Rv0537c Still unknown · low

Annotation: from legacy to revised

Curation note: 2026-10-02 (atlas-side reconciliation of the mtbc/Rv0537c back-propagation P52.2, status: unpublished, not peer-reviewed). Atlas-side reconciliation of the L1 disruption counts in the preceding note (computed on the atlas, not a result of the dedicated project). Both caches apply the same frequency floor, max(3, int(0.001 x n)), to different n: 142 strains for the pooled census (n = 142,601) and 25 for the L1 census (n = 25,332). Read directly on the per-strain SPDI files of the L1 and L_1 trees (one lineage since P90.19): NC_000962.3:629097:G:GC has 27 carriers (23 L1, 4 L_1), above the L1 floor and below the pooled one; NC_000962.3:628862:GT:G has 15, below both; no other indel of the gene exceeds 5 carriers, and none of the 12 substitutions reaching 25 carriers in L1 creates a stop codon. The single disrupting site of the L1 layer (disrupt_sites 1) is therefore 629097:G:GC, a one-base insertion that lengthens a CC run to CCC, and the pooled layer's 0 disrupted strains and frameshift 0 mean 'no indel above 142 strains', not 'no frameshift'. This reconciles 0 against 1; it does not validate the signal: no reads were checked. The L1 layer still reports 30 occurrences against 27 carriers today; its cache dates from 2026-08-04 and the base has changed since (25,054 genomes under the L1 and L_1 trees now against n = 25,332 in the cache), which is compatible with the gap of 3 but does not demonstrate it. The L1 candidate remains an unvalidated frameshift and must not be cited as a natural knock-out. 2026-10-02 (mtbc/Rv0537c project, back-propagation P52.2, destination C1, status: unpublished, not peer-reviewed). Independent rescan of the candidate L1 signal in the layer above. The dedicated Rv0537c project scanned all 145,209 strains of bdd/actuelle (2026-09-13) and found two rare frameshift indels almost exclusive to L1: NC_000962.3:628862:GT:G (15 carriers, 13 in L1) and NC_000962.3:629097:G:GC (27 carriers, 23 in L1). The layer above reports 30 disrupted occurrences among 25,332 L1 strains (one site in its source cache of 2026-08-04); the two sets of counts do not match and the gap is not reconciled. Both indels lie below the frequency floor of the pooled census (0.1% of strains, about 145), which is consistent with the pooled conservation layer reporting no disrupted strain. The first indel sits next to a TTTT homopolymer, a known source of false frameshift calls in short-read data. Neither indel was checked against raw reads, so the L1 signal remains an unvalidated candidate and should not be cited as a natural knock-out. Apart from these indels, no variant other than the synonymous p.Leu276Leu reaches fixation or near-fixation in the large African and animal clade (p.Pro282Ser is found in 161 of 1,364 L6 strains only). 2026-10-02 (mtbc/Rv0537c project, back-propagation P52.2, destination C1, status: unpublished, not peer-reviewed). Independent check of the vancomycin handle in a second screen. In the CRISPRi chemical-genetics screen of Li et al. 2022 (Nat Microbiol 7:766-779, doi 10.1038/s41564-022-01130-y; 4,053 genes, 9 drugs), Rv0537c is depleted under vancomycin in the same direction as the MtbTnDB phenotype (log2FC -0.806, rank 284 of 4,053, 10 of 10 guides concordant, the 10 guides covering only 7 distinct sites), but it is not called a hit for any of the 9 drugs: the weakest gene the authors call under vancomycin has |log2FC| = 1.000, a threshold measured back from their published calls. A vancomycin phenotype is common in that screen (1,110 of 4,053 genes, 27.4%, are called sensitised). In matched comparisons the dedicated project could not use the profile to separate a permeability-barrier