PSPPH_4093 encodes the YajQ-family protein of Pseudomonas savastanoi pv. phaseolicola 1448A, a 159-residue soluble cytoplasmic protein built from two tandem RNP-like domains, each a four-stranded antiparallel beta-sheet packed against two helices. YajQ proteins are found in most bacteria and in neither archaea nor eukaryotes, and their one firmly established biochemical property is nucleotide binding; the preferred ligand is not conserved across the family, with the Pseudomonas aeruginosa and Stenotrophomonas maltophilia members binding cyclic di-GMP while the Escherichia coli, Clostridium and Bacillus cereus members prefer ATP or GTP. Where a YajQ protein has been characterised in its own cell it behaves as a nucleotide-controlled accessory factor for transcription: the Xanthomonas campestris member binds cyclic di-GMP and modulates the promoter occupancy of a LysR-family regulator, and the Pseudomonas aeruginosa member is required for host-cell adhesion and lung colonisation. The ligand and the cellular partners of the Pseudomonas savastanoi protein itself have not been measured. What this protein is known for is a function it performs for a virus rather than for the cell: the dsRNA bacteriophage phi6 requires it, and YajQ binds the phage core through P1, the major structural protein, altering the core conformation so that the encapsidated viral RNA-dependent RNA polymerase P2 transcribes genomic segment L early in infection. YajQ does not transcribe anything itself and does not stimulate free P2; phi6 cannot replicate in a yajQ knockout, and escapes the requirement only by acquiring two mutations in the polymerase gene.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000120 | ACCEPT | Summary: Nucleotide binding is the one biochemical property established for the YajQ family, and this electronic row sits at the granularity the evidence for this protein supports. The UniProt entry asserts it as a curated UniRule/HAMAP statement (MF_00632) together with YajQ family membership, and the family-level grounding is direct: Escherichia coli YajQ was isolated as a nucleotide-binding protein by dye pseudoaffinity chromatography and its ligand binding then measured by NMR and isothermal titration calorimetry (PMID:12381839). The fold is consistent, two tandem RNP-like domains of the kind found in nucleic-acid-binding proteins (PMID:12943362). Reason: Kept at the parent term deliberately rather than refined, which is the unusual call here. The obvious refinement would be a cyclic-di-GMP binding term, since the closest characterised relative of this protein is Pseudomonas aeruginosa PA4395, a cyclic-di-GMP receptor. But the single study that established that specificity also showed the family does not conserve it: affinity for cyclic di-GMP was seen only in the Pseudomonas aeruginosa and Stenotrophomonas maltophilia proteins, while the Escherichia coli, Clostridium and Bacillus cereus proteins preferred ATP or GTP (PMID:25329577). No ligand has been measured for Q48EH2. Refining the term would therefore propagate a property across exactly the split the source study documents, so GO:0000166 is as precise as the evidence for this protein allows and is accepted as a core function. Supporting Evidence: file:PSE14/PSPPH_4093/PSPPH_4093-uniprot.txt FUNCTION: Nucleotide-binding protein. file:PSE14/PSPPH_4093/PSPPH_4093-uniprot.txt SIMILARITY: Belongs to the YajQ family. file:PSE14/PSPPH_4093/PSPPH_4093-uniprot.txt HAMAP; MF_00632; YajQ; 1. PMID:12381839 We used dye pseudoaffinity chromatography, two-dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide-binding proteins, YnaF and YajQ. PMID:12381839 In the absence of significant similarities of YajQ to any solved structure, we determined its structural and ligand-binding properties by NMR and isothermal titration calorimetry. PMID:25329577 Interestingly, affinity for cyclic di-GMP binding was only seen in YajQ family proteins from P. aeruginosa (PA4395) and S. maltophilia (Smlt4090) (Table S1). YajQ family proteins from E. coli, Clostridium sp. and B. cereus by contrast exhibited a greater affinity for ATP and/or GTP than for any cyclic mono- or di-nucleotide. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: A TreeGrafter electronic assignment that happens to have direct experimental backing for this very protein. GFP fusions to this YajQ give uniform fluorescence throughout uninfected cells, redistributing into puncta only when the cell is infected by a phi6-type phage that depends on YajQ (PMID:20164238). The UniProt record declares no transmembrane segment and no signal peptide, so there is nothing competing with a soluble cytoplasmic assignment. Reason: The row was examined as a synthesis row rather than taken on trust: what PANTHER PTN002411992 rests on is the cytoplasmic localisation of characterised YajQ-family proteins, and for this gene product the GFP experiment in PMID:20164238 confirms it independently, in the right organism, for the uninfected cell. Cytosol rather than a membrane or periplasmic compartment is also what the sequence predicts. Accepted as the location where the protein acts, including where it meets the incoming phage core. Supporting Evidence: PMID:20164238 Green fluorescent protein (GFP) fusions with YajQ produce uniform fluorescence in uninfected cells and in cells infected with viruses not dependent on YajQ. file:PSE14/PSPPH_4093/PSPPH_4093-notes.md The UniProt record for Q48EH2 declares no transmembrane segment and no signal peptide, its only sequence feature being the full-length chain PRO_0000261963, which is consistent with the cytosolic assignment. |
