Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization

Christopher Mulligan; David J Kelly; Gavin H Thomas

doi:10.1159/000099643

Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization

Christopher Mulligan, David J Kelly, Gavin H Thomas

Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Tripartite ATP-independent periplasmic (TRAP) transporters are a family of extracytoplasmic solute receptor-dependent secondary transporters that are widespread in the prokaryotic world but which have not been extensively studied. Here, we present results of a genome-wide analysis of TRAP sequences and genome organization from application of TRAPDb, a relational database created for the collection, curation and analysis of TRAP sequences. This has revealed a specific enrichment in the number of TRAP transporters in several bacteria which is consistent with increased use of TRAP transporters in saline environments. Additionally, we report a number of new organizations of TRAP transporter genes and proteins which suggest the recruitment of TRAP transporter components for use in other biological contexts.

Original language	English
Pages (from-to)	218-26
Number of pages	9
Journal	Journal of molecular microbiology and biotechnology
Volume	12
Issue number	3-4
DOIs	https://doi.org/10.1159/000099643
Publication status	Published - 2007

Bibliographical note

Keywords

Bacteria/enzymology
Biological Transport/genetics
Carrier Proteins/chemistry
Computational Biology/methods
Databases, Genetic
Gene Order
Genes, Bacterial
Genome, Bacterial
Models, Molecular
Periplasmic Proteins/chemistry
Synteny

Access to Document

10.1159/000099643

Cite this

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title = "Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization",

abstract = "Tripartite ATP-independent periplasmic (TRAP) transporters are a family of extracytoplasmic solute receptor-dependent secondary transporters that are widespread in the prokaryotic world but which have not been extensively studied. Here, we present results of a genome-wide analysis of TRAP sequences and genome organization from application of TRAPDb, a relational database created for the collection, curation and analysis of TRAP sequences. This has revealed a specific enrichment in the number of TRAP transporters in several bacteria which is consistent with increased use of TRAP transporters in saline environments. Additionally, we report a number of new organizations of TRAP transporter genes and proteins which suggest the recruitment of TRAP transporter components for use in other biological contexts.",

keywords = "Bacteria/enzymology, Biological Transport/genetics, Carrier Proteins/chemistry, Computational Biology/methods, Databases, Genetic, Gene Order, Genes, Bacterial, Genome, Bacterial, Models, Molecular, Periplasmic Proteins/chemistry, Synteny",

author = "Christopher Mulligan and Kelly, {David J} and Thomas, {Gavin H}",

year = "2007",

doi = "10.1159/000099643",

language = "English",

volume = "12",

pages = "218--26",

journal = "Journal of molecular microbiology and biotechnology",

issn = "1464-1801",

publisher = "S. Karger AG",

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}

Tripartite ATP-independent periplasmic transporters: application of a relational database for genome-wide analysis of transporter gene frequency and organization. / Mulligan, Christopher; Kelly, David J; Thomas, Gavin H.
In: Journal of molecular microbiology and biotechnology, Vol. 12, No. 3-4, 2007, p. 218-26.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Tripartite ATP-independent periplasmic transporters

T2 - application of a relational database for genome-wide analysis of transporter gene frequency and organization

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AU - Kelly, David J

AU - Thomas, Gavin H

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AB - Tripartite ATP-independent periplasmic (TRAP) transporters are a family of extracytoplasmic solute receptor-dependent secondary transporters that are widespread in the prokaryotic world but which have not been extensively studied. Here, we present results of a genome-wide analysis of TRAP sequences and genome organization from application of TRAPDb, a relational database created for the collection, curation and analysis of TRAP sequences. This has revealed a specific enrichment in the number of TRAP transporters in several bacteria which is consistent with increased use of TRAP transporters in saline environments. Additionally, we report a number of new organizations of TRAP transporter genes and proteins which suggest the recruitment of TRAP transporter components for use in other biological contexts.

KW - Bacteria/enzymology

KW - Biological Transport/genetics

KW - Carrier Proteins/chemistry

KW - Computational Biology/methods

KW - Databases, Genetic

KW - Gene Order

KW - Genes, Bacterial

KW - Genome, Bacterial

KW - Models, Molecular

KW - Periplasmic Proteins/chemistry

KW - Synteny

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