role from a cell-wall-activity role: on the peptidoglycan-screen axis (higher percentile means flatter) the median is 50.7 for 66 envelope transporters and lipid-barrier genes against 59.5 for 25 peptidoglycan enzymes (Mann-Whitney p = 0.078, the direction opposite to the permeability prediction); the vancomycin target ddlA is flatter (98.2) than Rv0537c (73.3); and Rv0537c lies 0.01 log2 unit from Rv1096, an accessory peptidoglycan deacetylase (-0.806 against -0.792). The profile is that of a non-essential accessory envelope gene with low reactivity and narrow specificity. This weakens but does not remove the vancomycin handle, and it supports neither mechanism. 2026-10-02 (mtbc/Rv0537c project, back-propagation P52.2, destination C1, status: unpublished, not peer-reviewed). Independent rescan of the candidate L1 signal in the layer above. The dedicated Rv0537c project scanned all 145,209 strains of bdd/actuelle (2026-09-13) and found two rare frameshift indels almost exclusive to L1: NC_000962.3:628862:GT:G (15 carriers, 13 in L1) and NC_000962.3:629097:G:GC (27 carriers, 23 in L1). The layer above reports 30 disrupted occurrences among 25,332 L1 strains (one site in its source cache of 2026-08-04); the two sets of counts do not match and the gap is not reconciled. Both indels lie below the frequency floor of the pooled census (0.1% of strains, about 145), which is consistent with the pooled conservation layer reporting no disrupted strain. The first indel sits next to a TTTT homopolymer, a known source of false frameshift calls in short-read data. Neither indel was checked against raw reads, so the L1 signal remains an unvalidated candidate and should not be cited as a natural knock-out. Apart from these indels, no variant other than the synonymous p.Leu276Leu reaches fixation or near-fixation in the large African and animal clade (p.Pro282Ser is found in 161 of 1,364 L6 strains only). 2026-10-02 (mtbc/Rv0537c project, back-propagation P52.2, destination C1, status: unpublished, not peer-reviewed). Independent check of the vancomycin handle in a second screen. In the CRISPRi chemical-genetics screen of Li et al. 2022 (Nat Microbiol 7:766-779, doi 10.1038/s41564-022-01130-y; 4,053 genes, 9 drugs), Rv0537c is depleted under vancomycin in the same direction as the MtbTnDB phenotype (log2FC -0.806, rank 284 of 4,053, 10 of 10 guides concordant, the 10 guides covering only 7 distinct sites), but it is not called a hit for any of the 9 drugs: the weakest gene the authors call under vancomycin has |log2FC| = 1.000, a threshold measured back from their published calls. A vancomycin phenotype is common in that screen (1,110 of 4,053 genes, 27.4%, are called sensitised). In matched comparisons the dedicated project could not use the profile to separate a permeability-barrier role from a cell-wall-activity role: on the peptidoglycan-screen axis (higher percentile means flatter) the median is 50.7 for 66 envelope transporters and lipid-barrier genes against 59.5 for 25 peptidoglycan enzymes (Mann-Whitney p = 0.078, the direction opposite to the permeability prediction); the vancomycin target ddlA is flatter (98.2) than Rv0537c (73.3); and Rv0537c lies 0.01 log2 unit from Rv1096, an accessory peptidoglycan deacetylase (-0.806 against -0.792). The profile is that of a non-essential accessory envelope gene with low reactivity and narrow specificity. This weakens but does not remove the vancomycin handle, and it supports neither mechanism. P52.5 (2026-09-30): fiche flagged as hand-reviewed at the closure of the dedicated project mtbc/clos/Rv0537c (iteration 6, state of 2026-09-12). The project's findings were compared with this fiche (P52.1, 2026-09-29) and no divergence was found.

