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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.
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BMC Genomics

ISSN: 1471-2164

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