id: Q9RSY6 gene_symbol: Q9RSY6 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:243230 label: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 description: >- Small ribosomal subunit protein bS1 (30S ribosomal protein S1, RpsA), encoded by DR_1983 on chromosome 1 of Deinococcus radiodurans R1, is a 629-residue cytoplasmic RNA-binding protein of the 30S ribosomal subunit. It belongs to the bacterial bS1 family (PANTHER PTHR10724:SF7, the same subfamily as Escherichia coli RpsA) and consists of an approximately 100-residue disordered, polar N-terminal extension followed by five tandem S1/OB-fold domains (residues 122-539) and a disordered Gly-rich C-terminal tail. By homology to E. coli bS1, the N-terminal S1 domains anchor the protein to the 30S platform (via uS2), while the more C-terminal S1 domains bind single-stranded regions of mRNA leaders upstream of the Shine-Dalgarno element, recruiting and unfolding mRNAs so that they can be positioned on the 30S subunit at the start of translation initiation. In D. radiodurans itself, purified RpsA binds RNA oligonucleotides in vitro, with a modest preference (micromolar Kd) for 8-oxoguanine-containing RNA, co-purifies with polynucleotide phosphorylase independently of RNA, and the gene could not be deleted, consistent with an essential role. existing_annotations: - term: id: GO:0003729 label: mRNA binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- PAINT places mRNA binding at node PTN000076677, seeded by experimental annotations of E. coli RpsA (P0AG67), Arabidopsis chloroplast RPS1 (AT5G30510) and P46837. Q9RSY6 shares PANTHER subfamily PTHR10724:SF7 with E. coli RpsA, and has five S1/OB-fold domains of the RNA-binding type. In E. coli, bS1 binds single-stranded regions of most leadered mRNAs at the first step of initiation; purified D. radiodurans RpsA binds RNA oligonucleotides in vitro. mRNA binding is the core molecular activity of bS1. action: ACCEPT reason: >- Target is inside the bS1 clade that inherited the function (same PANTHER subfamily as the experimentally characterised E. coli protein), retains the tandem S1 RNA-binding domain architecture, and has its own in vitro RNA binding data. Core function. supported_by: - reference_id: PMID:38474204 supporting_text: >- The vital function of bS1 as a component of the 30S subunit is the recognition and binding of various mRNAs at the first step of translation initiation - reference_id: PMID:35856907 supporting_text: >- all four proteins exhibited higher binding affinity to the 8-oxoG-containing oligoribonucleotide than the control oligoribonucleotide - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: 'PANTHER; PTHR10724:SF7; SMALL RIBOSOMAL SUBUNIT PROTEIN BS1C; 1.' - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:Pfam"] supporting_text: 'Pfam; PF00575; S1; 5.' - term: id: GO:0003735 label: structural constituent of ribosome evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: >- PAINT node PTN000076677, seeded by E. coli RpsA, which has IDA support for this term. bS1 is a bona fide 30S subunit protein that binds at the final step of 30S assembly via its N-terminal S1 domains, which contact uS2. Its association is more dynamic than that of most r-proteins, but GO conventionally annotates ribosomal proteins, including bS1, with this term. Q9RSY6 carries the bS1-specific family signatures (IPR050437, PRINTS RIBOSOMALS1, NCBIfam PRK06299/PRK06676). action: ACCEPT reason: >- Sound phylogenetic inference within the bS1 subfamily; consistent with the ribosomal-protein family signatures of the target. Retained as part of the core ribosomal role. supported_by: - reference_id: PMID:38474204 supporting_text: >- bS1 binds to the 30S subunit at the final step of the assembly via domains D1–D2 that form contacts with r-proteins, especially with uS2 - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:InterPro"] supporting_text: 'InterPro; IPR050437; Ribos_protein_bS1-like.' - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:PRINTS"] supporting_text: 'PRINTS; PR00681; RIBOSOMALS1.' - term: id: GO:0006412 label: translation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- PAINT node PTN000076677, seeded by E. coli RpsA. bS1 acts directly in translation as an mRNA-recruiting component of the 30S subunit. Its specific step is translation initiation, but PAINT curators propagated only the general term, and E. coli RpsA itself carries no translational-initiation annotation; for a ribosomal constituent, translation is an appropriate level, so the term is accepted rather than refined. action: ACCEPT reason: >- bS1 does part of the work of translation (mRNA capture and positioning on the 30S subunit). Inherited from within the correct subfamily. supported_by: - reference_id: PMID:38474204 supporting_text: >- it is an integral and essential component of translation machinery in all members of Proteobacteria, Cyanobacteria, Actinobacteria, and many other bacterial