| GO:0039696 RNA-templated viral transcription | IDA PMID:18836083 The role of host protein YajQ in the temporal control of tra... | MODIFY | Summary: CACAO row, IDA, PMID:18836083. What the cited paper shows for this gene: bacteriophage phi6 carries three dsRNA genomic segments inside a core particle that also contains an RNA-dependent RNA polymerase; that virion polymerase transcribes segments M and S in vitro, but segment L is highly transcribed early in infection, and the host protein encoded by yajQ is what activates L transcription. YajQ does not touch the enzyme directly: it binds P1, the major structural protein of the core, and the core conformation is what controls polymerase activity. The paper's own full text names the locus as PSPPH_4093, so the gene attribution is the authors' own and not an ortholog guess. Whether the term matches: only with the qualifier doing a great deal of work. GO:0039696 is defined as a transcription process that uses viral RNA as a template and sits under viral transcription and viral gene expression, so it names the activity of the polymerase, which here is phage protein P2. YajQ performs none of it. Reason: The claim is right and the term is the wrong side of the host/virus boundary, and there is now a term that fixes it. GO:0140181 host-mediated activation of viral RNA-templated transcription was created on 2025-06-12 with PMID:18836083, this paper, as its definition xref, two months after this row was made on 2025-04-25, and it still has no annotations at all. The row and the term therefore come from the same source and were never joined up. GO:0140181 says precisely what the paper shows, in the interspecies branch where a host factor belongs, at the granularity that matches phi6 being a dsRNA phage, and it takes involved_in, as all 1425 annotations to its parent GO:0043923 do. Two things are worth stating about what is not wrong here. The branch is not wrong: phi6 is a double-stranded RNA phage, so RNA-templated transcription really is the process being activated, and nothing about this gene belonging to a bacterium puts the row on the wrong side of the DNA/RNA distinction. And the qualifier is not the defect on this row. acts_upstream_of_or_within_positive_effect is a legal GO biological-process relation and it is the right relation for a product that influences a process it does not execute, so it happens to fit GO:0039696 as written. That fit should not be read as a considered judgement, though: across the CACAO corpus the hedge appears on every 2025-2026 row for terms whose earlier CACAO rows used involved_in, so it is a campaign-wide default rather than a per-row call, and these rows are dated 2025-04-25. The point is only that the qualifier question on this row is moot, because a term naming the wrong actor does not get repaired by a relation. The defect is the choice of term, filed as WRONG_TERM against CACAO with GO:0140181 as the correction. Proposed replacements: host-mediated activation of viral RNA-templated transcription Supporting Evidence: PMID:18836083 A host protein encoded by yajQ is responsible for the activation of L transcription. PMID:18836083 The virion RNA polymerase in the core particle transcribes segments M and S in vitro. PMID:18836083 YajQ acts indirectly on the polymerase by binding to P1, the major structural protein of the core. PMID:18836083 Bacteriophage Phi6 contains three dsRNA genomic segments L, M, and S. PMID:20164238 Transcription of genomic segment L is activated by the interaction of host protein YajQ with the capsid structure. file:PSE14/PSPPH_4093/PSPPH_4093-notes.md QuickGO reports that GO:0140181 host-mediated activation of viral RNA-templated transcription was created on 2025-06-12, carries PMID:18836083 as its definition xref, and had zero annotations when queried on 2026-11-01. file:PSE14/PSPPH_4093/PSPPH_4093-notes.md GO:0039696 RNA-templated viral transcription is defined as a transcription process that uses viral RNA as a template, and its ancestors are GO:0019083 viral transcription, GO:0019080 viral gene expression and GO:0016032 viral process, so the term names the activity of whatever polymerase does the transcribing. |
