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Guzina, Jelena, i Marko Djordjevic. "Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs". Journal of Bacteriology 198, nr 14 (2.05.2016): 1927–38. http://dx.doi.org/10.1128/jb.00244-16.
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ABSTRACTExtracytoplasmicfunction (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both −35 and −10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended −10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ2, which is responsible for the interaction with the identified extension of the −10 element. Interestingly, a similar protein motif is found C-terminal of domain σ2in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the −10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable −35 element and σ4domain, which we identify in a homologous phage, 7-11, indicating that the extended −10 element can compensate for the lack of −35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested.IMPORTANCEECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors.
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Fang, Chengli, Lingting Li, Liqiang Shen, Jing Shi, Sheng Wang, Yu Feng i Yu Zhang. "Structures and mechanism of transcription initiation by bacterial ECF factors". Nucleic Acids Research 47, nr 13 (27.05.2019): 7094–104. http://dx.doi.org/10.1093/nar/gkz470.
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Abstract Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) σ factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 Å of Escherichia coli transcription initiation complex comprising σE—the most-studied bacterial ECF σ factor (Ec σE-RPo), and a crystal structure at 3.1 Å of Mycobacterium tuberculosis transcription initiation complex with a chimeric σH/E (Mtb σH/E-RPo). The structure of Ec σE-RPo reveals key interactions essential for assembly of E. coli σE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli σE. Moreover, both structures show that the non-conserved linkers (σ2/σ4 linker) of the two ECF σ factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF σ factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such σ2/σ4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF σ factors-mediated transcription initiation.
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Thakur, Krishan Gopal, Anagha Madhusudan Joshi i B. Gopal. "Structural and Biophysical Studies on Two Promoter Recognition Domains of the Extra-cytoplasmic Function σ Factor σC from Mycobacterium tuberculosis". Journal of Biological Chemistry 282, nr 7 (4.12.2006): 4711–18. http://dx.doi.org/10.1074/jbc.m606283200.
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σ factors are transcriptional regulatory proteins that bind to the RNA polymerase and dictate gene expression. The extracytoplasmic function (ECF) σ factors govern the environment dependent regulation of transcription. ECF σ factors have two domains σ2 and σ4 that recognize the -10 and -35 promoter elements. However, unlike the primary σ factor σA, the ECF σ factors lack σ3, a region that helps in the recognition of the extended -10 element and σ1.1, a domain involved in the autoinhibition of σA in the absence of core RNA polymerase. Mycobacterium tuberculosis σC is an ECF σ factor that is essential for the pathogenesis and virulence of M. tuberculosis in the mouse and guinea pig models of infection. However, unlike other ECF σ factors, σC does not appear to have a regulatory anti-σ factor located in the same operon. We also note that M. tuberculosis σC differs from the canonical ECF σ factors as it has an N-terminal domain comprising of 126 amino acids that precedes the σC2 and σC4 domains. In an effort to understand the regulatory mechanism of this protein, the crystal structures of the σC2 and σC4 domains of σC were determined. These promoter recognition domains are structurally similar to the corresponding domains of σA despite the low sequence similarity. Fluorescence experiments using the intrinsic tryptophan residues of σC2 as well as surface plasmon resonance measurements reveal that the σC2 and σC4 domains interact with each other. Mutational analysis suggests that the Pribnow box-binding region of σC2 is involved in this interdomain interaction. Interaction between the promoter recognition domains in M. tuberculosis σC are thus likely to regulate the activity of this protein even in the absence of an anti-σ factor.
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Ho, Theresa D., i Craig D. Ellermeier. "PrsW Is Required for Colonization, Resistance to Antimicrobial Peptides, and Expression of Extracytoplasmic Function σ Factors in Clostridium difficile". Infection and Immunity 79, nr 8 (31.05.2011): 3229–38. http://dx.doi.org/10.1128/iai.00019-11.
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ABSTRACTClostridium difficileis an anaerobic, Gram-positive, spore-forming, opportunistic pathogen that is the most common cause of hospital-acquired infectious diarrhea. In numerous pathogens, stress response mechanisms are required for survival within the host. Extracytoplasmic function (ECF) σ factors are a major family of signal transduction systems, which sense and respond to extracellular stresses. We have identified threeC. difficileECF σ factors. These ECF σ factors, CsfT, CsfU, and CsfV, induce their own expressions and are negatively regulated by their cognate anti-σ factors, RsiT, RsiU, and RsiV, respectively. The levels of expression of these ECF σ factors increase following exposure to the antimicrobial peptides bacitracin and/or lysozyme. The expressions of many ECF σ factors are controlled by site 1 and site 2 proteases, which cleave anti-σ factors. Using a retargeted group II intron, we generated aC. difficilemutation inprsW, a putative site 1 protease. TheC. difficile prsWmutant exhibited decreased levels of expression of CsfT and CsfU but not of CsfV. When expressed in a heterologous host,C. difficilePrsW was able to induce the degradation of RsiT but not of RsiU. When theprsWmutant was tested in competition assays against its isogenic parent in the hamster model ofC. difficileinfection, we found that theprsWmutant was 30-fold less virulent than the wild type. TheprsWmutant was also significantly more sensitive to bacitracin and lysozyme than the wild type inin vitrocompetition assays. Taken together, these data suggest that PrsW likely regulates the activation of the ECF σ factor CsfT inC. difficileand controls the resistance ofC. difficileto antimicrobial peptides that are important for survival in the host.