In the literature (TB corpus sweep) named only in full text

No TB publication mentions this locus tag in its title or abstract (sweep of a ~330k-abstract PubMed TB corpus). A full-text search does however find 3 paper(s) naming this gene in their body text — see the full-text field below. The gene remains dark on function, but it is not unmentioned, and this page no longer claims that it is.

Scope of the sweep: What was actually swept: the H37Rv locus tag and the ortholog locus tags (M. bovis Mb…, M. marinum MMAR_…, M. smegmatis MSMEG_…, M. leprae ML…, M. abscessus MAB_…), plus the gene name where one exists. NOT swept: protein and enzyme names, including family shorthands such as Ldt(Mt4) or VapC28, and their orthographic variants. An absent locus-tag mention is therefore evidence about the TAG, and only indirect evidence about the protein (P18.14).

An antigen status or a virulence phenotype is NOT a molecular function: the verdict stays unchanged. This layer adds the missing context, it does not requalify the gene. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole), MULTI-ALIAS sweep of title+abstract: the H37Rv locus tag AND every ortholog identifier (M. bovis Mb…, M. marinum MMAR_…, M. smegmatis MSMEG_…, M. leprae ML…, M. abscessus MAB_…), each hit VERIFIED against the abstract text (word-boundary regex). phase73, 2026-07-13.

Integrative functional lead (multi-layer synthesis, hypothesis) 2 convergent handles

candidate cell-envelope / antibiotic-stress-associated inducible membrane protein (newly defined domain DUF7937), to validate

Synthesised across all evidence layers (conservation, operon, STRING, regulon, phenotype, localisation, structure, vulnerability) under an anti-oversell decision checklist. A functional hypothesis to validate, not an established function. P16.3d individual pocket examination, 2026-08-01.

Binding-pocket screen (P2Rank, geometric prediction) confident pocket · p = 0.778

Read with care. This protein (477 aa) is above the size where the detector has real power (P16.3b calibration). A pocket cleared this layer's confidence threshold of best_probability >= 0.70 (probability 0.778) -- see the integrative_lead / structural notes on this fiche for the individual read-out (P16.3d). On the same calibration panel, 18.9% of proteins annotated as non-catalytic also clear 0.70 above 200 aa (81.1% specificity), so a cleared threshold is a lead, not evidence of catalysis. P16.3e, calibration phase72b_pocket_calibration.py, 2026-08-03.

CRISPRi vulnerability

Vulnerability index 1.31 (95% CI -0.49 to 4.47). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.

Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, supplementary Table S2 'mmc3.xlsx', bulk import via Europe PMC -- supersedes the per-gene pebble.rockefeller.edu scrape of phase46_crispri_vulnerability.py).

Caveat on this estimate. Bosch et al. flag this gene's vulnerability estimate as NOT certain, and here that call has a mechanical cause visible in the library itself: every guide targeting this gene is >=21 nt (str_span=0.198 on a 0-1 scale, near the genome floor), and guide repression strength saturates from 21 nt on -- so the library never sampled a partial knockdown for this gene, only the near-maximal repression plateau. The dose-response fit (and this VI) is therefore essentially unconstrained by data, not merely uncertain -- a limitation of the CRISPRi library design for the non-essential class (Bosch et al. 2021), not a defect in this specific measurement. n_guides=10 is descriptive only and does not predict this. Do not cite this VI as a standalone vulnerability claim.

Orthologues (reciprocal best hits across mycobacteria)

Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.

Curated reference (UniProt)

Functional vocabulary (eggNOG-mapper, orthology transfer)

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 142 601 strains, snapshot of 2026-09-29)

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Lineage-specific relaxation (candidate, one evidence handle) 1 lineage(s)

Candidate lineage-specific loss-of-function signal: rare/absent in the other well-sampled lineages (<5%) but risen in the listed lineage(s). ONE handle, not a verdict change (P8 two-handle policy) -- the general phenomenon of lineage-specific gene loss reflecting ecotype-specific selective pressure is already established at genome scale (Silva-Pereira et al. 2024); this signal on an individual dark gene needs an independent second handle before any requalification.

Caveat: Sample-size heterogeneity across MTBC lineages (up to 4 orders of magnitude, 16 smaller lineages excluded for n<500); essentiality is NOT resolvable per lineage (TnSeq data is H37Rv-only). For the two smallest adequate lineages (L5 n=630, L6 n=1364) the frequency floor bottoms out at the absolute minimum of 3 carrier strains -- a handful of strains from a SINGLE transmission cluster (clonal outbreak) can pass this floor without representing independent evolutionary origins of the disrupting allele; no phylogenetic correction for clonal sampling was applied. Treat low-count hits in these two lineages with extra caution.

