification. This supports the classification of Borgs as a cohesive genetic entity.

4. Many Borg-encoded proteins are more highly expressed in situ than those of the Methanoperedens host, including cytochrome OmcZ proteins that can assemble into electrically conductive nanowires. This indicates Borgs augment the metabolic capacity of their hosts.

5. Methanoperedens and Borgs have distinct DNA methylation patterns, suggesting a mechanism to distinguish self vs non-self DNA. Borgs may also encode viral capsid proteins, raising the possibility they exist outside host cells.

    

   Key points
   

   • OmcZ is the only cytochrome known to form microbial nanowires that facilitate long-range (>10 μm) extracellular electron transfer between cells.

   • Nanowires act as electric cables to shuttle electrons from methane oxidation to external electron acceptors like iron minerals. This enhances the host Methanoperedens' metabolic capacity.

   • Borg and Methanoperedens OmcZ proteins have conserved structural features that allow OmcZ to self-assemble into highly conductive nanowires:

   • They contain key heme-binding histidine pairs that bring hemes close together. This confers ~1000x higher conductivity than other nanowires.

   • Surface residues are highly conserved, providing stability even under denaturing conditions like low pH.

   • The Borg genomes contain the entire conserved gene cluster needed for nanowire assembly - OmcZ plus protease and isomerase for processing.

   • Metatranscriptomics shows the Borg-encoded OmcZ is expressed at 3-6x higher levels than the host's OmcZ.

   • The authors suggest this shows Borgs augment Methanoperedens' ability to couple methane oxidation with extracellular electron transfer to soil minerals.

   • Some Borg OmcZ lack a motif to trap soluble electron acceptors, implying they interact with insoluble acceptors.

   • OmcZ phylogeny indicates horizontal transfer between Borgs and Methanoperedens.

    

   Areas for Further Research:

1. Elucidating the specific Methanoperedens hosts for each Borg type through culture-based experiments or sequencing of single cells containing Borgs.

2. Determining the subcellular localization of Borgs through microscopy techniques like fluorescence in situ hybridization. Do Borgs exist strictly inside host cells or also outside?

3. Further characterizing the DNA methylation patterns in Borgs and Methanoperedens and how they regulate replication and gene expression of Borgs. Do the patterns confer immunity against Borgs?

4. Exploring the possibility of Borgs as gene transfer agents. Can they package host or non-host DNA and transfer it between cells? This could expand host metabolism.

5. Investigating the diversity of Borgs in other environments like freshwater wetlands, permafrost, or marine sediments. How widespread are they and what new metabolic potentials do they encode

    

   OmcZ Filaments Display Unique Heme Arrangement: The packing of hemes, the heme:heme angles, and between-subunit heme coordination in OmcZ was found to be quite different from other forms. In contrast to the linear heme chains in OmcS and OmcE, OmcZ displayed a branched heme arrangement, leading to a highly surface-exposed heme in every subunit. This could play a significant role in the formation of conductive biofilm networks and the higher measured conductivity of OmcZ filaments.

   Extracellular Cytochrome Polymers Evolved Independently Multiple Times: The unique structure of OmcZ filaments suggests that conductive cytochrome polymers evolved independently on more than one occasion from different ancestral multiheme proteins. This discovery challenges the previous understanding of the evolution of these polymers.