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Luo, Yun, Kei Asai, Yoshito Sadaie i John D. Helmann. "Transcriptomic and Phenotypic Characterization of a Bacillus subtilis Strain without Extracytoplasmic Function σ Factors". Journal of Bacteriology 192, nr 21 (3.09.2010): 5736–45. http://dx.doi.org/10.1128/jb.00826-10.
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ABSTRACT Bacillus subtilis encodes seven extracytoplasmic function (ECF) σ factors. Three (σM, σW, and σX) mediate responses to cell envelope-active antibiotics. The functions of σV, σY, σZ, and σYlaC remain largely unknown, and strong inducers of these σ factors and their regulons have yet to be defined. Here, we define transcriptomic and phenotypic differences under nonstress conditions between a strain carrying deletions in all seven ECF σ factor genes (the Δ7ECF mutant), a ΔMWX triple mutant, and the parental 168 strain. Our results identify >80 genes as at least partially dependent on ECF σ factors, and as expected, most of these are dependent on σM, σW, or σX, which are active at a significant basal level during growth. Several genes, including the eps operon encoding enzymes for exopolysaccharide (EPS) production, were decreased in expression in the Δ7ECF mutant but affected less in the ΔMWX mutant. Consistent with this observation, the Δ7ECF mutant (but not the ΔMWX mutant) showed reduced biofilm formation. Extending previous observations, we also note that the ΔMWX mutant is sensitive to a variety of antibiotics and the Δ7ECF mutant is either as sensitive as, or slightly more sensitive than, the ΔMWX strain to these stressors. These findings emphasize the overlapping nature of the seven ECF σ factor regulons in B. subtilis, confirm that three of these (σM, σW, and σX) play the dominant role in conferring intrinsic resistance to antibiotics, and provide initial insights into the roles of the remaining ECF σ factors.
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Ho, Theresa D., Jessica L. Hastie, Peter J. Intile i Craig D. Ellermeier. "The Bacillus subtilis Extracytoplasmic Function σ Factor σVIs Induced by Lysozyme and Provides Resistance to Lysozyme". Journal of Bacteriology 193, nr 22 (19.08.2011): 6215–22. http://dx.doi.org/10.1128/jb.05467-11.
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Bacteria encounter numerous environmental stresses which can delay or inhibit their growth. Many bacteria utilize alternative σ factors to regulate subsets of genes required to overcome different extracellular assaults. The largest group of these alternative σ factors are the extracytoplasmic function (ECF) σ factors. In this paper, we demonstrate that the expression of the ECF σ factor σVinBacillus subtilisis induced specifically by lysozyme but not other cell wall-damaging agents. A mutation insigVresults in increased sensitivity to lysozyme killing, suggesting that σVis required for lysozyme resistance. Using reverse transcription (RT)-PCR, we show that the previously uncharacterized geneyrhL(here referred to asoatAforO-acetyltransferase) is in a four-gene operon which includessigVandrsiV. In quantitative RT-PCR experiments, the expression ofoatAis induced by lysozyme stress. Lysozyme induction ofoatAis dependent upon σV. Overexpression ofoatAin asigVmutant restores lysozyme resistance to wild-type levels. This suggests that OatA is required for σV-dependent resistance to lysozyme. We also tested the ability of lysozyme to induce the other ECF σ factors and found that only the expression ofsigVis lysozyme inducible. However, we found that the other ECF σ factors contributed to lysozyme resistance. We found thatsigXandsigMmutations alone had very little effect on lysozyme resistance but when combined with asigVmutation resulted in significantly greater lysozyme sensitivity than thesigVmutation alone. This suggests thatsigV,sigX, andsigMmay act synergistically to control lysozyme resistance. In addition, we show that two ECF σ factor-regulated genes,dltAandpbpX, are required for lysozyme resistance. Thus, we have identified three independent mechanisms whichB. subtilisutilizes to avoid killing by lysozyme.
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Luo, Yun, i John D. Helmann. "Extracytoplasmic Function σ Factors with Overlapping Promoter Specificity Regulate Sublancin Production in Bacillus subtilis". Journal of Bacteriology 191, nr 15 (22.05.2009): 4951–58. http://dx.doi.org/10.1128/jb.00549-09.
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ABSTRACT Bacillus subtilis harbors seven extracytoplasmic function (ECF) σ factors. At least three ECF σ factors (σM, σW, and σX) are induced by, and provide resistance to, antibiotics and other agents eliciting cell envelope stress. Here, we report that ECF σ factors also contribute to antibiotic production. B. subtilis 168 strains that are lysogenic for the SPβ bacteriophage produce sublancin, which inhibits the growth of other, nonlysogenic strains. Genetic studies demonstrate that synthesis of sublancin is largely dependent on σX, with a smaller contribution from σM. A sigM sigX double mutant is unable to produce sublancin. This defect is primarily due to the fact that the sublancin biosynthesis is positively activated by the transition state regulator and AbrB paralog Abh, which counteracts transcriptional repression of the sublancin biosynthesis operon by AbrB. Ectopic expression of abh bypasses the requirement for σM or σX in sublancin synthesis, as does an abrB mutation. In addition to their major role in regulating sublancin expression by activating abh transcription, σX and σM also have a second role as positive regulators of sublancin expression that is independent of AbrB and Abh. Since sublancin resistance in nonlysogens is largely dependent on σW, ECF σ factors control both sublancin production and resistance.