Reference: Silva-Pereira TT, Soler-Camargo NC, Sá Guimarães AM 2024, Microbiology Spectrum, doi:10.1128/spectrum.02289-23

Outgroup conservation (beyond the MTBC) Mycobacterium

Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.

Essentiality (transposon mutagenesis)

Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.

Mutant phenotypes (conditional Tn-seq, MtbTnDB)

Conditional fitness of transposon-disruption mutants across 2 significant condition(s) (|log2FC|≥1, q≤0.05), from the standardized MtbTnDB compendium. A negative log2FC means the mutant is depleted — the gene contributes to fitness in that condition. An in-vivo defect for a "hypothetical" is strong evidence it matters for infection, even without a known molecular function. Disruption (Tn insertion), not a clean deletion; genetic-interaction screens excluded.

Provenance note on a condition above. `marP_KO_vs_marP_WT` carries no source in MtbTnDB's own metadata (col_desc.tsv leaves paper_title/paper_URL empty). Traced by the `Rv0537c` companion project (2026-09-12): Weizhen Xu, PhD thesis, Weill Cornell Medicine, 2017, hdl:1813/64728 ("Genetic Screening In Mycobacterium Tuberculosis Utilizing Transposon Insertion Sequencing"), whose abstract describes a TnSeq genetic-interaction screen naming marP. Never published as a peer-reviewed article.

Provenance note on a condition above. This gene's displayed phenotypes include both `marP_KO_vs_marP_WT` and a drug-exposure condition from Xu et al. 2017 (AAC 61(12):e01334-17). Both trace to the same experimenter (Weizhen Xu) and very likely the same transposon insertion library -- read them as ONE handle, not two independent ones, when assessing convergence for an `integrative_lead` flip.

Proteomics (mass spectrometry) detected

Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Read the dataset count as abundance, not as replication. Measured across this atlas (3,491 detected proteins), the number of datasets a protein appears in tracks its abundance almost monotonically: median 1.2 ppm at 1 dataset of 16, 27 ppm at 10, 392 ppm at 15, 1,325 ppm at 16 — three orders of magnitude. A high count therefore says the protein is abundant more than it says several independent experiments confirmed it. What the count does establish, at any value, is that the product exists.

Predicted localisation (DeepTMHMM + lipobox)

Transmembrane topology and signal peptide from DeepTMHMM (deep-learning reference predictor); lipoproteins from a (myco)bacterial lipobox motif. A sequence-based prediction of subcellular context.

Physico-chemical properties (computed, ProtParam)

Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.

Domains (Pfam, hmmscan --cut_ga)

HHpred profile-profile (no confident hit): No confident hit, pure noise. Remains dark. top hits 3 weak hits only, best 43.2%, E=440. Remote homology search on the deep UniRef30 profile (MPI Toolkit), run for the residual dark set.

3D structure (interactive — Mol*/pdbe-molstar)

No experimental structure is deposited for this gene: showing the AlphaFold DB predicted model (mean pLDDT 80.6, confident), coloured by per-residue confidence (dark blue = very high, orange/red = low — treat low-confidence regions as unreliable, especially termini and loops). Drag to rotate, scroll to zoom.

Genomic context (neighbours & predicted operon)

Neighbours from the H37Rv annotation (- strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).

Published operon evidence (two independent sources)

Two independent published operon maps, cited alongside the distance heuristic above: an association corroborating or contradicting the heuristic, never proof of shared function. REMap's RNA-seq coverage continuity is the most direct of the three signals; Roback's logistic regression and the intergenic-distance heuristic are statistical proxies.

Transcriptional regulation (signed TRN: ChIP-seq + TFOE)

Regulatory edges from the ISB signed transcriptional regulatory network (TF ChIP-seq binding, Minch 2015 + TF-overexpression response, Rustad 2014). An edge is regulatory evidence (binding and/or expression change), not necessarily direct. For a "hypothetical", membership in a known regulon (e.g. DosR dormancy, PhoP virulence) is a physiological-context lead, not a function.

Condition: Condition-blind by construction. These edges come from transcription-factor OVEREXPRESSION in a single laboratory condition, so a listed regulator is not a claim that it governs this gene in every circumstance. Measured counter-examples exist within this atlas (see Rv2516c, where the DosR regulon collapses under moxifloxacin while the gene itself rises). Read a regulator as 'capable of shifting this gene', and look for the condition before building a hypothesis on it.

