InforLorV4, PascalFrancis, Corpus, bibRecord, 000156

In silico prediction of horizontal gene transfer in Streptococcus thermophilus

Identifieur interne : 000156 ( PascalFrancis/Corpus ); précédent : 000155; suivant : 000157

In silico prediction of horizontal gene transfer in Streptococcus thermophilus

Auteurs : Catherine Eng ; Annabelle Thibessard ; Morten Danielsen ; Thomas Bovbjerg Rasmussen ; Jean-François Mari ; Pierre Leblond

Source :

Archives of microbiology [ 0302-8933 ] ; 2011.

RBID : Pascal:11-0189733

Descripteurs français

Pascal (Inist)
- Streptococcus salivarius subsp. thermophilus, Transfert génétique, Génome.

English descriptors

KwdEn :
- Genetic transfer, Genome, Streptococcus salivarius subsp. thermophilus.

Abstract

A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.

Notice en format standard (ISO 2709)

Pour connaître la documentation sur le format Inist Standard.

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A02	`01`			`@0 AMICCW`
A03		`1`		`@0 Arch. microbiol.`
A05				`@2 193`
A06				`@2 4`
A08	`01`	`1`	`ENG`	`@1 In silico prediction of horizontal gene transfer in Streptococcus thermophilus`
A11	`01`	`1`		`@1 ENG (Catherine)`
A11	`02`	`1`		`@1 THIBESSARD (Annabelle)`
A11	`03`	`1`		`@1 DANIELSEN (Morten)`
A11	`04`	`1`		`@1 RASMUSSEN (Thomas Bovbjerg)`
A11	`05`	`1`		`@1 MARI (Jean-François)`
A11	`06`	`1`		`@1 LEBLOND (Pierre)`
A14	`01`			`@1 Genetique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Universite de Lorraine, Faculté des Sciences et Technologies, BP 239 @2 54506 Vandœuvre-lès-Nancy @3 FRA @Z 1 aut. @Z 2 aut. @Z 6 aut.`
A14	`02`			`@1 LORIA, UMR CNRS 7503 et INRIA Lorraine, Campus scientifique, BP 70239 @2 54506 Vandœuvre-lès-Nancy @3 FRA @Z 1 aut. @Z 5 aut.`
A14	`03`			`@1 Department of Assays, Chr. Hansen A/S @2 Hørsholm @3 DNK @Z 3 aut. @Z 4 aut.`
A14	`04`			`@1 Department of Physiology, innovation, Chr. Hansen A/S @2 Hørsholm @3 DNK @Z 3 aut. @Z 4 aut.`
A20				`@1 287-297`
A21				`@1 2011`
A23	`01`			`@0 ENG`
A43	`01`			`@1 INIST @2 856 @5 354000194473910060`
A44				`@0 0000 @1 © 2011 INIST-CNRS. All rights reserved.`
A45				`@0 3/4 p.`
A47	`01`	`1`		`@0 11-0189733`
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A64	`01`	`1`		`@0 Archives of microbiology`
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C01	`01`		`ENG`	@0 A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.
C02	`01`	`X`		`@0 002A05B15`
C03	`01`	`X`	`FRE`	`@0 Streptococcus salivarius subsp. thermophilus @2 NS @5 01`
C03	`01`	`X`	`ENG`	`@0 Streptococcus salivarius subsp. thermophilus @2 NS @5 01`
C03	`01`	`X`	`SPA`	`@0 Streptococcus salivarius subsp. thermophilus @2 NS @5 01`
C03	`02`	`X`	`FRE`	`@0 Transfert génétique @5 05`
C03	`02`	`X`	`ENG`	`@0 Genetic transfer @5 05`
C03	`02`	`X`	`SPA`	`@0 Transferencia genética @5 05`
C03	`03`	`X`	`FRE`	`@0 Génome @5 06`
C03	`03`	`X`	`ENG`	`@0 Genome @5 06`
C03	`03`	`X`	`SPA`	`@0 Genoma @5 06`
C07	`01`	`X`	`FRE`	`@0 Streptococcaceae @2 NS`
C07	`01`	`X`	`ENG`	`@0 Streptococcaceae @2 NS`
C07	`01`	`X`	`SPA`	`@0 Streptococcaceae @2 NS`
C07	`02`	`X`	`FRE`	`@0 Micrococcales @2 NS`
C07	`02`	`X`	`ENG`	`@0 Micrococcales @2 NS`
C07	`02`	`X`	`SPA`	`@0 Micrococcales @2 NS`
C07	`03`	`X`	`FRE`	`@0 Bactérie`
C07	`03`	`X`	`ENG`	`@0 Bacteria`
C07	`03`	`X`	`SPA`	`@0 Bacteria`
C07	`04`	`X`	`FRE`	`@0 Bactérie lactique @5 13`
C07	`04`	`X`	`ENG`	`@0 Lactic acid bacteria @5 13`
C07	`04`	`X`	`SPA`	`@0 Bacteria láctica @5 13`
N21				`@1 122`
N44	`01`			`@1 OTO`
N82				`@1 OTO`