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Wecke, Tina, Birgit Veith, Armin Ehrenreich i Thorsten Mascher. "Cell Envelope Stress Response in Bacillus licheniformis: Integrating Comparative Genomics, Transcriptional Profiling, and Regulon Mining To Decipher a Complex Regulatory Network". Journal of Bacteriology 188, nr 21 (25.08.2006): 7500–7511. http://dx.doi.org/10.1128/jb.01110-06.
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ABSTRACT The envelope is an essential structure of the bacterial cell, and maintaining its integrity is a prerequisite for survival. To ensure proper function, transmembrane signal-transducing systems, such as two-component systems (TCS) and extracytoplasmic function (ECF) σ factors, closely monitor its condition and respond to harmful perturbations. Both systems consist of a transmembrane sensor protein (histidine kinase or anti-σ factor, respectively) and a corresponding cytoplasmic transcriptional regulator (response regulator or σ factor, respectively) that mediates the cellular response through differential gene expression. The regulatory network of the cell envelope stress response is well studied in the gram-positive model organism Bacillus subtilis. It consists of at least two ECF σ factors and four two-component systems. In this study, we describe the corresponding network in a close relative, Bacillus licheniformis. Based on sequence homology, domain architecture, and genomic context, we identified five TCS and eight ECF σ factors as potential candidate regulatory systems mediating cell envelope stress response in this organism. We characterized the corresponding regulatory network by comparative transcriptomics and regulon mining as an initial screening tool. Subsequent in-depth transcriptional profiling was applied to define the inducer specificity of each identified cell envelope stress sensor. A total of three TCS and seven ECF σ factors were shown to be induced by cell envelope stress in B. licheniformis. We noted a number of significant differences, indicative of a regulatory divergence between the two Bacillus species, in addition to the expected overlap in the respective responses.
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Mascher, Thorsten, Anna-Barbara Hachmann i John D. Helmann. "Regulatory Overlap and Functional Redundancy among Bacillus subtilis Extracytoplasmic Function σ Factors". Journal of Bacteriology 189, nr 19 (3.08.2007): 6919–27. http://dx.doi.org/10.1128/jb.00904-07.
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ABSTRACT Bacillus subtilis encodes seven extracytoplasmic function (ECF) σ factors that regulate partially overlapping regulons related to cell envelope homeostasis and antibiotic resistance. Here, we investigated their physiological role by constructing a mutant set of single, double, triple, and quadruple ECF σ factor deletions in the undomesticated B. subtilis strain NCIB3610. This mutant set was subsequently screened for defects in motility, multicellular differentiation, and sensitivity to more than 200 chemicals by using Phenotype MicroArrays. A quadruple mutant strain, harboring deletions of the sigV, sigY, sigZ, and ylaC gene, behaved indistinguishably from the wild-type strain, indicative of either regulatory redundancy or very specific functions of these four ECF σ factors. In contrast, a triple mutant, inactivated for the sigM, sigW, and sigX genes (but none of the corresponding double mutants), showed a biphasic growth behavior and a complete loss of multicellular differentiation, as judged by both colony formation and the inability to form a pellicle. This triple mutant also displayed a greatly increased sensitivity to detergents and several cell wall antibiotics including β-lactams, polymyxin B, and d-cycloserine. In several cases, these antibiotic-sensitive phenotypes are significantly enhanced in the triple mutant strain relative to strains lacking only one or two σ factors.
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de Dios, Rubén, Eduardo Santero i Francisca Reyes-Ramírez. "Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses". International Journal of Molecular Sciences 22, nr 8 (9.04.2021): 3900. http://dx.doi.org/10.3390/ijms22083900.
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The ability of bacterial core RNA polymerase (RNAP) to interact with different σ factors, thereby forming a variety of holoenzymes with different specificities, represents a powerful tool to coordinately reprogram gene expression. Extracytoplasmic function σ factors (ECFs), which are the largest and most diverse family of alternative σ factors, frequently participate in stress responses. The classification of ECFs in 157 different groups according to their phylogenetic relationships and genomic context has revealed their diversity. Here, we have clustered 55 ECF groups with experimentally studied representatives into two broad classes of stress responses. The remaining 102 groups still lack any mechanistic or functional insight, representing a myriad of systems yet to explore. In this work, we review the main features of ECFs and discuss the different mechanisms controlling their production and activity, and how they lead to a functional stress response. Finally, we focus in more detail on two well-characterized ECFs, for which the mechanisms to detect and respond to stress are complex and completely different: Escherichia coli RpoE, which is the best characterized ECF and whose structural and functional studies have provided key insights into the transcription initiation by ECF-RNAP holoenzymes, and the ECF15-type EcfG, the master regulator of the general stress response in Alphaproteobacteria.
