Limits...
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

Gene set enrichment analysis of differently expressed genes. a Non-directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, respectively, indicating significantly overrepresented functional categories among the significantly differently expressed genes. b Directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, indicating significant gene expression asymmetries. In both panels, the heat map depicts significantly enriched COG functional categories in red coloring. The kind of comparison (cross-condition for strain MC58 and cross-strain for each condition) is indicated for each column of the heat maps, and the corresponding FDRs are color coded and given in the respective inserts. The associated tree is based on average linkage clustering of the functional categories using the Spearman rank correlation coefficient
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Gene set enrichment analysis of differently expressed genes. a Non-directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, respectively, indicating significantly overrepresented functional categories among the significantly differently expressed genes. b Directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, indicating significant gene expression asymmetries. In both panels, the heat map depicts significantly enriched COG functional categories in red coloring. The kind of comparison (cross-condition for strain MC58 and cross-strain for each condition) is indicated for each column of the heat maps, and the corresponding FDRs are color coded and given in the respective inserts. The associated tree is based on average linkage clustering of the functional categories using the Spearman rank correlation coefficient

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
Gene set enrichment analysis of differently expressed genes. a Non-directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, respectively, indicating significantly overrepresented functional categories among the significantly differently expressed genes. b Directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, indicating significant gene expression asymmetries. In both panels, the heat map depicts significantly enriched COG functional categories in red coloring. The kind of comparison (cross-condition for strain MC58 and cross-strain for each condition) is indicated for each column of the heat maps, and the corresponding FDRs are color coded and given in the respective inserts. The associated tree is based on average linkage clustering of the functional categories using the Spearman rank correlation coefficient
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Gene set enrichment analysis of differently expressed genes. a Non-directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, respectively, indicating significantly overrepresented functional categories among the significantly differently expressed genes. b Directional comparison of significantly differently expressed gene sets according to the COG functional classification scheme for cross-condition and cross-strain comparisons, indicating significant gene expression asymmetries. In both panels, the heat map depicts significantly enriched COG functional categories in red coloring. The kind of comparison (cross-condition for strain MC58 and cross-strain for each condition) is indicated for each column of the heat maps, and the corresponding FDRs are color coded and given in the respective inserts. The associated tree is based on average linkage clustering of the functional categories using the Spearman rank correlation coefficient
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 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