The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase

BACKGROUND: Corynebacterium glutamicum is a gram-positive soil bacterium widely used for the industrial production of amino acids. There is great interest in the examination of the molecular mechanism of transcription control. One of these control mechanisms are sigma factors. C. glutamicum ATCC 13032 has seven putative sigma factor-encoding genes, including sigA and sigB. The sigA gene encodes the essential primary sigma factor of C. glutamicum and is responsible for promoter recognition of house-keeping genes. The sigB gene codes for the non-essential sigma factor SigB that has a proposed role in stress reponse. RESULTS: The sigB gene expression was highest at transition between exponential growth and stationary phase, when the amount of sigA mRNA was already decreasing. Genome-wide transcription profiles of the wild-type and the sigB mutant were recorded by comparative DNA microarray hybridizations. The data indicated that the mRNA levels of 111 genes are significantly changed in the sigB-proficient strain during the transition phase, whereas the expression profile of the sigB-deficient strain showed only minor changes (26 genes). The genes that are higher expressed during transition phase only in the sigB-proficient strain mainly belong to the functional categories amino acid metabolism, carbon metabolism, stress defense, membrane processes, and phosphorus metabolism. The transcription start points of six of these genes were determined and the deduced promoter sequences turned out to be indistinguishable from that of the consensus promoter recognized by SigA. Real-time reverse transcription PCR assays revealed that the expression profiles of these genes during growth were similar to that of the sigB gene itself. In the sigB mutant, however, the transcription profiles resembled that of the sigA gene encoding the house-keeping sigma factor. CONCLUSION: During transition phase, the sigB gene showed an enhanced expression, while simultaneously the sigA mRNA decreased in abundance. This might cause a replacement of SigA by SigB at the RNA polymerase core enzyme and in turn results in increased expression of genes relevant for the transition and the stationary phase, either to cope with nutrient limitation or with the accompanying oxidative stress. The increased expression of genes encoding anti-oxidative or protection functions also prepares the cell for upcoming limitations and environmental stresses

The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae

Gross R, Guzman CA, Sebaihia M, et al. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics. 2008;9(1): 449.Background: Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. Results: In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. Conclusion: The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches

Charakterisierung des Sigmafaktors SigB aus Corynebacterium glutamicum und seiner Rolle bei der Genexpression in der Transitionsphase des Wachstums

Larisch C. Charakterisierung des Sigmafaktors SigB aus Corynebacterium glutamicum und seiner Rolle bei der Genexpression in der Transitionsphase des Wachstums. Bielefeld (Germany): Bielefeld University; 2006.Im Genom von Corynebacterium glutamicum konnten sieben Gene identifiziert werden, die für Sigmafaktoren kodieren. Diese ließen sich in essentielle (SigA), nicht-essentielle (SigB) und alternative Sigmafaktoren (SigC, SigD, SigE, SigH, SigM) unterteilen. Im Rahmen dieser Arbeit sollte der nicht-essentielle Sigmafaktor SigB im Hinblick auf seine Rolle in der globalen Genexpression sowohl bei Antwort auf Stressfaktoren als auch beim Übergang vom exponentiellen Wachstum zur stationären Phase untersucht werden. Die zunächst durchgeführte Charakterisierung des sigB-Gens mittels Expressionsanalysen zeigte, dass die höchste Expression während des Übergangs von der exponentiellen zur stationären Phase erfolgt. Ebenso konnte gezeigt werden, dass die sigB-Expression durch Kälte- und Ethanolstress deutlich erhöht wird. Durch eine gezielte Gendeletion im Restriktions- und Modifikations-defekten Stamm RES167 konnte eine sigB-Mutante (C. glutamicum CL1) konstruiert werden, mit deren Hilfe durch Wachstumstests und Lebendtiterbestimmungen gezeigt werden konnte, dass SigB ebenfalls an der Bewältigung von Ethanol- und Kältestress beteiligt ist. Des weiteren konnte durch ein IPTG-induzierbares sigB-Überexpressionsplasmid ein Einfluss von sigB auf das Wachstum gezeigt werden. Nach der Etablierung einer Glukose-limitierten batch-Fermentation wurde in diesem kontrollierten und Stress-armen System das SigB-Regulon im Wildtyp und in der sigB-Deletionsmutante mittels DNA-Microarray-Hybridisierungen bestimmt. Dabei waren 153 Gene auffällig, deren verstärkte Expression beim Übergang von der exponentiellen zur stationären Phase von der Anwesenheit von sigB abhing. Die Gene dieses Regulationsnetzwerks kodieren für eine Vielzahl von Funktionen im Metabolismus, bei Membranprozessen und der Genregulation. Die verstärkte Expression dieser Gene bereitet die Zelle vermutlich auf die veränderten Verhältnisse vor, die während der Stationärphase in der Zelle auftreten können. Durch bioinformatische Analysen konnte diesem Regulationsnetzwerk eine Promotor-Konsensussequenz zugeordnet werden, an die die RNA-Polymerase durch SigB binden kann. Für die Gene cg0096, cg1083, cg1417, cg2418, cg3141 und cg3330 konnte diese Promotorsequenz mittels RACE-PCR verifiziert werden. Es lassen sich allerdings keine signifikanten Unterschiede zwischen einer SigB-Promotor-Konsensussequenz und der von SigA-Promotoren feststellen, so dass der nicht-essentielle Sigmafaktor SigB vermutlich eine Unterklasse der SigA-Promotoren erkennt. Es konnte gezeigt werden, dass das Expressionsprofil der kartierten sechs Gene im Stamm RES167 mit dem des sigB-Gens übereinstimmt, wohingegen das Profil dieser Gene in Abwesenheit des sigB-Gens im Stamm CL1 über das Wachstum dem Expressionsprofil des Gens sigA entspricht

The Extracytoplasmic Function-Type Sigma Factor SigM of Corynebacterium glutamicum ATCC 13032 Is Involved in Transcription of Disulfide Stress-Related Genes▿

The gene for the extracytoplasmic function (ECF) sigma factor SigM was deleted from the chromosome of the gram-positive soil bacterium Corynebacterium glutamicum to elucidate the role of the SigM protein in the regulation of gene expression. Comparative DNA microarray hybridizations of the C. glutamicum wild type and sigM-deficient mutant C. glutamicum DN1 revealed 23 genes with enhanced expression in the sigM-proficient strain, encoding functions in the assembly of iron-sulfur clusters (suf operon), thioredoxin reductase (trxB), thioredoxins (trxC, trxB1), chaperones (groES, groEL, clpB), and proteins involved in the heat shock response (hspR, dnaJ, grpE). Deletion of the sigM gene rendered the C. glutamicum cells more sensitive to heat, cold, and the presence of the thiol oxidant diamide. Transcription of the sigM gene increased under different stress conditions, including heat shock, cold shock, and disulfide stress caused by diamide treatment, suggesting a regulatory role for SigM under thiol-oxidative stress conditions. Stress-responsive promoters were determined upstream of the suf operon and of the trxB, trxC, and trxB1 genes. The deduced SigM consensus promoter is characterized by the −35 hexamer gGGAAT and the −10 hexamer YGTTGR. Transcription of the sigM gene is apparently controlled by the ECF sigma factor SigH, since a sigH mutant was unable to enhance the expression of sigM and the SigM regulon under thiol-oxidative stress conditions. A typical SigH-responsive promoter was mapped upstream of the sigM gene. The ECF sigma factor SigM is apparently part of a regulatory cascade, and its transcription is controlled by SigH under conditions of thiol-oxidative stress