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Pinto, Daniela, Qiang Liu i Thorsten Mascher. "ECF σ factors with regulatory extensions: the one‐component systems of the σ universe". Molecular Microbiology 112, nr 2 (26.06.2019): 399–409. http://dx.doi.org/10.1111/mmi.14323.
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Todor, Horia, Hendrik Osadnik, Elizabeth A. Campbell, Kevin S. Myers, Hao Li, Timothy J. Donohue i Carol A. Gross. "Rewiring the specificity of extracytoplasmic function sigma factors". Proceedings of the National Academy of Sciences 117, nr 52 (14.12.2020): 33496–506. http://dx.doi.org/10.1073/pnas.2020204117.
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Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators’ DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid–nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Masloboeva, Nadezda, Luzia Reutimann, Philipp Stiefel, Rainer Follador, Nadja Leimer, Hauke Hennecke, Socorro Mesa i Hans-Martin Fischer. "Reactive Oxygen Species-Inducible ECF σ Factors of Bradyrhizobium japonicum". PLoS ONE 7, nr 8 (16.08.2012): e43421. http://dx.doi.org/10.1371/journal.pone.0043421.
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Mascher, Thorsten. "Signaling diversity and evolution of extracytoplasmic function (ECF) σ factors". Current Opinion in Microbiology 16, nr 2 (kwiecień 2013): 148–55. http://dx.doi.org/10.1016/j.mib.2013.02.001.
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Lee, Yong Heon, Ki Hyun Nam i John D. Helmann. "A Mutation of the RNA Polymerase β′ Subunit (rpoC) Confers Cephalosporin Resistance in Bacillus subtilis". Antimicrobial Agents and Chemotherapy 57, nr 1 (15.10.2012): 56–65. http://dx.doi.org/10.1128/aac.01449-12.
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ABSTRACTIn bacteria, mutations affecting the major catalytic subunits of RNA polymerase (encoded byrpoBandrpoC) emerge in response to a variety of selective pressures. Here we isolated aBacillus subtilisstrain with high-level resistance to cefuroxime (CEF). Whole-genome resequencing revealed only one missense mutation affecting an invariant residue in close proximity to the C-terminal DNA-binding domain of RpoC (G1122D). Genetic reconstruction experiments demonstrate that this substitution is sufficient to confer CEF resistance. The G1122D mutation leads to elevated expression of stress-responsive regulons, including those of extracytoplasmic function (ECF) σ factors (σM, σW, and σX) and the general stress σ factor (σB). The increased CEF resistance of therpoCG1122Dstrain is lost in thesigM rpoCG1122Ddouble mutant, consistent with a major role for σMin CEF resistance. However, asigMmutant is very sensitive to CEF, and this sensitivity is still reduced by the G1122D mutation, suggesting that other regulatory effects are also important. Indeed, the ability of the G1122D mutation to increase CEF resistance is further reduced in a triple mutant strain lacking three ECF σ factors (σM, σW, and σX), which are known from prior studies to control overlapping sets of genes. Collectively, our findings highlight the ability of mutations in RNA polymerase to confer antibiotic resistance by affecting the activity of alternative σ factors that control cell envelope stress-responsive regulons.
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Cao, Min, i John D. Helmann. "Regulation of the Bacillus subtilis bcrC Bacitracin Resistance Gene by Two Extracytoplasmic Function σ Factors". Journal of Bacteriology 184, nr 22 (15.11.2002): 6123–29. http://dx.doi.org/10.1128/jb.184.22.6123-6129.2002.
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ABSTRACT Bacitracin resistance is normally conferred by either of two major mechanisms, the BcrABC transporter, which pumps out bacitracin, or BacA, an undecaprenol kinase that provides C55-isoprenyl phosphate by de novo synthesis. We demonstrate that the Bacillus subtilis bcrC (ywoA) gene, encoding a putative bacitracin transport permease, is an important bacitracin resistance determinant. A bcrC mutant strain had an eightfold-higher sensitivity to bacitracin. Expression of bcrC initiated from a single promoter site that could be recognized by either of two extracytoplasmic function (ECF) σ factors, σX or σM. Bacitracin induced expression of bcrC, and this induction was dependent on σM but not on σX. Under inducing conditions, expression was primarily dependent on σM. As a consequence, a sigM mutant was fourfold more sensitive to bacitracin, while the sigX mutant was only slightly sensitive. A sigX sigM double mutant was similar to a bcrC mutant in sensitivity. These results support the suggestion that one function of B. subtilis ECF σ factors is to coordinate antibiotic stress responses.
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Teng, Shiyu, Tingting Wu, Donghao Gao, Siyi Wu, Yaqian Xiao, Yan Long i Zhixiong Xie. "Insight into the Global Negative Regulation of Iron Scavenger 7-HT Biosynthesis by the SigW/RsiW System in Pseudomonas donghuensis HYS". International Journal of Molecular Sciences 24, nr 2 (7.01.2023): 1184. http://dx.doi.org/10.3390/ijms24021184.