Additional regulons (curated, outside the TFOE-derived TRN)

Curated from primary literature not covered by the ISB signed TRN (Minch 2015 / Rustad 2014): Zur regulon (Maciag et al. 2007, PMID 17098899), SigG regulon (Gaudion et al. 2013, PMID 23871545), LexA/SOS regulon (Smollett et al. 2012, PMID 22528497) — added P16.25 (2026-08-18); CRP regulon (Kahramanoglou et al. 2014, PMID 24957601) — added P16.25b (2026-09-27). Confidence and caveats are per-edge and carried from the source paper — read them before citing a specific gene as "regulated by" its listed TF. An entry reading "binding site only — direction not determined" is not a regulation claim: it records a measured ChIP-seq binding site for which the source reports no expression change, and the absence of such a change is not evidence of absent regulation.

Node colour = verdict, dashed = still uncharacterised; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.

Closest characterised functional partner: Rv0538 (membrane protein), medium confidence (score 556, all STRING channels except text-mining; the partner is chosen on its genomic-context evidence). Read this as a lead toward a shared pathway or operon, not as evidence of a physical complex: when this atlas co-folded 98 such context-only pairs, their predicted interfaces were no more confident than those of length-matched control pairs.

All 1 partner(s) at medium confidence are shown. None rests on an interaction measured in M. tuberculosis itself.

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Where the experimental evidence comes from, and why it matters here. STRING's experimental channel fuses interactions measured in M. tuberculosis with interactions measured in another organism and transferred to this pair by orthology. The two are not equivalent for this atlas, whose standing rule is that better studied elsewhere is not a function established in M. tuberculosis. Measured on the served network: of the 38 229 partner pairs shown across the atlas, 13 483 partner rows carry a non-zero experimental channel, and only 106 pairs rest on an interaction measured in M. tuberculosis itself — 0.3 % of the network. Those 106 are long-established complexes (ESX-1/ESAT-6, RNA polymerase with CarD and RbpA, the Pup–Mpa proteasome, gyrase, Emb, GarA with PknB and PknG, the Rel modules); no still-uncharacterised gene is among them. The reason is not a gap in this atlas but in the literature: there is almost no experimental interactome of this bacterium, IntAct holding 134 curated protein pairs for a ~4 000-gene proteome. A exp (transferred) badge is therefore a lead, never a measurement, and an absence of badge is not evidence that the pair does not interact.

Evidence

• Legacy H37Rv annotation: integral membrane protein
• MTBC0 PGAP product: hypothetical protein
• Pfam (hmmscan --cut_ga): DUF7937 PF25592.2 (E=2e-113)
• (initial automatic assignment: auto-curated by rules from PGAP + Pfam + Foldseek; superseded by hand review)

Ancestral MTBC0 protein sequence

>mtbc0_000566|Rv0537c|
MGLSSDDTRRREVVRDLAAGALLIGALFFPWNLYFGFRIPDSSKTVFGLLLAVTSLSLASLAVTFAGRRSQLRLGLNVPYLLLVLAFVVFDAIQTIRLGGTVHVPGGVGPGGWLGITGALLSAQPALTGATTDEGSHSRWLRATQFLGYASMLGAALSTGFNLSWRVRYALEPAAGASGFGKQNLAVIDTAVVYGVVALAAVLVASRWLLRPTAAEALSTVALGGSTLIAGSIVWSLPIGREIDAFHGIAQNTSTAGVGYEGYLVWAAAAAMCAPLTLFRSPNAPPIDKTVWRAASRNGLLLIAVWCLGSVAMRLTDLVVAVLLNYPFSRYDSMALAAFDLATAVLAIWLRFNMATEALPARLISSLCGLLCTFTVSRVIVGVVLAPRFQASSGGSAHPVYGNDLAQQITSTFDVVLCGLALSILAAAIVIGRLRQLPQPPHTPALSRPAGSPRIFRSAGSTHPVRPKIYRPPDHSS