Format Inist (serveur)

NO :	PASCAL 11-0189733 INIST
ET :	In silico prediction of horizontal gene transfer in Streptococcus thermophilus
AU :	ENG (Catherine); THIBESSARD (Annabelle); DANIELSEN (Morten); RASMUSSEN (Thomas Bovbjerg); MARI (Jean-François); LEBLOND (Pierre)
AF :	Genetique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Universite de Lorraine, Faculté des Sciences et Technologies, BP 239/54506 Vandœuvre-lès-Nancy/France (1 aut., 2 aut., 6 aut.); LORIA, UMR CNRS 7503 et INRIA Lorraine, Campus scientifique, BP 70239/54506 Vandœuvre-lès-Nancy/France (1 aut., 5 aut.); Department of Assays, Chr. Hansen A/S/Hørsholm/Danemark (3 aut., 4 aut.); Department of Physiology, innovation, Chr. Hansen A/S/Hørsholm/Danemark (3 aut., 4 aut.)
DT :	Publication en série; Niveau analytique
SO :	Archives of microbiology; ISSN 0302-8933; Coden AMICCW; Allemagne; Da. 2011; Vol. 193; No. 4; Pp. 287-297; Bibl. 3/4 p.
LA :	Anglais
EA :	A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.
CC :	002A05B15
FD :	Streptococcus salivarius subsp. thermophilus; Transfert génétique; Génome
FG :	Streptococcaceae; Micrococcales; Bactérie; Bactérie lactique
ED :	Streptococcus salivarius subsp. thermophilus; Genetic transfer; Genome
EG :	Streptococcaceae; Micrococcales; Bacteria; Lactic acid bacteria
SD :	Streptococcus salivarius subsp. thermophilus; Transferencia genética; Genoma
LO :	INIST-856.354000194473910060
ID :	11-0189733

