Diverse bacteriohemerythrin genes of <i>Methylomonas denitrificans</i> FJG1 provide insight into the survival and activity of methanotrophs in low oxygen ecosystems
Bibliographic record
Abstract
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 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. IMPORTANCE Aerobic 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 seven 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 neighborhoods 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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".