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Table 3 Proposed substrate classess of predicted glycosyltransferases in Lactobacillus rhamnosus GG

From: A network-based approach to identify substrate classes of bacterial glycosyltransferases

Query-GT locus tag Query-GT localization Enriched GO categories Membrane association Partner GTs Proposed substrate class of the query-GT Potential protein substrate Evidence Reference
LGG_00280 C EPS biosynthesis LGG_00278 (hypothetical protein) LGG_02043 LGG_00281 LGG_00283 LGG_00295 LGG_00279 LGG_01999 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_00281 C EPS biosynthesis; PS transport LGG_00278 (hypothetical protein) LGG_00280 LGG_00295 LGG_01057 LGG_00279 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_00295 C EPS biosynthesis LGG_00296 (integral membrane protein) LGG_00280 LGG_02043 LGG_00281 LGG_02869 LGG_01057 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_01062* C EPS biosynthesis - LGG_02026 LGG_02023 LGG_02025 Extracellularsaccharides - - -
LGG_02040$ C EPS biosynthesis; nucleotide-sugar metabolism - LGG_02042 LGG_02046 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_02042 C EPS biosynthesis; nucleotide-sugar metabolism - LGG_02040 Extracellularsaccharides - Conservation Kankainen et al., 2009 [44]
LGG_02043 TM Peptidyl-tyrosine dephosphorylation, regulation of catalytic acitivity, EPS biosynthesis - LGG_01992 LGG_02047 Extracellularsaccharides - Experimental validation Lebeer et al., 2009 [37]; Kankainen et al., 2009 [44]
LGG_02045 C Polysaccharide biosynthesis; polysaccharide transport LGG_00282 (polysaccharide transporter) LGG_00998 LGG_00999 LGG_02046 LGG_02047 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_02046 C EPS biosynthesis; polysaccharide transport LGG_02049 (polysaccharide transporter) LGG_02045 LGG_02047 LGG_01999 Extracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_02047 C Polysaccharide biosynthesis; polysaccharide transport LGG_02043 (undecaprenyl-P-β-glucosephosphotransferase) LGG_02043 LGG_02045 LGG_02046 LGG_02869 LGG_00295 LGG_01057 Extracellular saccharides - Experimental validation This work
LGG_01062* C Glycogen biosynthesis - LGG_02026 LGG_02023 LGG_02025 Intracellular saccharides - - -
LGG_02023 C Glycogen biosynthesis; pyrimidine nucleoside metabolism - LGG_02026 LGG_01062 LGG_02024 LGG_02025 Intracellular saccharides - Conservation Kankainen et al., 2009 [44]
LGG_02024 C Glycogen biosynthesis; response to antibiotic - LGG_02023 LGG_02025 LGG_02026 Intracellular saccharides - Conservation Kiel et al., 1994 [42]; Kankainen et al., 2009 [44]
LGG_02025 C Glycogen biosynthesis - LGG_02023 LGG_02024 LGG_02026 Intracellular saccharides - Conservation Ballicora et al., 2003 [56]; Kankainen et al., 2009 [44]
LGG_02026 C Glycogen biosynthesis - LGG_02023 LGG_02024 LGG_02025 Intracellular saccharides - Conservation Ballicora et al., 2003 [56]; Kankainen et al., 2009 [44]
LGG_00998 C Carbohydrate metabolism; lipids metabolism LGG_00995 (hypothetical protein) LGG_02045 LGG_00999 Lipid - Conservation Kankainen et al., 2009 [44]
LGG_00999 C Carbohydrate metabolism; lipids metabolism LGG_00995 (hypothetical protein) LGG_02045 LGG_00998 Lipid - Conservation Kankainen et al., 2009 [44]
LGG_01057* C Carbohydrate metabolism; lipids metabolism LGG_02004 (sugar or LPS synthesis transferase) LGG_02004 LGG_00280 LGG_02043 LGG_02869 LGG_00295 LGG_02046 LGG_02047 Lipid - - -
LGG_00794 TM PG-based cell wall biogenesis - - Peptidoglycan - Conservation Kankainen et al., 2009 [44]
LGG_01283 C PG-based cell wall biogenesis LGG_01192 (rod shape-determining protein RodA) LGG_01487 Peptidoglycan - Conservation Mengin-Lecreulx et al., 1991 [26]; Kankainen et al., 2009 [44]
LGG_01487 TM PG-based cell wall biogenesis - LGG_01283 Peptidoglycan - Conservation Kankainen et al., 2009 [44]
LGG_01538* TM PG biosynthetic process; regulation of cell shape; dephosphorylation; response to antibiotics - LGG_00280 Peptidoglycan - - -
LGG_01783 TM PG-based cell wall biogenesis - - Peptidoglycan - Conservation Di Guilmi et al., 2003 [17]; Kankainen et al., 2009 [44]
LGG_00794* TM Regulation of cell shape; cell cycle - - Protein LGG_01280 (cell division protein FtsI) - -
LGG_00825* C Protein translation LGG_00751 (SNARE associated golgi protein) LGG_00826 Protein LGG_00829 (YkuJ protein) - -
LGG_00826* C Protein translation; amino acid transport LGG_00751 (SNARE associated golgi protein) LGG_00825 LGG_02047 Protein LGG_00829 (YkuJ protein) - -
LGG_01147* C DNA metabolic process LGG_01146 (predicted ORF) - Protein LGG_01145 (DNA-entry nuclease) - -
LGG_01283* C Regulation of cell shape; response to antibiotic, cell division LGG_01192 (rod shape-determining protein RodA) LGG_01487 Protein LGG_01280 (cell division protein FtsI) - -
LGG_01487* TM Regulation of cell shape; cell division - LGG_01283 Protein LGG_01706 (cell division protein/penicillin-binding protein 2); LGG_01280 (cell division protein FtsI); LGG_00254 (D-alanyl-D-alanine carboxypeptidase) - -
LGG_01783* TM Regulation of cell shape; cell cycle - - Protein LGG_01280 (cell division protein FtsI)   
  1. Locus tag: gene identifier of the predicted GT used as query in STRING to obtain a query-dependent subnetwork. Localization: indicates whether the query-GT was predicted to be a cytoplasmic (C) or a transmembrane protein (TM). Enriched GO categories: GO categories enriched amongst the members of the query-dependent subnetwork of the indicated query-GT. Only categories showing an enrichment value of p < 0.05 are shown (according to a hypergeometric test corrected for multiple testing using False Discovery Rate). Membrane association: refers to edges between the query-GT and members of its subnetwork predicted to be transmembrane proteins. Partner GTs: predicted/experimentally validated GTs that belong to the subnetwork of the query-GT. Proposed substrate class of the query-GT: inferred from the GO enrichment analysis of the query-dependent subnetwork of the indicated query-GT derived from STRING. Novel substrate predictions derived from this study are indicated by a star (*) next to the locus tag of the corresponding query-GT. Potential protein substrate: it refers to edges between the query-GT and members of its subnetwork predicted to have N- or O-glycosylation sites. Such proteins are therefore suggested to be potential substrates of the query-GT in the cases where proteins are the proposed substrate. Evidence: level of evidence for the predicted substrate class of the query-GT. Conservation: shows significant sequence conservation with a GT for which the substrate specificity has been experimentally validated in closely related species. Experimental validation: the substrate specificity of the GT has been experimentally validated in Lactobacillus rhamnosus GG. Reference: publication(s) supporting the predicted substrate class of the query-GT.