sigma factors
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2022 ◽  
Vol 79 (2) ◽  
Author(s):  
Jan Blumenstein ◽  
Robert Rädisch ◽  
Václav Štěpánek ◽  
Michal Grulich ◽  
Hana Dostálová ◽  
...  

2022 ◽  
Vol 12 ◽  
Author(s):  
Yehong Huang ◽  
Wurihan Wurihan ◽  
Bin Lu ◽  
Yi Zou ◽  
Yuxuan Wang ◽  
...  

Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.


2021 ◽  
Author(s):  
Zheng Jiang ◽  
Zengfang Zhuang ◽  
Kaixia Mi

Understanding how Mycobacterium tuberculosis has evolved into a professional pathogen is helpful in studying its pathogenesis and for designing vaccines. We investigated how the evolutionary adaptation of M. smegmatis mc251 to an important clinical stressor H2O2 allows bacteria undergo coordinated genetic mutations, resulting in increased pathogenicity. Whole-genome sequencing identified a mutation site in the fur gene, which caused increased expression of katG. Using a Wayne dormancy model, mc251 showed a growth advantage over its parental strain mc2155 in recovering from dormancy under anaerobic conditions. Meanwhile, the high level of KatG in mc251 was accompanied by a low level of ATP, which meant that mc251 is at a low respiratory level. Additionally, the redox-related protein Rv1996 showed different phenotypes in different specific redox states in M. smegmatis mc2155, mc251, M. bovis BCG and M. tuberculosis mc27000. In conclusion, our study shows that the same gene presents different phenotypes under different physiological conditions. This may partly explain why M. smegmatis and M. tuberculosis have similar virulence factors and signaling transduction systems such as two-component systems and sigma factors, but due to the different redox states in the corresponding bacteria, M. smegmatis is a nonpathogen, while M. tuberculosis is a pathogen. As mc251 overcomes its shortcomings of rapid removal, it can be potentially developed as a vaccine vector.


2021 ◽  
Author(s):  
Ryo Kariyazono ◽  
Takashi Osanai

Sigma factors are the subunits of bacterial RNA polymerase that govern the expression of genes by recognizing the promoter sequence. Cyanobacteria, which are oxygenic phototrophic eubacteria, have multiple alternative sigma factors that respond to various environmental stresses. The subgroup highly homologous to the primary sigma factor (SigA) is called the group 2 sigma factor. The model cyanobacterium, Synechocystis sp. PCC 6803, has four group 2 sigma factors (SigB-E) conserved within the phylum Cyanobacteria. Among the group 2 sigma factors in Synechocystis sp. PCC 6803, SigE is unique because it alters metabolism by inducing the expression of genes related to sugar catabolism and nitrogen metabolism. However, the features of promoter sequence of the SigE regulon remains elusive. Here, we identified the direct targets of SigA and SigE by chromatin immunoprecipitation sequencing (ChIP-seq). We then showed that the binding sites of SigE and SigA overlapped substantially, but SigE exclusively localized to SigE-dependent promoters. We also found consensus sequences from SigE-dependent promoters and confirmed their importance. ChIP-seq analysis showed both the redundancy and specificity of SigE compared with SigA, integrating information obtained from a previously adopted genetic approach and in vitro assays. The features of SigE elucidated in our study indicate its similarity with group 2 sigma factors of other bacteria, even though they are evolutionally irrelevant. Our approach is also applicable to other organisms and organelles, such as plant plastids, which have multiple group 2 sigma factors.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yu Kanesaki ◽  
Mitsuo Ogura

Abstract Objective We observed that the addition of glucose enhanced the expression of sigX and sigM, encoding extra-cytoplasmic function sigma factors in Bacillus subtilis. Several regulatory factors were identified for this phenomenon, including YqfO, CshA (RNA helicase), and YlxR (nucleoid-associated protein). Subsequently, the relationships among these regulators were analyzed. Among them, YqfO is conserved in many bacterial genomes and may function as a metal ion insertase or metal chaperone, but has been poorly characterized. Thus, to further characterize YqfO, we performed RNA sequencing (RNA-seq) analysis of YqfO in addition to CshA and YlxR. Results We first performed comparative RNA-seq to detect the glucose-responsive genes. Next, to determine the regulatory effects of YqfO in addition to CshA and YlxR, three pairs of comparative RNA-seq analyses were performed (yqfO/wt, cshA/wt, and ylxR/wt). We observed relatively large regulons (approximately 420, 780, and 180 for YqfO, CshA, and YlxR, respectively) and significant overlaps, indicating close relationships among the three regulators. This study is the first to reveal that YqfO functions as a global regulator in B. subtilis.


