ttgB

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005886 plasma membrane	IEA GO_REF:0000120	ACCEPT	Summary: TtgB is an inner membrane protein with 12 predicted transmembrane helices. UniProt annotates TtgB to cell inner membrane as a multi-pass membrane protein (ECO:0000305). The GO term GO:0005886 (plasma membrane) is the correct GO term for the bacterial inner/cytoplasmic membrane. This is well-supported by the domain architecture (IPR001036 Acriflavine resistance protein; 12 TM helices in the UniProt feature table) and by its function as the inner membrane component of the TtgABC tripartite efflux system (PMID:12743835). The deep research file confirms TtgB localizes to the inner membrane and functionally couples to the periplasmic adaptor (TtgA) and an outer-membrane channel (TtgC) (file:PSEPK/ttgB/ttgB-deep-research-falcon.md). Reason: UniProt explicitly states "Cell inner membrane; Multi-pass membrane protein" (ECO:0000305). The 12 predicted transmembrane helices in the UniProt feature table confirm integral membrane localization. GO:0005886 (plasma membrane) is the standard GO mapping for bacterial inner membrane. This is a core cellular component annotation. Supporting Evidence: file:PSEPK/ttgB/ttgB-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane file:PSEPK/ttgB/ttgB-deep-research-falcon.md TtgB (PP_1385; Q88N31) is the inner-membrane RND transporter/IMP
GO:0009636 response to toxic substance	IEA GO_REF:0000117	MODIFY	Summary: TtgB, as part of the TtgABC efflux pump, actively extrudes toxic xenobiotic compounds from the cell including antibiotics and bipyridyl compounds. This is a response to toxic substances, but the term is quite broad. A more specific term such as GO:1990961 (xenobiotic detoxification by transmembrane export across the plasma membrane) would precisely describe the mechanism by which TtgB responds to toxic substances. The deep research confirms that TtgABC is required for detoxification of bipyridyl compounds and contributes to antibiotic tolerance (file:PSEPK/ttgB/ttgB-deep-research-falcon.md). Reason: While TtgB is indeed involved in response to toxic substances, this term is too vague for the specific efflux-based detoxification mechanism. GO:1990961 (xenobiotic detoxification by transmembrane export across the plasma membrane) precisely describes the mechanism: reducing toxicity by exporting xenobiotics across the plasma membrane. This matches TtgABC's demonstrated function in extruding chloramphenicol (PMID:22143519), bipyridyl compounds (PMID:32973714), and other xenobiotics from KT2440. Proposed replacements: xenobiotic detoxification by transmembrane export across the plasma membrane Supporting Evidence: PMID:32973714 the deletion of ttgB made the strain susceptible to 2,2'-bipyridyl and natural bipyridyl derivatives such as caerulomycin A, indicating that TtgABC is required for detoxification of compounds of the bipyridyl family PMID:22143519 survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol
GO:0015562 efflux transmembrane transporter activity	IEA GO_REF:0000002	ACCEPT	Summary: TtgB is the inner membrane transporter of the RND-type TtgABC efflux pump. This is its core molecular function: active efflux of substrates across the inner membrane, driven by the proton motive force. The term GO:0015562 (efflux transmembrane transporter activity) correctly captures this function. InterPro domain IPR004764 (MdtF-like) and IPR001036 (Acriflavine resistance protein) both support RND efflux transporter activity. The deep research confirms TtgB as the inner-membrane transporter enabling pmf-driven extrusion of multiple toxic small molecules (file:PSEPK/ttgB/ttgB-deep-research-falcon.md). Reason: This is the core molecular function of TtgB. It is the substrate-translocating inner membrane component of the TtgABC RND efflux pump. InterPro mapping from IPR004764 is appropriate. Multiple publications confirm efflux transporter function: TtgABC overexpression causes multidrug resistance via efflux (PMID:32840000), TtgABC knockout compromises chloramphenicol resistance (PMID:22143519), and TtgB possesses multidrug-binding capacity (PMID:17498746). Supporting Evidence: PMID:32840000 Mutants of the first type were more resistant to fluoroquinolones and beta-lactams except imipenem, and overproduced the efflux system TtgABC PMID:17498746 TtgR and the TtgB efflux pump proteins possess multidrug-binding capacity, and their concerted action is responsible for the multidrug resistance phenotype
