Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure

Abstract

Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a lowpressure analog for structure II gas clathrate. When grown in the presence of CbpAs, THF clathrate was polycrystalline and platelike instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a plate-like structure during gas clathrate transportation. ACKNOWLEDGMENTWe thank William Waite (USGS) for helpful suggestions. ABBREVIATIONSCbp: clathrate-binding protein; eGFP: enhanced green fluorescent protein; THF, tetrahydrofuran.

Microbial metabolism and adaptations in Atribacteria‐dominated methane hydrate sediments

“…Other probable environmental stress adaptations include glycosylation and membrane modifications. It is also possible that these microbes can produce secondary metabolites that modify gas hydrate properties; we recently showed experimentally that recombinant Chloroflexi proteins from metagenomic sequences native to methane hydrate‐bearing sediments alter the structure of clathrates (Johnson et al ., 2020). More experiments are required to resolve the complex metabolic pathways and biosynthetic potential of life in methane hydrates, with important implications for stability of gas hydrates on our own planet (e.g.…”

Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments

“…Other probable environmental stress adaptations may include glycosylation and membrane modifications. It is also possible that these microbes can produce secondary metabolites that modify gas hydrate properties; we recently showed experimentally that recombinant Chloroflexi proteins from metagenomic sequences native to methane hydrate-bearing sediments alter the structure of clathrates (Johnson et al, 2020). More experiments are required to resolve the complex metabolic pathways and biosynthetic potential of life in methane hydrates, with important implications for stability of gas hydrates on our own planet (e.g.…”

What is the role of microbes in gas hydrate formation and stability?

“…Some amino acids function as hydrate promoters, while others are inhibitors (Bavoh et al, 2019; Bhattacharjee & Linga, 2021). Recombinantly expressed clathrate‐binding proteins (CbpAs) encoded in genomes of hydrate bacteria bind to and change the morphology of tetrahydrofuran hydrate (Johnson et al, 2020) and methane hydrate (Huard et al, in review). The activity of proteins as hydrate inhibitors has also been demonstrated in natural samples from a hydrate deposit in the South China Sea (Liu et al, 2021).…”