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7-Hydroxytropolone (7-HT) is a unique iron scavenger synthesized by Pseudomonas donghuensis HYS that has various biological activities in addition to functioning as a siderophore. P. donghuensis HYS is more pathogenic than P. aeruginosa toward Caenorhabditis elegans, an observation that is closely linked to the biosynthesis of 7-HT. The nonfluorescent siderophore (nfs) gene cluster is responsible for the orderly biosynthesis of 7-HT and represents a competitive advantage that contributes to the increased survival of P. donghuensis HYS; however, the regulatory mechanisms of 7-HT biosynthesis remain unclear. This study is the first to propose that the ECF σ factor has a regulatory effect on 7-HT biosynthesis. In total, 20 ECF σ factors were identified through genome-wide scanning, and their responses to extracellular ferrous ions were characterized. We found that SigW was both significantly upregulated under high-iron conditions and repressed by an adjacent anti-σ factor. RNA-Seq results suggest that the SigW/RsiW system is involved in iron metabolism and 7-HT biosynthesis. Combined with the siderophore phenotype, we also found that SigW could inhibit siderophore synthesis, and this inhibition can be relieved by RsiW. EMSA assays proved that SigW, when highly expressed, can directly bind to the promoter region of five operons of the nfs cluster to inhibit the transcription of the corresponding genes and consequently suppress 7-HT biosynthesis. In addition, SigW not only directly negatively regulates structural genes related to 7-HT synthesis but also inhibits the transcription of regulatory proteins, including of the Gac/Rsm cascade system. Taken together, our results highlight that the biosynthesis of 7-HT is negatively regulated by SigW and that the SigW/RsiW system is involved in mechanisms for the regulation of iron homeostasis in P. donghuensis HYS. As a result of this work, we identified a novel mechanism for the global negative regulation of 7-HT biosynthesis, complementing our understanding of the function of ECF σ factors in Pseudomonas.
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Kędzierska-Mieszkowska, Sabina, i Zbigniew Arent. "Immunoreactivity of a Putative ECF σ Factor, LIC_10559, from Leptospira interrogans with Sera from Leptospira-Infected Animals". Pathogens 12, nr 4 (25.03.2023): 512. http://dx.doi.org/10.3390/pathogens12040512.
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L. interrogans belongs to highly invasive spirochaetes causing leptospirosis in mammals, including humans. During infection, this pathogen is exposed to various stressors, and therefore, it must reprogram its gene expression to survive in the host and establish infection in a short duration of time. Host adaptation is possible thanks to molecular responses where appropriate regulators and signal transduction systems participate. Among the bacterial regulators, there are σ factors, including ECF (extracytoplasmic function) σ factors. The L. interrogans genome encodes 11 putative ECF σE-type factors. Currently, none of them has been characterized biochemically, and their functions are still unknown. One of them, LIC_10559, is the most likely to be active during infection because it is only found in the highly pathogenic Leptospira. The aim of this study was to achieve LIC_10559 overexpression to answer the question whether it may be a target of the humoral immune response during leptospiral infections. The immunoreactivity of the recombinant LIC_10559 was evaluated by SDS-PAGE, ECL Western blotting and ELISA assay using sera collected from Leptospira-infected animals and uninfected healthy controls. We found that LIC_10559 was recognized by IgG antibodies from the sera of infected animals and is, therefore, able to induce the host’s immune response to pathogenic Leptospira. This result suggests the involvement of LIC_10559 in the pathogenesis of leptospirosis.
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Stockwell, S. B., L. Reutimann i M. L. Guerinot. "A Role for Bradyrhizobium japonicum ECF16 Sigma Factor EcfS in the Formation of a Functional Symbiosis with Soybean". Molecular Plant-Microbe Interactions® 25, nr 1 (styczeń 2012): 119–28. http://dx.doi.org/10.1094/mpmi-07-11-0188.
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Alternative sigma (σ) factors, proteins that recruit RNA polymerase core enzyme to target promoters, are one mechanism by which bacteria transcriptionally regulate groups of genes in response to environmental stimuli. A class of σ70 proteins, termed extracytoplasmic function (ECF) σ factors, are involved in cellular processes such as bacterial stress responses and virulence. Here, we describe an ECF16 σ factor, EcfS (Blr4928) from the gram-negative soil bacterium Bradyrhizobium japonicum USDA110, that plays a critical role in the establishment of a functional symbiosis with soybean. Nonpolar insertional mutants of ecfS form immature nodules that do not fix nitrogen, a defect that can be successfully complemented by expression of ecfS. Overexpression of the cocistronic gene, tmrS (blr4929), phenocopies the ecfS mutant in planta and, therefore, we propose that TmrS is a negative regulator of EcfS, a determination consistent with the prediction that it encodes an anti-σ factor. Microarray analysis of the ecfS mutant and tmrS overexpressor was used to identify 40 transcripts misregulated in both strains. These transcripts primarily encode proteins of unknown and transport-related functions and may provide insights into the symbiotic defect in these strains.
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Martinez-Malaxetxebarria, Irati, Rudy Muts, Linda van Dijk, Craig T. Parker, William G. Miller, Steven Huynh, Wim Gaastra, Jos P. M. van Putten, Aurora Fernandez-Astorga i Marc M. S. M. Wösten. "Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) σ Factors of Arcobacter butzleri". PLoS ONE 7, nr 9 (18.09.2012): e44796. http://dx.doi.org/10.1371/journal.pone.0044796.
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Li, Lingting, Vadim Molodtsov, Wei Lin, Richard H. Ebright i Yu Zhang. "RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription". Proceedings of the National Academy of Sciences 117, nr 11 (3.03.2020): 5801–9. http://dx.doi.org/10.1073/pnas.1920747117.