GO:0016020 membrane	IEA GO_REF:0000002	ACCEPT	Summary: GO:0016020 (membrane) is a very broad cellular component term. TtgB is indeed a membrane protein, but this annotation is redundant with the more specific GO:0005886 (plasma membrane) annotation already present. However, as an IEA annotation derived from InterPro domain mappings (IPR001036, IPR004764), it is technically correct and acceptable to retain alongside the more specific term. Reason: While this is a broad parent term and GO:0005886 (plasma membrane) is more specific, it is acceptable to retain IEA annotations at broader levels. The InterPro domains IPR001036 (Acriflavine resistance protein) and IPR004764 (MdtF-like) correctly map to membrane localization. TtgB has 12 predicted transmembrane helices confirming integral membrane insertion. Supporting Evidence: file:PSEPK/ttgB/ttgB-uniprot.txt SUBCELLULAR LOCATION: Cell inner membrane
GO:0022857 transmembrane transporter activity	IEA GO_REF:0000002	ACCEPT	Summary: GO:0022857 (transmembrane transporter activity) is a parent term of the more specific GO:0015562 (efflux transmembrane transporter activity) which is also annotated. TtgB does have transmembrane transporter activity, but this is redundant with the more specific efflux term. As an IEA from InterPro (IPR001036), it is acceptable to retain this broader annotation. Reason: This is a correct but general parent term of GO:0015562 (efflux transmembrane transporter activity). Since both annotations are IEA, retaining the broader term from a different InterPro mapping (IPR001036 vs IPR004764) is acceptable. TtgB unambiguously has transmembrane transporter activity as the RND inner membrane component of the TtgABC efflux pump. Supporting Evidence: file:PSEPK/ttgB/ttgB-uniprot.txt Probable efflux pump membrane transporter TtgB
GO:0042908 xenobiotic transport	IEA GO_REF:0000120	MODIFY	Summary: GO:0042908 (xenobiotic transport) is a biological process term describing the transport of xenobiotics. TtgABC exports antibiotics (chloramphenicol, fluoroquinolones, beta-lactams), plant antimicrobials (phloretin), and bipyridyl compounds, all of which are xenobiotics. This term is correct. A more specific child term GO:0006855 (xenobiotic transmembrane transport) would be more precise since TtgB specifically performs transmembrane transport of xenobiotics. Reason: While xenobiotic transport is correct, the more specific term GO:0006855 (xenobiotic transmembrane transport) better describes TtgB's function. TtgB transports xenobiotics specifically across the inner membrane (as part of the tripartite TtgABC system spanning both membranes). The substrates confirmed as xenobiotics in KT2440 include chloramphenicol (PMID:22143519), bipyridyl compounds (PMID:32973714), fluoroquinolones and beta-lactams (PMID:32840000), and plant antimicrobials such as phloretin (PMID:17466326). Proposed replacements: xenobiotic transmembrane transport Supporting Evidence: PMID:22143519 survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol PMID:32973714 the deletion of ttgB made the strain susceptible to 2,2'-bipyridyl and natural bipyridyl derivatives such as caerulomycin A, indicating that TtgABC is required for detoxification of compounds of the bipyridyl family
GO:0042910 xenobiotic transmembrane transporter activity	IEA GO_REF:0000118	ACCEPT	Summary: GO:0042910 (xenobiotic transmembrane transporter activity) is the most specific and accurate molecular function term currently assigned to TtgB. It describes the ability to transport xenobiotics across a membrane, which is precisely what TtgB does as the RND transporter of the TtgABC efflux pump. The TreeGrafter assignment via PANTHER is well-supported. TtgB exports antibiotics (ampicillin, chloramphenicol, fluoroquinolones), plant antimicrobials, and bipyridyl compounds -- all xenobiotics. The deep research confirms TtgABC exports 2,2'-bipyridyl, caerulomycin A, chloramphenicol, bile salts, and deoxycholate (file:PSEPK/ttgB/ttgB-deep-research-falcon.md). Reason: This is an excellent annotation from TreeGrafter that captures the core molecular function at the right level of specificity. TtgB specifically transports xenobiotic compounds (antibiotics, plant antimicrobials, bipyridyls) across the inner membrane. The broad substrate specificity spanning multiple xenobiotic classes makes this term more appropriate than any single substrate-specific transporter term. Literature demonstrates TtgB possesses multidrug-binding capacity (PMID:17498746) and exports diverse xenobiotic classes (PMID:22143519, PMID:32973714, PMID:32840000). Supporting Evidence: PMID:17498746 TtgR and the TtgB efflux pump proteins possess multidrug-binding capacity, and their concerted action is responsible for the multidrug resistance phenotype PMID:32840000 Mutants of the first type were more resistant to fluoroquinolones and beta-lactams except imipenem, and overproduced the efflux system TtgABC