| GO:1903902 positive regulation of viral life cycle | IDA PMID:18836083 The role of host protein YajQ in the temporal control of tra... | MODIFY | Summary: CACAO row, IDA, PMID:18836083, same paper and same date as the row above. What the cited paper shows for this gene: yajQ knockouts do not support phi6 replication, and phi6 escapes the requirement only by acquiring two mutations in the RNA-dependent RNA polymerase gene, so the host protein is genuinely required for, and promotes, the phage life cycle. Whether the term matches: in substance yes, and this row is not in the same difficulty as the GO:0039696 row, because a positive-regulation term is something a host factor can legitimately carry. The problem is that it is uninformative about which part of the life cycle and by what route, when the paper pins both down to activation of segment-L transcription on the viral core. Reason: Correct but general, so MODIFY rather than KEEP_AS_NON_CORE. The replacement is GO:0140181 host-mediated activation of viral RNA-templated transcription, the same term the GO:0039696 row moves to, which merges two rows built from one experiment into the single statement that experiment supports. GO:0140181 is not a descendant of GO:1903902, since it sits in the interspecies branch under GO:0043923 rather than under regulation of viral life cycle, so this is a lateral correction rather than a refinement. Separately, this row does have a genuine qualifier defect, and unlike the GO:0039696 row it is the AcrIIA5 pattern: acts_upstream_of_or_within_positive_effect on a term that already means positive regulation stacks a second regulatory layer on a regulatory term, and YajQ is the entity doing the regulating, so involved_in is correct. Both defects are filed below. The claim itself is kept, not weakened: the knockout and the escape mutations are strong, and the only thing changing is which term and relation carry them. Proposed replacements: host-mediated activation of viral RNA-templated transcription Supporting Evidence: PMID:18836083 Knockout mutants of yajQ do not support the replication of Phi6, although they do support the replication of distantly related members of the Cystoviridae. PMID:18836083 Phi6 can mutate to independence of YajQ. This requires two mutations in the gene for the RNA-dependent RNA polymerase. PMID:18836083 A host protein encoded by yajQ is responsible for the activation of L transcription. file:PSE14/PSPPH_4093/PSPPH_4093-notes.md GO:0140181 is not a descendant of GO:1903902 positive regulation of viral life cycle; it sits in the interspecies branch under GO:0043923, GO:0044794, GO:0044788, GO:0035821 and GO:0044419, so replacing GO:1903902 with it is a lateral correction rather than a refinement. |
| GO:0046790 virion binding | IDA PMID:18836083 The role of host protein YajQ in the temporal control of tra... | NEW | Summary: Proposed addition. The molecular step YajQ itself performs is binding a structural component of the phage particle: it binds P1, the major structural protein of the phi6 core, which is how an indirect effect on the encapsidated polymerase is produced. GO:0046790 is defined as binding to a virion, either by binding to components of the capsid or the viral envelope, which is this interaction. The follow-up study makes the particle association visible in the cell: GFP-YajQ becomes punctate on infection by YajQ-dependent phage and the host protein stays with the infecting particles throughout infection. Reason: Added because the review's two process rows both rest on a binding event that no row records, and because this gene carries no molecular-function term beyond family-level nucleotide binding. The participation test is met on the right side: YajQ is the entity that does the binding, so this is its own activity rather than an effect attributed to it, which is exactly the distinction the GO:0039696 row failed. GO:0046790 is also the informative alternative to bare GO:0005515 protein binding, which this gene does not carry and should not acquire. Deliberately not proposed as a core function: binding a bacteriophage capsid protein is the phage exploiting a host surface, not a function YajQ evolved to perform, and the core-function block records only the conserved cellular property. Supporting Evidence: PMID:18836083 YajQ acts indirectly on the polymerase by binding to P1, the major structural protein of the core. PMID:18836083 The RNA is located inside a core particle composed of multiple copies of a major structural protein, an RNA-dependent RNA polymerase, a hexameric NTPase, and an auxiliary protein. PMID:20164238 It appears that the host protein binds to the infecting particles and remains with them during the entire infection period. PMID:20164238 Punctate fluorescence develops when cells are infected with YajQ-dependent viruses. |
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Download this section (compressed HTML)Q: Which nucleotide does PSPPH_4093 actually bind? Its closest characterised relative, Pseudomonas aeruginosa PA4395, is a cyclic-di-GMP receptor, but the same study found Escherichia coli, Clostridium and Bacillus cereus YajQ proteins preferring ATP or GTP, so the ligand cannot be inferred from family membership.
