1887

Abstract

Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions. To assess diversity and predict function associated with different T6SSs, comparative genomic analysis of 34 genomes was performed. This identified 70 T6SSs, with at least one locus in every strain, except for A1501. By comparing 11 core genes of the T6SS, it was possible to identify five main phylogenetic clusters, with strains typically carrying T6SSs from more than one clade. In addition, most strains encode additional and genes, which encode extracellular structural components of the secretion apparatus. Using a combination of phylogenetic and meta-analysis of transcriptome datasets it was possible to associate specific subsets of VgrG and Hcp proteins with each T6SS clade. Moreover, a closer examination of the genomic context of genes in multiple strains highlights a number of additional genes associated with these regions. It is proposed that these genes may play a role in secretion or alternatively could be new T6S effectors.

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2011-06-01
2019-10-22
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T6SS component frequencies. Prevalence (expressed as percentage) of each gene within every T6SS locus identified [ PDF] (96 kb) Genomic dissimilarities between T6SS loci and associated genomes. This Excel file(42 kb) shows the dinucleotide frequency and the GC percentage of T6SS loci of PAO1, Pf-5, Pf0-1, KT2440, W619, pv. DC3000 and pv. B728a. Rows in bold indicates that the region differs significantly in GC percentage and dinucleotide frequency compared to the overall genome signature. Transcriptome datasets used in this study. This Excel file(40 kb) shows the transcriptomes used in the expression clustering analysis. Numbers represent the percentage of T6S structural genes that are significantly differentially expressed under each condition. Only conditions where at least 50% of the genes were altered (shown in bold) were used for each analysis. Accessory T6SS genes specific to each cluster. Presence of each accessory T6S gene within the different T6S phylogenetic clusters is highlighted with Y. [ Excel file] (36 kb) Expression clusters of T6SS-related genes in [ Excel file, 73 kb]. List of genes co-regulated with each T6S locus (clusters 1.1, 3 and 4A) of PAO1. A total of 36, 90 and 96 genes were co-regulated with the phylogenetic clusters 1.1 (HSI-II), 3 (HSI-I) and 4A (HSI-III), respectively (highlighted with Y). Genes co-regulated with cluster 3 have been compared with orthologous genes of Pf-5 differentially regulated in a mutant (Hassan , 2010). Predicted transmembrane helices, canonical hydrophobic signal peptide and exported protein identified with PhoA-fusions (Lewenza ., 2005) are reported for each gene product. Inactivation of the GacA response regulator in Pf-5 has far-reaching transcriptomic consequences. , 899-915. Genome-wide identification of exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. , 321-329.

PDF

T6SS component frequencies. Prevalence (expressed as percentage) of each gene within every T6SS locus identified [ PDF] (96 kb) Genomic dissimilarities between T6SS loci and associated genomes. This Excel file(42 kb) shows the dinucleotide frequency and the GC percentage of T6SS loci of PAO1, Pf-5, Pf0-1, KT2440, W619, pv. DC3000 and pv. B728a. Rows in bold indicates that the region differs significantly in GC percentage and dinucleotide frequency compared to the overall genome signature. Transcriptome datasets used in this study. This Excel file(40 kb) shows the transcriptomes used in the expression clustering analysis. Numbers represent the percentage of T6S structural genes that are significantly differentially expressed under each condition. Only conditions where at least 50% of the genes were altered (shown in bold) were used for each analysis. Accessory T6SS genes specific to each cluster. Presence of each accessory T6S gene within the different T6S phylogenetic clusters is highlighted with Y. [ Excel file] (36 kb) Expression clusters of T6SS-related genes in [ Excel file, 73 kb]. List of genes co-regulated with each T6S locus (clusters 1.1, 3 and 4A) of PAO1. A total of 36, 90 and 96 genes were co-regulated with the phylogenetic clusters 1.1 (HSI-II), 3 (HSI-I) and 4A (HSI-III), respectively (highlighted with Y). Genes co-regulated with cluster 3 have been compared with orthologous genes of Pf-5 differentially regulated in a mutant (Hassan , 2010). Predicted transmembrane helices, canonical hydrophobic signal peptide and exported protein identified with PhoA-fusions (Lewenza ., 2005) are reported for each gene product. Inactivation of the GacA response regulator in Pf-5 has far-reaching transcriptomic consequences. , 899-915. Genome-wide identification of exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. , 321-329.