2021 ◽  
Author(s):  
Daniel A Schwartz ◽  
Brent K Lehmkuhl ◽  
Jay T Lennon

By entering a reversible state of reduced metabolic activity, dormant microorganisms are able to tolerate suboptimal conditions that would otherwise reduce their fitness. Dormancy may also benefit bacteria by serving as a refuge from parasitic infections. Here we focus on dormancy in the Firmicutes, where endospore development is transcriptionally regulated by the expression of sigma factors. A disruption of this process could influence the survivorship and reproduction of phages that infect spore-forming hosts with implications for coevolutionary dynamics. Here, we characterized the distribution and diversity of sigma factors in nearly 3,500 phage genomes. Homologs of sporulation-specific sigma factors were identified in phages that infect spore-forming hosts. Unlike sigma factors required for phage reproduction, the sporulation-like sigma factors were non-essential for lytic infection. However, when expressed in the spore-forming Bacillus subtilis, sigma factors from phages activated the bacterial sporulation gene network and reduced spore yield. Our findings suggest that the acquisition of host-like transcriptional regulators may allow phages to manipulate a complex and ancient trait in one of the most abundant cell types on Earth.


2021 ◽  
Author(s):  
Harsh Goar ◽  
Partha Paul ◽  
Hina Khan ◽  
Dibyendu SARKAR

The main purpose of this study is to understand how mycobacteria can sense numerous stress conditions and mount an appropriate stress response. Recent studies suggest that at low pH M. tuberculosis encounters reductive stress, and in response, modulates redox homeostasis by utilizing the phoPR regulatory system. However, the mechanism of integrated regulation of stress response remains unknown. To probe how PhoP contributes to redox stress response, we find that a PhoP-depleted M. tuberculosis shows a significantly enhanced susceptibility to redox stress relative to the WT bacilli. In keeping with these results, PhoP was shown to contribute to mycothiol redox state. Because SigH, one of the alternative sigma factors of mycobacteria, is known to control expression of redox inducible genes, we probed whether previously-reported PhoP-SigH interaction accounts for mycobacterial redox stress response. We had shown that under acidic conditions PhoP functions in maintaining pH homeostasis via its interaction with SigE. In striking contrast, here we show that under redox stress, direct recruitment of SigH, but not PhoP-SigH interaction, controls expression of mycobacterial thioredoxin genes, a major mycobacterial anti-oxidant system. Together, these unexpected results uncover novel stress-specific enhanced or reduced interaction events of sigma factors and PhoP, as the underlying mechanisms of an adaptive programme, which couples low pH conditions and mycobacterial thiol redox homeostasis.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hamed Tahmasebi ◽  
Sanaz Dehbashi ◽  
Mohammad Reza Arabestani

AbstractIron is a limiting factor in such a condition that usually is sequestered by the host during polymicrobial infections of Pseudomonas aeruginosa and Staphylococcus aureus. This study aimed to investigate the interaction of S. aureus and P. aeruginosa, which alters iron-related sigma factors regulation and antibiotic resistance. The antibiotic resistance of P. aeruginosa and S. aureus was investigated in a L929 cell culture model. The expression level of pvdS, hasI (P. aeruginosa sigma factors), and sigS (S. aureus sigma factor) genes was determined using Quantitative Real-Time PCR. pvdS and hasI were downregulated during co-culture with S. aureus, while the susceptibility to carbapenems increased (p-value < 0.0001). Also, there was a direct significant relationship between resistance to vancomycin with sigS. Regarding the findings of the current study, iron-related sigma factors of P. aeruginosa and S. aureus play a role in induction susceptibility to various antibiotics, including carbapenems and vancomycin.


2021 ◽  
Author(s):  
Juying Long ◽  
Mayuri Sadoine ◽  
Confeng Song ◽  
Yugander Arra ◽  
Wolf B Frommer ◽  
...  

Virulence of Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial leaf blight of rice, depends on induction of host SWEET sucrose efflux transporters. It remained unknown whether secreted sucrose serves bacterial nutrition or host defense. Here we identified the sux sucrose uptake/utilization locus of Xoo and demonstrate that it is necessary and sufficient for sucrose acquisition. Induction of sux genes during infection closely tracked induction of rice SWEET11a. sux mutants were defective in swimming, swarming, extracellular polysaccharide (EPS) production and biofilm formation. EPS synthesis in mutants was restored by the quorum-sensing factor DSF. Notably, transcripts for rate limiting steps in DSF production were unaffected by sucrose, transcripts of the DSF receptor were sucrose-inducible and increased during infection, indicating sensitization to DSF in response to sucrose supply. Sucrose induced the sigma factors transcripts for RpoN1 and RpoN2 that regulate swimming, EPS and virulence. Furthermore, in contrast to Xanthomonas axonopodis pv. manihotis, virulence of Xoo depended critically on sux gene function. Together, pathogen-induced sucrose efflux from host cells likely induces bacterial sigma factors and sensitizes quorum signaling necessary for biofilm formation and colonization of the xylem, serves as energy source for swimming against the xylem stream, and as nutrient for growth.


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