Suggested experts: J. Maxwell Dow, Shi-Qi An
Q: Does PSPPH_4093 have a LysR-family partner in Pseudomonas savastanoi, as XC_3703 does in Xanthomonas campestris, and is the phi6 core protein P1 recognised by the same surface that such a partner would use?
Suggested experts: J. Maxwell Dow, Shi-Qi An
Q: What does a yajQ knockout cost the uninfected cell? Both phi6 papers characterise the knockout only as non-permissive for the phage, so the native cellular role of this protein in this organism is unaddressed.
Suggested experts: Leonard Mindich, Xueying Qiao
Q: Does YajQ binding change the phi6 core conformation directly, and does nucleotide occupancy of YajQ gate that activity? If a nucleotide ligand switches the P1 interaction, the host's second-messenger state would set the phage's early transcription programme.
Suggested experts: Leonard Mindich, Xueying Qiao
Q: The two mutations that make phi6 independent of YajQ fall in the polymerase gene rather than in P1. Do they reproduce the core conformation that YajQ induces, and would a P1 mutant be viable at all?
Suggested experts: Leonard Mindich, Xueying Qiao
Experiment: Purify recombinant Q48EH2 and measure binding affinity for cyclic di-GMP, cyclic di-AMP, cyclic AMP, GTP, ATP, GDP and ADP by isothermal titration calorimetry, running Pseudomonas aeruginosa PA4395 and Escherichia coli YajQ in parallel as the two known family behaviours. The result settles whether GO:0000166 can be refined to a specific nucleotide-binding term for this ortholog.
Hypothesis: PSPPH_4093 binds a nucleotide ligand, and whether that ligand is cyclic di-GMP or a linear nucleoside triphosphate cannot be predicted from the Pseudomonas aeruginosa ortholog.
Type: Isothermal titration calorimetry ligand panel
Experiment: Map the P1 contact by hydrogen-deuterium exchange mass spectrometry or cross-linking mass spectrometry on YajQ-bound phi6 core particles, then make point mutants in the mapped surface and score them in parallel for phi6 plaque support in a yajQ knockout background and for co-purification with host proteins by pull-down proteomics. Separation of the two phenotypes would show the phage has found a distinct site; coincidence would show it is mimicking a cellular ligand.
Hypothesis: The YajQ surface that binds phi6 P1 is a surface the protein normally presents to a cellular partner, so phage dependence and the native cellular interaction map to the same residues.
Type: Interaction-site mapping with separation-of-function mutants
Experiment: Reconstitute the published in vitro transcription assay with purified phi6 nucleocapsids and recombinant YajQ, and compare segment-L transcript output with YajQ pre-loaded with each ligand from the calorimetry panel, and with ligand-binding-site mutants. A ligand-dependent shift in L transcription would link host second-messenger state to phage early gene expression.
Hypothesis: Nucleotide occupancy of YajQ gates its activation of phi6 segment-L transcription.
Type: In vitro nucleocapsid transcription with defined YajQ ligand states
Experiment: Phenotype the yajQ knockout LM4470 and a clean deletion in strain 1448A without phage: growth across carbon sources and temperatures, biofilm formation, motility, adhesion, and virulence on the bean host, with RNA-seq of knockout versus wild type to find the regulon. The Xanthomonas and Pseudomonas aeruginosa work predicts a transcriptional and adhesion phenotype; a clean result would mean the protein is dispensable to the cell and known only as a phage cofactor.
Hypothesis: PSPPH_4093 has a cellular function independent of phage infection that the existing literature has not examined.
Type: Comparative phenotyping and transcriptomics of a yajQ deletion
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