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Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

View Article: PubMed Central - PubMed

ABSTRACT

Background: Commensal bacteria like Neisseria meningitidis sometimes cause serious disease. However, genomic comparison of hyperinvasive and apathogenic lineages did not reveal unambiguous hints towards indispensable virulence factors. Here, in a systems biological approach we compared gene expression of the invasive strain MC58 and the carriage strain α522 under different ex vivo conditions mimicking commensal and virulence compartments to assess the strain-specific impact of gene regulation on meningococcal virulence.

Results: Despite indistinguishable ex vivo phenotypes, both strains differed in the expression of over 500 genes under infection mimicking conditions. These differences comprised in particular metabolic and information processing genes as well as genes known to be involved in host-damage such as the nitrite reductase and numerous LOS biosynthesis genes. A model based analysis of the transcriptomic differences in human blood suggested ensuing metabolic flux differences in energy, glutamine and cysteine metabolic pathways along with differences in the activation of the stringent response in both strains. In support of the computational findings, experimental analyses revealed differences in cysteine and glutamine auxotrophy in both strains as well as a strain and condition dependent essentiality of the (p)ppGpp synthetase gene relA and of a short non-coding AT-rich repeat element in its promoter region.

Conclusions: Our data suggest that meningococcal virulence is linked to transcriptional buffering of cryptic genetic variation in metabolic genes including global stress responses. They further highlight the role of regulatory elements for bacterial virulence and the limitations of model strain approaches when studying such genetically diverse species as N. meningitidis.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-017-3616-7) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Genes significantly differently expressed and/or regulated in cross-condition and/or cross-strain comparisons. a Venn diagram comparing sets of genes in strain MC58 differently expressed between conditions as indicated. The total number of genes compared was 1987. b Venn diagrams comparing sets of genes differently expressed between strains as indicated with each diagram. The total number of genes compared in each panel was 1450. c Heatmap depicting cross-condition and cross-strain gene expression differences and hierarchical clustering of significantly differently expressed genes. Average linkage clustering based on the Spearman rank correlation of all 828 genes significantly differently expressed and/or regulated in at least one cross-condition and/or cross-strain comparison (FDR < 0.05). Grey lines correspond to genes that were absent in the α522 genome sequence and therefore excluded from the cross-strain comparisons
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Fig1: Genes significantly differently expressed and/or regulated in cross-condition and/or cross-strain comparisons. a Venn diagram comparing sets of genes in strain MC58 differently expressed between conditions as indicated. The total number of genes compared was 1987. b Venn diagrams comparing sets of genes differently expressed between strains as indicated with each diagram. The total number of genes compared in each panel was 1450. c Heatmap depicting cross-condition and cross-strain gene expression differences and hierarchical clustering of significantly differently expressed genes. Average linkage clustering based on the Spearman rank correlation of all 828 genes significantly differently expressed and/or regulated in at least one cross-condition and/or cross-strain comparison (FDR < 0.05). Grey lines correspond to genes that were absent in the α522 genome sequence and therefore excluded from the cross-strain comparisons

Mentions: Of the 1987 genes assayed in the cross-condition comparisons in strain MC58, 429 genes were differently expressed between saliva and blood and 151 between blood and CSF, respectively (Fig. 1a, c and Additional file 1: Figure S2A). Gene set enrichment analysis (GSA) showed that genes differently expressed between saliva and blood were significantly enriched for genes coding for nucleotide transport and metabolism (COG F) (Table 2), whereas genes differently expressed between blood and CSF were just slightly enriched for genes involved in posttranslational modification, protein turnover and chaperones (COG O, OR = 2.7, FDR > 0.10) (Fig. 2a). GSA further showed significant differences also in the directionality of gene expression changes (Fig. 2b). The 173 genes that showed higher expression levels in saliva compared to blood were enriched for genes involved in energy metabolism and conversion (COG C), posttranslational modification, protein turnover and chaperones (COG O) and cell envelope and outer membrane biogenesis (COG M). However, genes that were more highly expressed in blood than in saliva and CSF, respectively, were significantly enriched predominantly for genes coding for proteins without any COG functional annotation so far, suggesting that our knowledge about the mechanisms employed by meningococci to survive in human blood are still quite limited.Fig. 1


Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Genes significantly differently expressed and/or regulated in cross-condition and/or cross-strain comparisons. a Venn diagram comparing sets of genes in strain MC58 differently expressed between conditions as indicated. The total number of genes compared was 1987. b Venn diagrams comparing sets of genes differently expressed between strains as indicated with each diagram. The total number of genes compared in each panel was 1450. c Heatmap depicting cross-condition and cross-strain gene expression differences and hierarchical clustering of significantly differently expressed genes. Average linkage clustering based on the Spearman rank correlation of all 828 genes significantly differently expressed and/or regulated in at least one cross-condition and/or cross-strain comparison (FDR < 0.05). Grey lines correspond to genes that were absent in the α522 genome sequence and therefore excluded from the cross-strain comparisons
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5383966&req=5

Fig1: Genes significantly differently expressed and/or regulated in cross-condition and/or cross-strain comparisons. a Venn diagram comparing sets of genes in strain MC58 differently expressed between conditions as indicated. The total number of genes compared was 1987. b Venn diagrams comparing sets of genes differently expressed between strains as indicated with each diagram. The total number of genes compared in each panel was 1450. c Heatmap depicting cross-condition and cross-strain gene expression differences and hierarchical clustering of significantly differently expressed genes. Average linkage clustering based on the Spearman rank correlation of all 828 genes significantly differently expressed and/or regulated in at least one cross-condition and/or cross-strain comparison (FDR < 0.05). Grey lines correspond to genes that were absent in the α522 genome sequence and therefore excluded from the cross-strain comparisons
Mentions: Of the 1987 genes assayed in the cross-condition comparisons in strain MC58, 429 genes were differently expressed between saliva and blood and 151 between blood and CSF, respectively (Fig. 1a, c and Additional file 1: Figure S2A). Gene set enrichment analysis (GSA) showed that genes differently expressed between saliva and blood were significantly enriched for genes coding for nucleotide transport and metabolism (COG F) (Table 2), whereas genes differently expressed between blood and CSF were just slightly enriched for genes involved in posttranslational modification, protein turnover and chaperones (COG O, OR = 2.7, FDR > 0.10) (Fig. 2a). GSA further showed significant differences also in the directionality of gene expression changes (Fig. 2b). The 173 genes that showed higher expression levels in saliva compared to blood were enriched for genes involved in energy metabolism and conversion (COG C), posttranslational modification, protein turnover and chaperones (COG O) and cell envelope and outer membrane biogenesis (COG M). However, genes that were more highly expressed in blood than in saliva and CSF, respectively, were significantly enriched predominantly for genes coding for proteins without any COG functional annotation so far, suggesting that our knowledge about the mechanisms employed by meningococci to survive in human blood are still quite limited.Fig. 1

View Article: PubMed Central - PubMed

ABSTRACT

Background: Commensal bacteria like Neisseria meningitidis sometimes cause serious disease. However, genomic comparison of hyperinvasive and apathogenic lineages did not reveal unambiguous hints towards indispensable virulence factors. Here, in a systems biological approach we compared gene expression of the invasive strain MC58 and the carriage strain &alpha;522 under different ex vivo conditions mimicking commensal and virulence compartments to assess the strain-specific impact of gene regulation on meningococcal virulence.

Results: Despite indistinguishable ex vivo phenotypes, both strains differed in the expression of over 500 genes under infection mimicking conditions. These differences comprised in particular metabolic and information processing genes as well as genes known to be involved in host-damage such as the nitrite reductase and numerous LOS biosynthesis genes. A model based analysis of the transcriptomic differences in human blood suggested ensuing metabolic flux differences in energy, glutamine and cysteine metabolic pathways along with differences in the activation of the stringent response in both strains. In support of the computational findings, experimental analyses revealed differences in cysteine and glutamine auxotrophy in both strains as well as a strain and condition dependent essentiality of the (p)ppGpp synthetase gene relA and of a short non-coding AT-rich repeat element in its promoter region.

Conclusions: Our data suggest that meningococcal virulence is linked to transcriptional buffering of cryptic genetic variation in metabolic genes including global stress responses. They further highlight the role of regulatory elements for bacterial virulence and the limitations of model strain approaches when studying such genetically diverse species as N. meningitidis.

Electronic supplementary material: The online version of this article (doi:10.1186/s12864-017-3616-7) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus