Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

Nikolaos Strepis, Henry D. Naranjo, Jan Meier-Kolthoff, Markus Göker, Nicole Shapiro, Nikos Kyrpides, Hans Peter Klenk, Peter J. Schaap, Alfons J.M. Stams, Diana Z. Sousa*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

Original languageEnglish
Article number24
JournalBMC Genomics
Volume21
Issue number1
DOIs
Publication statusPublished - 8 Jan 2020

Fingerprint

Glycerol
Genome
Osmoregulation
Salinity
Genes
Operon
Microbial Drug Resistance
Shock
Carbon
Genotype
Carbohydrates
Phenotype
Temperature
Enzymes
1,3-propanediol
alginic acid
araban

Keywords

  • 1,3-propanediol
  • Comparative genomics
  • Halophilic
  • Protein domains
  • Psychrophilic

Cite this

Strepis, Nikolaos ; Naranjo, Henry D. ; Meier-Kolthoff, Jan ; Göker, Markus ; Shapiro, Nicole ; Kyrpides, Nikos ; Klenk, Hans Peter ; Schaap, Peter J. ; Stams, Alfons J.M. ; Sousa, Diana Z. / Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. In: BMC Genomics. 2020 ; Vol. 21, No. 1.
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title = "Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species",
abstract = "Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.",
keywords = "1,3-propanediol, Comparative genomics, Halophilic, Protein domains, Psychrophilic",
author = "Nikolaos Strepis and Naranjo, {Henry D.} and Jan Meier-Kolthoff and Markus G{\"o}ker and Nicole Shapiro and Nikos Kyrpides and Klenk, {Hans Peter} and Schaap, {Peter J.} and Stams, {Alfons J.M.} and Sousa, {Diana Z.}",
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Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. / Strepis, Nikolaos; Naranjo, Henry D.; Meier-Kolthoff, Jan; Göker, Markus; Shapiro, Nicole; Kyrpides, Nikos; Klenk, Hans Peter; Schaap, Peter J.; Stams, Alfons J.M.; Sousa, Diana Z.

In: BMC Genomics, Vol. 21, No. 1, 24, 08.01.2020.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

AU - Strepis, Nikolaos

AU - Naranjo, Henry D.

AU - Meier-Kolthoff, Jan

AU - Göker, Markus

AU - Shapiro, Nicole

AU - Kyrpides, Nikos

AU - Klenk, Hans Peter

AU - Schaap, Peter J.

AU - Stams, Alfons J.M.

AU - Sousa, Diana Z.

PY - 2020/1/8

Y1 - 2020/1/8

N2 - Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

AB - Background: The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. Results: In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. Conclusions: Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

KW - 1,3-propanediol

KW - Comparative genomics

KW - Halophilic

KW - Protein domains

KW - Psychrophilic

U2 - 10.1186/s12864-019-6410-x

DO - 10.1186/s12864-019-6410-x

M3 - Article

VL - 21

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 24

ER -

Strepis N, Naranjo HD, Meier-Kolthoff J, Göker M, Shapiro N, Kyrpides N et al. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics. 2020 Jan 8;21(1). 24. https://doi.org/10.1186/s12864-019-6410-x