phyla - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:NCBIfam"] supporting_text: 'NCBIfam; NF004952; PRK06299.1-2; 1.' - term: id: GO:0022627 label: cytosolic small ribosomal subunit evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: part_of review: summary: >- PAINT node PTN000076734 (bacteria, taxon:2), seeded by E. coli RpsA, which has multiple IDA/IPI annotations to the 30S subunit. D. radiodurans is a bacterium with cytoplasmic 70S ribosomes, so the bacterial 30S subunit is the cytosolic small ribosomal subunit. action: ACCEPT reason: >- Correct and appropriately specific complex membership, inherited within the bacterial bS1 clade. supported_by: - reference_id: PMID:38474204 supporting_text: >- The vital function of bS1 as a component of the 30S subunit is the recognition and binding of various mRNAs at the first step of translation initiation - reference_id: PMID:9451450 supporting_text: >- one of the proteins of the E coli 30S ribosomal - term: id: GO:0003676 label: nucleic acid binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: >- InterPro2GO mapping from IPR003029 (S1 domain). True, since the S1/OB-fold domains bind single-stranded RNA, but uninformative; the substrate is known to be RNA, specifically mRNA leaders, and the gene already carries GO:0003729 mRNA binding, a descendant of this term. action: MODIFY reason: >- Correct but too general. Refine to GO:0003729 mRNA binding, which the gene already carries by IBA and which is supported by the bS1 literature and by RNA-binding data for the D. radiodurans protein. proposed_replacement_terms: - id: GO:0003729 label: mRNA binding supported_by: - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:InterPro"] supporting_text: 'InterPro; IPR003029; S1_domain.' - reference_id: PMID:38474204 supporting_text: >- The S1 domain adopts an OB-fold that is highly specific for binding single-stranded nucleic acids. - term: id: GO:0003729 label: mRNA binding evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: enables review: summary: >- ARBA-generated electronic annotation for the same term as the IBA row. The ARBA rule itself is not independent evidence, but the claim is correct and is supported by the phylogenetic placement and bS1 biochemistry cited for the IBA row. action: ACCEPT reason: >- Same claim as the accepted IBA mRNA binding row; actions kept consistent. supported_by: - reference_id: PMID:38474204 supporting_text: >- bS1 does not have strict sequence specificity and binds most leadered mRNAs (including heterologous mRNAs) - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: located_in review: summary: >- ARBA-generated localization. Correct (bacterial ribosomes are cytoplasmic) but much less informative than the complex membership GO:0022627 cytosolic small ribosomal subunit already carried by this gene, which is part_of cytosol and therefore of cytoplasm. action: MODIFY reason: >- Correct but general; the specific supported location is the cytosolic small ribosomal subunit (GO:0022627), which the gene already carries by IBA. proposed_replacement_terms: - id: GO:0022627 label: cytosolic small ribosomal subunit supported_by: - reference_id: PMID:38474204 supporting_text: >- bS1 binds to the 30S subunit at the final step of the assembly via domains D1–D2 that form contacts with r-proteins, especially with uS2 core_functions: - description: >- mRNA-recruiting RNA-binding protein of the 30S ribosomal subunit; its C-terminal S1/OB-fold domains bind single-stranded regions of mRNA leaders and deliver mRNAs to the 30S subunit for translation initiation. molecular_function: id: GO:0003729 label: mRNA binding directly_involved_in: - id: GO:0006412 label: translation in_complex: id: GO:0022627 label: cytosolic small ribosomal subunit supported_by: - reference_id: PMID:38474204 supporting_text: >- The vital function of bS1 as a component of the 30S subunit is the recognition and binding of various mRNAs at the first step of translation initiation - reference_id: PMID:35856907 supporting_text: >- all four proteins exhibited higher binding affinity to the 8-oxoG-containing oligoribonucleotide than the control oligoribonucleotide - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: 'PANTHER; PTHR10724:SF7; SMALL RIBOSOMAL SUBUNIT PROTEIN BS1C; 1.' - description: >- Ribosomal protein of the 30S subunit, anchored to the platform through its N-terminal S1 domains contacting uS2. molecular_function: id: GO:0003735 label: structural constituent of ribosome directly_involved_in: - id: GO:0006412 label: translation in_complex: id: GO:0022627 label: cytosolic small ribosomal subunit supported_by: - reference_id: PMID:38474204 supporting_text: >- bS1 binds to the 30S subunit at the final step of the assembly via domains D1–D2 that form contacts with r-proteins, especially with uS2 - reference_id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt record_section: ["DR:InterPro"] supporting_text: 