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Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860

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Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860. / Rosa, Leonardo T.; Springthorpe, Victoria Jayne; Bianconi, Matheus E.; Thomas, Gavin Hugh; Kelly, David J.

In: Microbial Genomics, Vol. 4, No. 5, 01.05.2018, p. 1-7.

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Harvard

Rosa, LT, Springthorpe, VJ, Bianconi, ME, Thomas, GH & Kelly, DJ 2018, 'Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860', Microbial Genomics, vol. 4, no. 5, pp. 1-7. https://doi.org/10.1099/mgen.0.000176

APA

Rosa, L. T., Springthorpe, V. J., Bianconi, M. E., Thomas, G. H., & Kelly, D. J. (2018). Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860. Microbial Genomics, 4(5), 1-7. https://doi.org/10.1099/mgen.0.000176

Vancouver

Rosa LT, Springthorpe VJ, Bianconi ME, Thomas GH, Kelly DJ. Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860. Microbial Genomics. 2018 May 1;4(5):1-7. https://doi.org/10.1099/mgen.0.000176

Author

Rosa, Leonardo T. ; Springthorpe, Victoria Jayne ; Bianconi, Matheus E. ; Thomas, Gavin Hugh ; Kelly, David J. / Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860. In: Microbial Genomics. 2018 ; Vol. 4, No. 5. pp. 1-7.

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@article{d33b6995c6f84aab91f96f15007c96a0,
title = "Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860",
abstract = "Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the β-proteobacteria Bordetella and we observed similar expansions in other β-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points.",
author = "Rosa, {Leonardo T.} and Springthorpe, {Victoria Jayne} and Bianconi, {Matheus E.} and Thomas, {Gavin Hugh} and Kelly, {David J.}",
note = "{\textcopyright} 2018 The Authors.",
year = "2018",
month = may,
day = "1",
doi = "10.1099/mgen.0.000176",
language = "English",
volume = "4",
pages = "1--7",
journal = "Microbial Genomics",
issn = "2057-5858",
publisher = "Microbiology Society",
number = "5",

}

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TY - JOUR

T1 - Massive over-representation of solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family in the genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860

AU - Rosa, Leonardo T.

AU - Springthorpe, Victoria Jayne

AU - Bianconi, Matheus E.

AU - Thomas, Gavin Hugh

AU - Kelly, David J.

N1 - © 2018 The Authors.

PY - 2018/5/1

Y1 - 2018/5/1

N2 - Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the β-proteobacteria Bordetella and we observed similar expansions in other β-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points.

AB - Lineage-specific expansion (LSE) of protein families is a widespread phenomenon in many eukaryotic genomes, but is generally more limited in bacterial genomes. Here, we report the presence of 434 genes encoding solute-binding proteins (SBPs) from the tripartite tricarboxylate transporter (TTT) family, within the 8.2 Mb genome of the α-proteobacterium Rhodoplanes sp. Z2-YC6860, a gene family over-representation of unprecedented abundance in prokaryotes. Representing over 6 % of the total number of coding sequences, the SBP genes are distributed across the whole genome but are found rarely in low-GC islands, where the gene density for this family is much lower. This observation, and the much higher sequence identity between the 434 Rhodoplanes TTT SBPs compared with the average identity between homologues from different species, is indicative of a key role for LSE in the expansion. The TTT SBP genes were found in the vicinity of genes encoding membrane components of transport systems from different families, as well as regulatory proteins such as histidine-kinases and transcription factors, indicating a broad range of functions around the sensing, response and transport of organic compounds. A smaller expansion of TTT SBPs is known in some species of the β-proteobacteria Bordetella and we observed similar expansions in other β-proteobacterial lineages, including members of the genus Comamonas and the industrial biotechnology organism Cupriavidus necator, indicating that strong environmental selection can drive SBP duplication and specialisation from multiple evolutionary starting points.

U2 - 10.1099/mgen.0.000176

DO - 10.1099/mgen.0.000176

M3 - Article

VL - 4

SP - 1

EP - 7

JO - Microbial Genomics

JF - Microbial Genomics

SN - 2057-5858

IS - 5

ER -