Links to Exploration step

Pascal:11-0189733

Le document en format XML

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<front><div type="abstract" xml:lang="en">A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.</div>
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<fC01 i1="01" l="ENG"><s0>A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.</s0>
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<fC03 i1="01" i2="X" l="FRE"><s0>Streptococcus salivarius subsp. thermophilus</s0>
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<s5>01</s5>
</fC03>
<fC03 i1="01" i2="X" l="ENG"><s0>Streptococcus salivarius subsp. thermophilus</s0>
<s2>NS</s2>
<s5>01</s5>
</fC03>
<fC03 i1="01" i2="X" l="SPA"><s0>Streptococcus salivarius subsp. thermophilus</s0>
<s2>NS</s2>
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<s5>05</s5>
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<s5>05</s5>
</fC03>
<fC03 i1="02" i2="X" l="SPA"><s0>Transferencia genética</s0>
<s5>05</s5>
</fC03>
<fC03 i1="03" i2="X" l="FRE"><s0>Génome</s0>
<s5>06</s5>
</fC03>
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<s5>06</s5>
</fC03>
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<s2>NS</s2>
</fC07>
<fC07 i1="01" i2="X" l="SPA"><s0>Streptococcaceae</s0>
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</fC07>
<fC07 i1="03" i2="X" l="ENG"><s0>Bacteria</s0>
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<s5>13</s5>
</fC07>
<fC07 i1="04" i2="X" l="SPA"><s0>Bacteria láctica</s0>
<s5>13</s5>
</fC07>
<fN21><s1>122</s1>
</fN21>
<fN44 i1="01"><s1>OTO</s1>
</fN44>
<fN82><s1>OTO</s1>
</fN82>
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<server><NO>PASCAL 11-0189733 INIST</NO>
<ET>In silico prediction of horizontal gene transfer in Streptococcus thermophilus</ET>
<AU>ENG (Catherine); THIBESSARD (Annabelle); DANIELSEN (Morten); RASMUSSEN (Thomas Bovbjerg); MARI (Jean-François); LEBLOND (Pierre)</AU>
<AF>Genetique et Microbiologie, UMR UHP-INRA 1128, IFR 110 EFABA, Universite de Lorraine, Faculté des Sciences et Technologies, BP 239/54506 Vandœuvre-lès-Nancy/France (1 aut., 2 aut., 6 aut.); LORIA, UMR CNRS 7503 et INRIA Lorraine, Campus scientifique, BP 70239/54506 Vandœuvre-lès-Nancy/France (1 aut., 5 aut.); Department of Assays, Chr. Hansen A/S/Hørsholm/Danemark (3 aut., 4 aut.); Department of Physiology, innovation, Chr. Hansen A/S/Hørsholm/Danemark (3 aut., 4 aut.)</AF>
<DT>Publication en série; Niveau analytique</DT>
<SO>Archives of microbiology; ISSN 0302-8933; Coden AMICCW; Allemagne; Da. 2011; Vol. 193; No. 4; Pp. 287-297; Bibl. 3/4 p.</SO>
<LA>Anglais</LA>
<EA>A combination of gene loss and acquisition through horizontal gene transfer (HGT) is thought to drive Streptococcus thermophilus adaptation to its niche, i.e. milk. In this study, we describe an in silico analysis combining a stochastic data mining method, analysis of homologous gene distribution and the identification of features frequently associated with horizontally transferred genes to assess the proportion of the S. thermophilus genome that could originate from HGT. Our mining approach pointed out that about 17.7% of S. thermophilus genes (362 CDSs of 1,915) showed a composition bias; these genes were called 'atypical'. For 22% of them, their functional annotation strongly support their acquisition through HGT and consisted mainly in genes encoding mobile genetic recombinases, exopolysaccharide (EPS) biosynthesis enzymes or resistance mechanisms to bacteriophages. The distribution of the atypical genes in the Firmicutes phylum as well as in S. thermophilus species was sporadic and supported the HGT prediction for more than a half (52%, 189). Among them, 46 were found specific to S. thermophilus. Finally, by combining our method, gene annotation and sequence specific features, new genome islands were suggested in the S. thermophilus genome.</EA>
<CC>002A05B15</CC>
<FD>Streptococcus salivarius subsp. thermophilus; Transfert génétique; Génome</FD>
<FG>Streptococcaceae; Micrococcales; Bactérie; Bactérie lactique</FG>
<ED>Streptococcus salivarius subsp. thermophilus; Genetic transfer; Genome</ED>
<EG>Streptococcaceae; Micrococcales; Bacteria; Lactic acid bacteria</EG>
<SD>Streptococcus salivarius subsp. thermophilus; Transferencia genética; Genoma</SD>
<LO>INIST-856.354000194473910060</LO>
<ID>11-0189733</ID>
</server>
</inist>
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In silico prediction of horizontal gene transfer in Streptococcus thermophilus

In silico prediction of horizontal gene transfer in Streptococcus thermophilus

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