rne Family assigned · medium auto-curated
H37Rv Rv2444c · MTBC0 mtbc0_002603 ·
953 aa · 2766371–2769232 (-) ·
RefSeq NP_216960.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonuclease E |
|---|---|
| MTBC0 PGAP re-annotation | Rne/Rng family ribonuclease |
| Revised (this work) | Rne/Rng family ribonuclease. Pfam: RNase_E_G (PF10150.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71905
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribonuclease E |
| EC (curated) |
EC 3.1.26.12
|
| Curated function | Endoribonuclease that plays a central role in RNA processing and decay. Plays a major role in pre-16S rRNA maturation, probably generating the mature 5'-end, and a minor role in pre-5S and pre-23S rRNA maturation. Probably also processes tRNA (By similarity). RNase E and HupB jointly contribute to cellular adaptation to changing growth conditions and survival during antibiotic treatment and in the host. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | rne |
| eggNOG description | ribonuclease, Rne Rng family |
| Orthologous group | COG1530 |
| EC number |
EC 3.1.26.12
|
| KEGG orthology |
K08300, K08301
|
| KEGG pathways |
map03018
|
| KEGG modules |
M00394
|
| Gene Ontology (27) |
GO:0006139, GO:0006364, GO:0006396, GO:0006397, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009987, GO:0010467, GO:0016070, GO:0016071 +15 more
|
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, 145 209 strains)
| pN/pS | 0.138 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 4 missense, 0 nonsense, 0 frameshift |
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.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RNase_E_G | PF10150.15 | 8.8e-97 | 455–736 | Ribonuclease E/G family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplU (50S ribosomal protein L21), medium confidence from genomic context alone (score 599 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 968 | 846 | experimental:826 textmining:807 |
Rv1023 eno |
enolase | 801 | 776 | experimental:773 |
Rv1095 phoH2 |
phosphate starvation-inducible protein PsiH | 765 | 765 | coexpression:703 |
Rv1421 rapZ hyp |
hypothetical protein | 700 | 668 | experimental:652 |
Rv1340 rphA |
ribonuclease PH | 820 | 618 | database:500 textmining:549 |
Rv2442c rplU |
50S ribosomal protein L21 | 598 | 599 ctx | neighborhood:544 |
Rv2439c proB |
glutamate 5-kinase protein | 562 | 563 ctx | neighborhood:544 |
Rv3920c hyp |
hypothetical protein | 670 | 560 | experimental:471 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 570 | 552 ctx | neighborhood:549 |
Rv2441c rpmA |
50S ribosomal protein L27 | 573 | 547 ctx | neighborhood:544 |
Rv3923c rnpA |
ribonuclease P protein component | 591 | 537 | database:500 |
Rv2555c alaS |
alanine--tRNA ligase | 548 | 537 | coexpression:536 |
Rv2733c miaB |
(dimethylallyl)adenosine tRNA methylthiotransferase | 551 | 533 | |
Rv3282 hyp |
hypothetical protein | 519 | 519 | |
Rv2903c lepB |
signal peptidase | 516 | 517 | coexpression:439 |
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.
Evidence
- Legacy H37Rv annotation: ribonuclease E
- MTBC0 PGAP product: Rne/Rng family ribonuclease
- Pfam (hmmscan --cut_ga): RNase_E_G PF10150.15 (E=9e-97)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_216960.1)
- Domains: Pfam-A via hmmscan --cut_ga — RNase_E_G (PF10150.15)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1530 - Curated reference: UniProt P71905 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
55 functional partner(s); context anchor
rplU - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002603|Rv2444c|rne MIDGAPPSDPPEPSQHEELPDRLRVHSLARTLGTTSRRVLDALTALDGRVRSAHSTVDRVDAVRVRDLLATHLETAGVLAASVHAPEASEEPESRLMLETQETRNADVERPHYMPLFVAPQPIPEPLADDEDVDDGPDYVADDSDADDEGQLDRPANRRRRRGRRGRGRGRGEQGGSDGDPVDQQSEPRAQQFTSADAAETDDGDDRDSEDTEAGDNGEDENGSLEAGNRRRRRRRRRKSASGDDNDAALEGPLPDDPPNTVVHERVPRAGDKAGNSQDGGSGSTEIKGIDGSTRLEAKRQRRRDGRDAGRRRPPVLSEAEFLARREAVERVMVVRDRVRTEPPLPGTRYTQIAVLEDGIVVEHFVTSAASASLVGNIYLGIVQNVLPSMEAAFVDIGRGRNGVLYAGEVNWDAAGLGGADRKIEQALKPGDYVVVQVSKDPVGHKGARLTTQVSLAGRFLVYVPGASSTGISRKLPDTERQRLKEILREVVPSDAGVIIRTASEGVKEDDIRADVARLRERWEQIEAKAQETKEKAAGAAVALYEEPDVLVKVIRDLFNEDFVGLIVSGDEAWNTINEYVNSVAPELVSKLTKYESADGPDGQSAPDVFTVHRIDEQLAKAMDRKVWLPSGGTLVIDRTEAMTVIDVNTGKFTGAGGNLEQTVTKNNLEAAEEIVRQLRLRDIGGIVVIDFIDMVLESNRDLVLRRLTESLARDRTRHQVSEVTSLGLVQLTRKRLGTGLIEAFSTSCPNCSGRGILLHADPVDSAAATGRKSEPGARRGKRSKKSRSEESSDRSMVAKVPVHAPGEHPMFKAMAAGLSSLAGRGDEESGEPAAELAEQAGDQPPTDLDDTAQADFEDTEDTDEDEDELDADEDLEDLDDEDLDEDLDVEDSDSDDEDSDEDAADADVDEEDAAGLDGSPGEVDVPGVTELAPTRPRRRVAGRPAGPPIRLD