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All organisms—bacteria, archaea, and eukaryotes—have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the “σ-finger” of the bacterial transcription initiation factor σ. The structures reveal that—for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5′-triphosphate RNA and 5′-hydroxy RNA—the “σ-finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5′-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.
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Yeoman, Kay H., Alex G. May, Nicola G. deLuca, Daniel B. Stuckey i Andrew W. B. Johnston. "A Putative ECF σ Factor Gene, rpoI, Regulates Siderophore Production in Rhizobium leguminosarum". Molecular Plant-Microbe Interactions® 12, nr 11 (listopad 1999): 994–99. http://dx.doi.org/10.1094/mpmi.1999.12.11.994.
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A cloned Rhizobium leguminosarum gene, termed rpoI, when transferred to wild-type strains, caused overproduction of the siderophore vicibactin. An rpoI mutant was defective in Fe uptake but was unaffected in symbiotic N2 fixation. The RpoI gene product was similar in sequence to extra-cytoplasmic σ factors of RNA polymerase. Transcription of rpoI was reduced in cells grown in medium that was replete with Fe.
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Guariglia-Oropeza, Veronica, i John D. Helmann. "Bacillus subtilis σVConfers Lysozyme Resistance by Activation of Two Cell Wall Modification Pathways, Peptidoglycan O-Acetylation and d-Alanylation of Teichoic Acids". Journal of Bacteriology 193, nr 22 (16.09.2011): 6223–32. http://dx.doi.org/10.1128/jb.06023-11.
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The seven extracytoplasmic function (ECF) sigma (σ) factors ofBacillus subtilisare broadly implicated in resistance to antibiotics and other cell envelope stressors mediated, in part, by regulation of cell envelope synthesis and modification enzymes. We here define the regulon of σVas including at least 20 operons, many of which are also regulated by σM, σX, or σW. The σVregulon is strongly and specifically induced by lysozyme, and this induction is key to the intrinsic resistance ofB. subtilisto lysozyme. Strains with null mutations in eithersigVor all seven ECF σ factor genes (Δ7ECF) have essentially equal increases in sensitivity to lysozyme. Induction of σVin the Δ7ECF background restores lysozyme resistance, whereas induction of σM, σX, or σWdoes not. Lysozyme resistance results from the ability of σVto activate the transcription of two operons: the autoregulatedsigV-rsiV-oatA-yrhKoperon anddltABCDE. Genetic analyses reveal thatoatAanddltare largely redundant with respect to lysozyme sensitivity: single mutants are not affected in lysozyme sensitivity, whereas anoatA dltAdouble mutant is as sensitive as asigVnull strain. Moreover, thesigV oatA dltAtriple mutant is no more sensitive than theoatA dltAdouble mutant, indicating that there are no other σV-dependent genes necessary for lysozyme resistance. Thus, we suggest that σVconfers lysozyme resistance by the activation of two cell wall modification pathways: O-acetylation of peptidoglycan catalyzed by OatA andd-alanylation of teichoic acids by DltABCDE.
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Tamizi, Amin-Asyraf, Norliza Abu-Bakar, Aimera-Farhana Samsuddin, Lina Rozano, Rohaiza Ahmad-Redzuan i Abdul-Munir Abdul-Murad. "Characterisation and Mutagenesis Study of An Alternative Sigma Factor Gene (hrpL) from Erwinia mallotivora Reveal Its Central Role in Papaya Dieback Disease". Biology 9, nr 10 (3.10.2020): 323. http://dx.doi.org/10.3390/biology9100323.
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The alternative sigma (σ) factor E, RpoE or HrpL, has been reported to be involved in stress- and pathogenicity-related transcription initiation in Escherichia coli and many other Gram-negative bacteria, including Erwinia spp. and Pseudomonas spp. A previous study identified the hrpL/rpoE transcript as one of the significant differentially expressed genes (DEGs) during early E. mallotivora infection in papaya and those data serve as the basis of the current project. Here, the full coding DNA sequence (CDS) of hrpL from E. mallotivora (EmhrpL) was determined to be 549 bp long, and it encoded a 21.3 kDa HrpL protein that possessed two highly conserved sigma-70 (σ70) motifs—σR2 and σR4. Nucleotide sequence alignment revealed the hrpL from E. mallotivora shared high sequence similarity to rpoE/hrpL from E. tracheiphila (83%), E. pyrifoliae (81%), and E. tasmaniensis (80%). Phylogenetics analysis indicated hrpL from E. mallotivora to be monophyletic with rpoEs/hrpLs from Pantoea vagans, E. herbicola, and E. tracheiphila. Structural analysis postulated that the E. mallotivora’s alternative σ factor was non-transmembranic and was an extracytoplasmic function (ECF) protein—characteristics shared by other σ factors in different bacterial species. Notably, the protein–protein interaction (PPI) study through molecular docking suggested the σ factor could be possibly inhibited by an anti-σ. Finally, a knockout of hrpL in E. mallotivora (ΔEmhrpL) resulted in avirulence in four-month-old papaya plants. These findings have revealed that the hrpL is a necessary element in E. mallotivora pathogenicity and also predicted that the gene can be inhibited by an anti-σ.
