Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.01.07.574550

Diverse bacteriohemerythrin genes of Methylomonas denitrificans FJG1 provide insight into the survival and activity of proteobacterial methanotrophs under hypoxia

Weiblen, C.·Sauvageau, D.·Stein, L. Y.
View original source ↗Export metadata ↓

Abstract

Proteobacterial methanotrophs are dependent on the oxidation of methane for ATP production and assimilation of carbon into biomass. Interestingly, some types of gammaproteobacterial methanotrophs thrive in oxygen-depleted zones of lakes and other aquatic ecosystems despite their reliance on oxygen to support methane oxidation. The model gammaproteobacterial methanotroph, Methylomonas denitrificans FJG1, oxidizes methane coupled to nitrate reduction under hypoxia and highly upregulates its expression of bacteriohemerythrin (Bhr). Bhr is a homolog of eukaryotic hemerythrin, which is a protein associated with oxygen binding. Ten bhr homologs were identified in the genome of M. denitrificans FJG1, requiring phylogenetic and gene expression analyses to pinpoint which homolog is likely responsible for delivering oxygen to support methane oxidation to under low oxygen conditions. This study examined the prevalence and phylogeny of the 10 bhr homologs from M. denitrificans FJG1 in the genomes of other methanotrophs and across the Bacteria. The homolog denoted "bhr-00" was specific to methanotroph genomes, was highly expressed in M. denitrificans FJG1 under hypoxia, and its predicted structure was nearly identical to a purified oxygen-scavenging hemerythrin protein from Methylococcus capsulatus Bath. Other bhr homologs upregulated from denitrifying cultures of M. denitrificans FJG1 included those with gene neighborhoods related to oxygen sensing, denitrification and chemotaxis. Together, this study uncovered potential multifunctional roles of bacteriohemerythrin genes of M. denitrificans FJG1 under low oxygen conditions and identified the bhr homolog that most likely enables and supports oxygen delivery to methane monooxygenase enzymes in anoxic ecosystems. ImportanceAerobic gammaproteobacterial methanotrophs can survive and grow in anoxic lakes, but mechanisms that provide them with oxygen to support methane oxidation remain uncharacterized. Methylomonas denitrificans FJG1 encodes 10 copies of bacteriohemerthyrin (bhr), of which 7 are expressed at the mRNA level under low oxygen conditions. Comparing the 10 bhr homologs from M. denitrificans FJG1 with those from other methanotrophs and bacterial genomes shows that two are specific to methanotrophs. Gene neighbourhoods surrounding conserved bhr genes in methanotrophs suggest a range of potential functions including oxygen respiration, oxygen sensing, chemotaxis, and nitrate reduction. The results from this study illuminate a previously undescribed diversity of structures and potential functions of bhr homologs in M. denitrificans FJG1 and related methanotrophic bacteria. The results pinpoint a methanotroph-specific homolog, bhr-00, that is likely responsible for oxygen binding and delivery to methane monooxygenase enzymes to promote methane oxidation in low oxygen ecosystems.

Source connections

Explore related subjects

microbiologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Weiblen, C., Sauvageau, D., Stein, L. Y.. 2024-01-07. Diverse bacteriohemerythrin genes of Methylomonas denitrificans FJG1 provide insight into the survival and activity of proteobacterial methanotrophs under hypoxia. https://doi.org/10.1101/2024.01.07.574550

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗
bioRxiv2026

Beta-lactam enhancement against methicillin-resistant Staphylococcus aureus by cell wall blockade is autolysis-dependent: a butyrolactone derivative as case in point

Methicillin-resistant Staphylococcus aureus (MRSA) is non-susceptible to beta-lactams. Blockade of cell wall biosynthesis is a potential target for beta-lactam enhancement but requires further investigation. A butyrolactone derivative enhanced beta-lactams against MRSA strains by reducing the availability of D-Ala-D-Ala. Unlike D-cycloserine, it did not inhibit D-Ala-D-Ala ligase (Ddl). Nor did it show an additive or synergistic effect when combined with cycloserine, indicating a unique mechanism for blocking cell wall precursor production that does not involve the traditional Lipid II pathway. Notably, beta-lactam potentiation by our chemical or D-cycloserine was highly dependent on the intrinsic autolytic ability of the tested MRSA strains. Strains that resisted lysis upon Triton X-100 exposure showed a minimal increase in beta-lactam susceptibility, whereas highly autolytic strains showed significant changes in their beta-lactam MICs. We have thus identified autolytic ability as the Achilles Heel in the strategy of targeting cell wall biosynthesis for beta-lactam potentiation.

microbiology↗
bioRxiv2026

Rapid and largely reversible shifts in the canine fecal metabolome during dietary change

Diet can rapidly change the fecal metabolome, but less is known about recovery after the original diet is restored. We used untargeted UPLC-MS metabolomics to analyze 72 fecal samples from nine Pumi dogs during an owner-managed switch from dry food to raw food and back to dry food. Diet phase accounted for a large proportion of variation in both ionization modes. More than 13,000 LC-MS features changed at the first sampling point after the switch to raw food, with a similarly large response after return to dry food. Among features significant in both comparisons, more than 99% changed in opposite directions. At the final sampling point, no positive-mode (ESI+) features and only 13 negative-mode (ESI-) features differed from the second dry-food baseline under the same threshold. BARF-associated patterns persisted in analyses excluding individual dogs and in pedigree-adjusted candidate models, although individual feature effects depended on normalization. Putative metabolites from several biochemical classes differed in their response and recovery. The fecal metabolome therefore changed rapidly and returned largely toward baseline, with differences among dogs.

microbiology↗