'InterPro; IPR050437; Ribos_protein_bS1-like.' suggested_questions: - question: >- Should bacterial bS1 orthologs carry GO:0006413 translational initiation? E. coli RpsA has no such annotation in GOA and PAINT propagated only GO:0006412 translation, although bS1's mechanistic role is at the mRNA-recruitment step of initiation. - question: >- Is the micromolar-affinity preference of D. radiodurans RpsA for 8-oxoguanine-containing RNA physiologically relevant, or a general property of its single-stranded RNA binding? - question: >- Does the D. radiodurans-specific ~100-residue disordered N-terminal extension, absent from E. coli bS1, alter how the protein anchors to the 30S subunit? suggested_experiments: - description: >- Cryo-EM of D. radiodurans 30S or 70S initiation complexes with mRNA to locate bS1, test whether its N-terminal S1 domain contacts uS2 as in E. coli, and map the five S1 domains onto the mRNA path. experiment_type: cryo-EM structural analysis - description: >- Conditional depletion of RpsA (the gene appears essential) followed by ribosome profiling to measure dependence of leadered versus leaderless mRNA translation on bS1 in D. radiodurans. experiment_type: ribosome profiling references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: PMID:10567266 title: Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. findings: - statement: >- The genome of Deinococcus radiodurans R1 was sequenced, providing the gene predictions including DR_1983 encoding bS1. reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Genome paper cited by the UniProt entry as the sequence source; gives the gene model only, no functional data. Retained for provenance; not used as support for any annotation. - id: PMID:35856907 title: PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in Deinococcus radiodurans. findings: - statement: >- Purified D. radiodurans RpsA (DR_1983) binds RNA oligonucleotides in vitro, with higher affinity for 8-oxoG-containing RNA, though with micromolar Kd (much weaker than PNPase or RhlB). supporting_text: >- RpsA and Rho showed relatively lower affinity to the 8-oxoG-modified oligoribonucleotides - statement: >- rpsA could not be deleted in D. radiodurans, consistent with an essential role. supporting_text: >- deletion of these proteins could not be achieved, likely due to their critical roles for cell viability in D. radiodurans - statement: >- RpsA co-purifies with PNPase in D. radiodurans independently of RNA. supporting_text: >- RpsA (the ribosomal protein S1) was also found to interact with PNPase in D. radiodurans in an RNA-independent fashion reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Only experimental study of the D. radiodurans protein itself (full text cached). Provides direct RNA-binding data and essentiality; the oxidized-RNA preference is modest and not used as a basis for a separate annotation. - id: PMID:38474204 title: Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. findings: - statement: >- bS1 recognises and binds mRNAs at the first step of translation initiation as a component of the 30S subunit; N-terminal domains anchor it to the 30S via uS2 and C-terminal domains bind RNA. supporting_text: >- The two N-terminal S1 domains (D1–D2) lost their RNA-binding functions during evolution and acquired an ability to form protein–protein interactions, while the C-terminal domains (D3-D6) provide the RNA-binding capacity of bS1. - statement: >- Autogenous repression of rpsA translation is conserved mainly in gamma-proteobacteria and is not transferred to D. radiodurans. supporting_text: >- which are highly conserved in several families of γ-proteobacteria reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Authoritative review of bS1 biology (mostly E. coli), used for the family-level mechanism transferred within PANTHER subfamily SF7. - id: PMID:9451450 title: Identification of ribosomal protein S1 as a poly(A) binding protein in Escherichia coli. findings: - statement: >- Purified E. coli S1, a 30S subunit protein, binds poly(A) and poly(C) RNA. supporting_text: >- The binding of S1 to poly(A) occurred reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Abstract-only cache. Experimental RNA binding by the E. coli ortholog in the same PANTHER subfamily. - id: file:DEIRA/Q9RSY6/Q9RSY6-uniprot.txt title: UniProt entry Q9RSY6 findings: - statement: >- Q9RSY6 is placed in PANTHER subfamily PTHR10724:SF7, the subfamily that also contains E. coli RpsA (P0AG67). record_section: ["DR:PANTHER"] supporting_text: 'PANTHER; PTHR10724:SF7; SMALL RIBOSOMAL SUBUNIT PROTEIN BS1C; 1.' - statement: >- The protein contains five S1 motif domains spanning residues 122-539, characteristic of the multi-domain architecture of bacterial S1 proteins. record_section: ["DR:Pfam"] supporting_text: 'Pfam; PF00575; S1; 5.' - statement: >- The N-terminal ~100 residues are predicted to be disordered. record_section: ["FT:REGION"] supporting_text: 'REGION 1..100'