EXCEL

T6SS component frequencies. Prevalence (expressed as percentage) of each gene within every T6SS locus identified [ PDF] (96 kb) Genomic dissimilarities between T6SS loci and associated genomes. This Excel file(42 kb) shows the dinucleotide frequency and the GC percentage of T6SS loci of PAO1, Pf-5, Pf0-1, KT2440, W619, pv. DC3000 and pv. B728a. Rows in bold indicates that the region differs significantly in GC percentage and dinucleotide frequency compared to the overall genome signature. Transcriptome datasets used in this study. This Excel file(40 kb) shows the transcriptomes used in the expression clustering analysis. Numbers represent the percentage of T6S structural genes that are significantly differentially expressed under each condition. Only conditions where at least 50% of the genes were altered (shown in bold) were used for each analysis. Accessory T6SS genes specific to each cluster. Presence of each accessory T6S gene within the different T6S phylogenetic clusters is highlighted with Y. [ Excel file] (36 kb) Expression clusters of T6SS-related genes in [ Excel file, 73 kb]. List of genes co-regulated with each T6S locus (clusters 1.1, 3 and 4A) of PAO1. A total of 36, 90 and 96 genes were co-regulated with the phylogenetic clusters 1.1 (HSI-II), 3 (HSI-I) and 4A (HSI-III), respectively (highlighted with Y). Genes co-regulated with cluster 3 have been compared with orthologous genes of Pf-5 differentially regulated in a mutant (Hassan , 2010). Predicted transmembrane helices, canonical hydrophobic signal peptide and exported protein identified with PhoA-fusions (Lewenza ., 2005) are reported for each gene product. Inactivation of the GacA response regulator in Pf-5 has far-reaching transcriptomic consequences. , 899-915. Genome-wide identification of exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. , 321-329.

EXCEL

T6SS component frequencies. Prevalence (expressed as percentage) of each gene within every T6SS locus identified [ PDF] (96 kb) Genomic dissimilarities between T6SS loci and associated genomes. This Excel file(42 kb) shows the dinucleotide frequency and the GC percentage of T6SS loci of PAO1, Pf-5, Pf0-1, KT2440, W619, pv. DC3000 and pv. B728a. Rows in bold indicates that the region differs significantly in GC percentage and dinucleotide frequency compared to the overall genome signature. Transcriptome datasets used in this study. This Excel file(40 kb) shows the transcriptomes used in the expression clustering analysis. Numbers represent the percentage of T6S structural genes that are significantly differentially expressed under each condition. Only conditions where at least 50% of the genes were altered (shown in bold) were used for each analysis. Accessory T6SS genes specific to each cluster. Presence of each accessory T6S gene within the different T6S phylogenetic clusters is highlighted with Y. [ Excel file] (36 kb) Expression clusters of T6SS-related genes in [ Excel file, 73 kb]. List of genes co-regulated with each T6S locus (clusters 1.1, 3 and 4A) of PAO1. A total of 36, 90 and 96 genes were co-regulated with the phylogenetic clusters 1.1 (HSI-II), 3 (HSI-I) and 4A (HSI-III), respectively (highlighted with Y). Genes co-regulated with cluster 3 have been compared with orthologous genes of Pf-5 differentially regulated in a mutant (Hassan , 2010). Predicted transmembrane helices, canonical hydrophobic signal peptide and exported protein identified with PhoA-fusions (Lewenza ., 2005) are reported for each gene product. Inactivation of the GacA response regulator in Pf-5 has far-reaching transcriptomic consequences. , 899-915. Genome-wide identification of exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. , 321-329.

EXCEL

T6SS component frequencies. Prevalence (expressed as percentage) of each gene within every T6SS locus identified [ PDF] (96 kb) Genomic dissimilarities between T6SS loci and associated genomes. This Excel file(42 kb) shows the dinucleotide frequency and the GC percentage of T6SS loci of PAO1, Pf-5, Pf0-1, KT2440, W619, pv. DC3000 and pv. B728a. Rows in bold indicates that the region differs significantly in GC percentage and dinucleotide frequency compared to the overall genome signature. Transcriptome datasets used in this study. This Excel file(40 kb) shows the transcriptomes used in the expression clustering analysis. Numbers represent the percentage of T6S structural genes that are significantly differentially expressed under each condition. Only conditions where at least 50% of the genes were altered (shown in bold) were used for each analysis. Accessory T6SS genes specific to each cluster. Presence of each accessory T6S gene within the different T6S phylogenetic clusters is highlighted with Y. [ Excel file] (36 kb) Expression clusters of T6SS-related genes in [ Excel file, 73 kb]. List of genes co-regulated with each T6S locus (clusters 1.1, 3 and 4A) of PAO1. A total of 36, 90 and 96 genes were co-regulated with the phylogenetic clusters 1.1 (HSI-II), 3 (HSI-I) and 4A (HSI-III), respectively (highlighted with Y). Genes co-regulated with cluster 3 have been compared with orthologous genes of Pf-5 differentially regulated in a mutant (Hassan , 2010). Predicted transmembrane helices, canonical hydrophobic signal peptide and exported protein identified with PhoA-fusions (Lewenza ., 2005) are reported for each gene product. Inactivation of the GacA response regulator in Pf-5 has far-reaching transcriptomic consequences. , 899-915. Genome-wide identification of exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. , 321-329.

EXCEL
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