GO:0055085 transmembrane transport	IEA GO_REF:0000120	ACCEPT	Summary: GO:0055085 (transmembrane transport) is a very broad biological process term. TtgB does participate in transmembrane transport, but this is redundant with the more specific GO:0042908 (xenobiotic transport) annotation and the proposed replacement GO:0006855 (xenobiotic transmembrane transport). As a general IEA annotation, it is acceptable but uninformative. Reason: This is a correct but very general parent BP term. TtgB undeniably performs transmembrane transport as the RND inner membrane transporter. While more specific terms like GO:0006855 (xenobiotic transmembrane transport) are more informative, retaining this broad IEA annotation is acceptable as it captures the fundamental process without being incorrect. Supporting Evidence: file:PSEPK/ttgB/ttgB-uniprot.txt Probable efflux pump membrane transporter TtgB
GO:0046677 response to antibiotic	IDA PMID:22143519 Mechanisms of resistance to chloramphenicol in Pseudomonas p...	NEW	Summary: TtgABC in KT2440 is specifically demonstrated to confer resistance to antibiotics including chloramphenicol (PMID:22143519), fluoroquinolones and beta-lactams (PMID:32840000), and ampicillin (PMID:28352264). The ttgB knockout shows compromised survival in the presence of chloramphenicol. This is a core biological process for TtgB in KT2440 that is not captured by any existing annotation. Reason: Antibiotic resistance is the primary demonstrated biological role of TtgABC in KT2440 (as opposed to solvent tolerance in DOT-T1E). Multiple publications demonstrate that TtgABC knockout impairs antibiotic resistance (PMID:22143519), and overexpression causes multidrug resistance (PMID:32840000). This annotation fills an important gap in the existing annotation set. Supporting Evidence: PMID:22143519 survival of a knockout mutant in the TtgABC resistance-nodulation-division (RND) efflux pump and mutants in the biosynthesis of pyrroloquinoline (PQQ) were compromised in the presence of chloramphenicol PMID:32840000 Mutants of the first type were more resistant to fluoroquinolones and beta-lactams except imipenem, and overproduced the efflux system TtgABC PMID:28352264 Among the genes involved in β-lactam resistance (Nakae et al., 1999; Quale et al., 2006; Kong et al., 2010), genes encoding resistance nodulation cell division (RND) efflux pumps/transporters (ttgABC, acrB2, and acrB3) and bacterial secretion systems, specifically, were increased by indole plus Amp or only indole (Supplementary Tables S5–S7), suggesting that they might contribute primarily to the acquisition of indole-induced Amp resistance
GO:1990281 efflux pump complex	ISS PMID:12743835 Comparative genomic analysis of solvent extrusion pumps in P...	NEW	Summary: TtgB is a subunit of the TtgABC tripartite efflux pump complex, which consists of TtgA (membrane fusion protein), TtgB (inner membrane RND transporter), and TtgC (outer membrane factor). GO:1990281 (efflux pump complex) is defined as "a protein complex that is capable of efflux transmembrane transporter activity." No current CC annotation captures the complex membership. The deep research file confirms the tripartite architecture (file:PSEPK/ttgB/ttgB-deep-research-falcon.md). Reason: TtgB functions exclusively as part of the TtgABC tripartite complex. The complex membership is a critical aspect of its biology -- TtgB alone cannot export substrates without TtgA and TtgC partners. This annotation fills a gap, as the current CC annotations only capture membrane localization but not complex membership. Supporting Evidence: PMID:12743835 Three efflux pumps belonging to the RND (resistance-nodulation-cell division) family of multidrug extrusion pumps are the main factor involved in the high intrinsic tolerance to toluene file:PSEPK/ttgB/ttgB-deep-research-falcon.md TtgA (PP_1386) is the periplasmic adaptor/MFP, TtgB (PP_1385; Q88N31) is the inner-membrane RND transporter/IMP, and TtgC (PP_1384) is the outer-membrane channel component
GO:0042710 biofilm formation	IMP PMID:24907323 Knockout of extracytoplasmic function sigma factor ECF-10 af...	NEW	Summary: Knockout of ECF-10 sigma factor leads to upregulation of ttgABC and enhanced biofilm formation in KT2440, suggesting TtgABC plays a role in biofilm development beyond simple antibiotic resistance (PMID:24907323). This is a non-core but documented function for TtgB in KT2440. Reason: PMID:24907323 demonstrates a link between TtgABC expression and biofilm formation in KT2440. The publication explicitly identifies a new role for TtgABC in biofilm development. This should be annotated as a non-core function. Supporting Evidence: PMID:24907323 the ECF-10 mutant exhibited enhanced formation of biofilms after 24 h of incubation