Project description:The extracytoplasmic function sigma factor SigH is responsible for heat and oxidative stress response in a biotechnologically -important bacterium Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, it has not been possible to fully determine the SigH regulon by previous transcriptome analyses. Here, we determined the direct genome-wide targets of SigH were determined by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-sigma factor of SigH. Seventy-five SigH-dependent promoters, including 39 new ones, were identified. Firstly, SigH-dependent heat induction was confirmed for several of the new targets, including two genes (ilvD and lipA) encoding Fe-S cluster containing enzymes. Internal SigH-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, and riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin probably due to the coordinated upregulation of these genes. A SigH-dependent promoter was also found upstream of znuC1 in the znuA1C1B1 operon encoding an ABC-type transporter for Zn uptake. Overexpression of znuC1B1 by deletion of rshA and by an IPTG-inducible promoter and similarly affected expression of Zn-responsive genes, indicating that SigH-dependent upregulation of part of the operon potentiates Zn uptake. probably through Zn overload, indicating new physiological roles of SigH. Furthermore, reporter assays demonstrated that rshA in the sigH-rshA operon was heat-inducible under the control of an internal SigH-dependent promoters, identified upstream of rshA within the sigH-rshA operon, while the sigH promoter was independent of SigH, suggesting negative autoregulation of SigH activity. Finally, a SigH-dependent promoter identified and upstream of sigA encoding the primary sigma factor , wereas highly heat-inducible, but much weaker than the known SigA-dependent one.. The promoter upstream of sigH was independent of SigH but showed weak heat-shock response. The known SigA-dependent sigA promoter was much stronger than the SigH-dependent one. Taken together with the fact that SigH also regulates sigB encoding the primary-like sigma factor, Tthese findings uncovered a complicated regulatory network of the sigma factors.

Project description:We have performred RNA-seq analysis of WT, ∆phoP and ∆sigH Mtb H37Rv under normal and redox (Diamide) stress, to investigate the role of PhoP and SigH in maintaning the redox homoeostasis of bacterium. RNA was extracted from exponentially growing mycobacterial cells in Middlebrook 7H9 media. Briefly, 25 ml of bacterial culture was grown to mid-log phase (OD600= 0.4 to 0.6) and combined with 40 ml of 5 M guanidinium thiocyanate solution containing 1% β-mercaptoethanol and 0.5% Tween 80. Cells were pelleted by centrifugation, and lysed by re-suspending in 1 ml Trizol (Ambion) in the presence of Lysing Matrix B (100 µm silica beads; MP Bio) using a FastPrep-24 bead beater (MP Bio) at a speed setting of 6.0 for 30 seconds. The procedure was repeated for 2-3 cycles with incubation on ice in between pulses. Next, cell lysates were centrifuged at 13000 rpm for 10 minutes; supernatant was collected and processed for RNA isolation using Direct-ZolTM RNA isolation kit (ZYMO) as per manufacturer’s recommendation. Following extraction, RNA was treated with DNAse I (Promega) to degrade contaminating DNA, and integrity was assessed using a Nanodrop (ND-1000, Spectrophotometer). RNA samples were further checked for intactness of 23S and 16S rRNA using formaldehyde-agarose gel electrophoresis, and Qubit fluoremeter (Invitrogen). RNA integrity was checked using Agilent 2200 Tape Station system (Agilent Technologies). Library construction, RNA-sequencing and data analysis have been carried out by Agrigenome Labs Private Limited (Cochin), India. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis. The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Although recent evidence suggests that at low pH M. tuberculosis encounters reductive stress, the mechanism of integrated regulation of stress response remains unknown. Unexpectedly, we find that PhoP contributes to mycothiol level and a PhoP-depleted bacilli shows enhanced susceptibility to redox stress. Because SigH is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. Our results suggest that while PhoP controls pH homeostasis via its interaction with SigE, SigH-dependent PhoP expression, but not PhoP -SigH interaction, and direct recruitment of SigH, but not PhoP controls expression of mycobacterial thioredoxin genes. Together, these results uncover novel stress-specific interaction events of sigma factors and PhoP or lack thereof, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol homeostasis.

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Slr0643, a S2P Homolog, Is Essential for Acid Acclimation in Cyanobacterium Synechocystis sp. PCC 6803

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