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Rey-Varela, Diego, Miguel Balado i Manuel L. Lemos. "The Sigma Factor AsbI Is Required for the Expression of Acinetobactin Siderophore Transport Genes in Aeromonas salmonicida". International Journal of Molecular Sciences 24, nr 11 (2.06.2023): 9672. http://dx.doi.org/10.3390/ijms24119672.
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Aeromonas salmonicida subsp. salmonicida (A. salmonicida), a Gram-negative bacterium causing furunculosis in fish, produces the siderophores acinetobactin and amonabactins in order to extract iron from its hosts. While the synthesis and transport of both systems is well understood, the regulation pathways and conditions necessary for the production of each one of these siderophores are not clear. The acinetobactin gene cluster carries a gene (asbI) encoding a putative sigma factor belonging to group 4 σ factors, or, the ExtraCytoplasmic Function (ECF) group. By generating a null asbI mutant, we demonstrate that AsbI is a key regulator that controls acinetobactin acquisition in A. salmonicida, since it directly regulates the expression of the outer membrane transporter gene and other genes necessary for Fe-acinetobactin transport. Furthermore, AsbI regulatory functions are interconnected with other iron-dependent regulators, such as the Fur protein, as well as with other sigma factors in a complex regulatory network.
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Kędzierska-Mieszkowska, Sabina, Katarzyna Potrykus, Zbigniew Arent i Joanna Krajewska. "Identification of σE-Dependent Promoter Upstream of clpB from the Pathogenic Spirochaete Leptospira interrogans by Applying an E. coli Two-Plasmid System". International Journal of Molecular Sciences 20, nr 24 (15.12.2019): 6325. http://dx.doi.org/10.3390/ijms20246325.
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There is limited information on gene expression in the pathogenic spirochaete Leptospira interrogans and genetic mechanisms controlling its virulence. Transcription is the first step in gene expression that is often determined by environmental effects, including infection-induced stresses. Alterations in the environment result in significant changes in the transcription of many genes, allowing effective adaptation of Leptospira to mammalian hosts. Thus, promoter and transcriptional start site identification are crucial for determining gene expression regulation and for the understanding of genetic regulatory mechanisms existing in Leptospira. Here, we characterized the promoter region of the L. interrogans clpB gene (clpBLi) encoding an AAA+ molecular chaperone ClpB essential for the survival of this spirochaete under thermal and oxidative stresses, and also during infection of the host. Primer extension analysis demonstrated that transcription of clpB in L. interrogans initiates at a cytidine located 41 bp upstream of the ATG initiation codon, and, to a lesser extent, at an adenine located 2 bp downstream of the identified site. Transcription of both transcripts was heat-inducible. Determination of clpBLi transcription start site, combined with promoter transcriptional activity assays using a modified two-plasmid system in E. coli, revealed that clpBLi transcription is controlled by the ECF σE factor. Of the ten L. interrogans ECF σ factors, the factor encoded by LIC_12757 (LA0876) is most likely to be the key regulator of clpB gene expression in Leptospira cells, especially under thermal stress. Furthermore, clpB expression may be mediated by ppGpp in Leptospira.
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Ahuja, Umesh, Bhumika Shokeen, Ning Cheng, Yeonjoo Cho, Charles Blum, Giovanni Coppola i Jeff F. Miller. "Differential regulation of type III secretion and virulence genes inBordetella pertussisandBordetella bronchisepticaby a secreted anti-σ factor". Proceedings of the National Academy of Sciences 113, nr 9 (16.02.2016): 2341–48. http://dx.doi.org/10.1073/pnas.1600320113.
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The BvgAS phosphorelay regulates ∼10% of the annotated genomes ofBordetella pertussisandBordetella bronchisepticaand controls their infectious cycles. The hierarchical organization of the regulatory network allows the integration of contextual signals to control all or specific subsets of BvgAS-regulated genes. Here, we characterize a regulatory node involving a type III secretion system (T3SS)-exported protein, BtrA, and demonstrate its role in determining fundamental differences in T3SS phenotypes amongBordetellaspecies. We show that BtrA binds and antagonizes BtrS, a BvgAS-regulated extracytoplasmic function (ECF) sigma factor, to couple the secretory activity of the T3SS apparatus to gene expression. InB. bronchiseptica, a remarkable spectrum of expression states can be resolved by manipulatingbtrA, encompassing over 80 BtrA-activated loci that include genes encoding toxins, adhesins, and other cell surface proteins, and over 200 BtrA-repressed genes that encode T3SS apparatus components, secretion substrates, the BteA effector, and numerous additional factors. InB. pertussis, BtrA retains activity as a BtrS antagonist and exerts tight negative control over T3SS genes. Most importantly, deletion ofbtrAinB. pertussisrevealed T3SS-mediated, BteA-dependent cytotoxicity, which had previously eluded detection. This effect was observed in laboratory strains and in clinical isolates from a recent California pertussis epidemic. We propose that the BtrA-BtrS regulatory node determines subspecies-specific differences in T3SS expression amongBordetellaspecies and thatB. pertussisis capable of expressing a full range of T3SS-dependent phenotypes in the presence of appropriate contextual cues.
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Mishra, Mukti Nath, Santosh Kumar, Namrata Gupta, Simarjot Kaur, Ankush Gupta i Anil K. Tripathi. "An extracytoplasmic function sigma factor cotranscribed with its cognate anti-sigma factor confers tolerance to NaCl, ethanol and methylene blue in Azospirillum brasilense Sp7". Microbiology 157, nr 4 (1.04.2011): 988–99. http://dx.doi.org/10.1099/mic.0.046672-0.
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Azospirillum brasilense, a plant-growth-promoting rhizobacterium, is exposed to changes in its abiotic environment, including fluctuations in temperature, salinity, osmolarity, oxygen concentration and nutrient concentration, in the rhizosphere and in the soil. Since extra-cytoplasmic function (ECF) sigma factors play an important role in stress adaptation, we analysed the role of ECF sigma factor (also known as RpoE or σ E) in abiotic stress tolerance in A. brasilense. An in-frame rpoE deletion mutant of A. brasilense Sp7 was carotenoidless and slow-growing, and was sensitive to salt, ethanol and methylene blue stress. Expression of rpoE in the rpoE deletion mutant complemented the defects in growth, carotenoid biosynthesis and sensitivity to different stresses. Based on data from reverse transcriptase-PCR, a two-hybrid assay and a pull-down assay, we present evidence that rpoE is cotranscribed with chrR and the proteins synthesized from these two overlapping genes interact with each other. Identification of the transcription start site by 5′ rapid amplification of cDNA ends showed that the rpoE–chrR operon was transcribed by two promoters. The proximal promoter was less active than the distal promoter, whose consensus sequence was characteristic of RpoE-dependent promoters found in alphaproteobacteria. Whereas the proximal promoter was RpoE-independent and constitutively expressed, the distal promoter was RpoE-dependent and strongly induced in response to stationary phase and elevated levels of ethanol, salt, heat and methylene blue. This study shows the involvement of RpoE in controlling carotenoid synthesis as well as in tolerance to some abiotic stresses in A. brasilense, which might be critical in the adaptation, survival and proliferation of this rhizobacterium in the soil and rhizosphere under stressful conditions.
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Ohki, Reiko, Kozue Tateno, Youji Okada, Haruo Okajima, Kei Asai, Yoshito Sadaie, Makiko Murata i Toshiko Aiso. "A Bacitracin-Resistant Bacillus subtilis Gene Encodes a Homologue of the Membrane-Spanning Subunit of the Bacillus licheniformis ABC Transporter". Journal of Bacteriology 185, nr 1 (1.01.2003): 51–59. http://dx.doi.org/10.1128/jb.185.1.51-59.2003.
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ABSTRACT Bacitracin is a peptide antibiotic nonribosomally produced by Bacillus licheniformis. The bcrABC genes which confer bacitracin resistance to the bacitracin producer encode ATP binding cassette (ABC) transporter proteins, which are hypothesized to pump out bacitracin from the cells. Bacillus subtilis 168, which has no bacitracin synthesizing operon, has several genes homologous to bcrABC. It was found that the disruption of ywoA, a gene homologous to bcrC, resulted in hypersensitivity to bacitracin. Resistance to other drugs such as surfactin, iturin A, vancomycin, tunicamycin, gramicidin D, valinomycin and several cationic dyes were not changed in the ywoA disruptant. Spontaneous bacitracin-resistant mutants (Bcr-1 and -2) isolated in the presence of bacitracin have a single base substitution from A to G in the ribosome binding region. Northern hybridization analysis and determination of the expression of ywoA-LacZ transcriptional fusion gene revealed that the transcription of the ywoA gene was dependent on extracytoplasmic function (ECF) σ factors σM and σX. Preincubation of wild-type cells in the presence of a low concentration of bacitracin induced increased resistance to bacitracin about two- to threefold, although the mechanism of this induction has not yet been elucidated. It has been reported that a commercially available bacitracin is a mixture of several components and also contains impurity. Bacitracin A was purified by reverse phase high-performance liquid chromatography (HPLC). Similar results were obtained with bacitracin A as those with crude bacitracin, indicating that contaminating substances were not responsible for the results obtained in this study.
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Huang, Xiaoluo, Daniela Pinto, Georg Fritz i Thorsten Mascher. "Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum". Journal of Bacteriology 197, nr 15 (18.05.2015): 2517–35. http://dx.doi.org/10.1128/jb.00176-15.
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ABSTRACTSignal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function σ factors (ECFs). SinceActinobacteriaare particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies.IMPORTANCEIn the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance.
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Casas-Pastor, Delia, Angelika Diehl i Georg Fritz. "Coevolutionary Analysis Reveals a Conserved Dual Binding Interface between Extracytoplasmic Function σ Factors and Class I Anti-σ Factors". mSystems 5, nr 4 (4.08.2020). http://dx.doi.org/10.1128/msystems.00310-20.
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ABSTRACT Extracytoplasmic function σ factors (ECFs) belong to the most abundant signal transduction mechanisms in bacteria. Among the diverse regulators of ECF activity, class I anti-σ factors are the most important signal transducers in response to internal and external stress conditions. Despite the conserved secondary structure of the class I anti-σ factor domain (ASDI) that binds and inhibits the ECF under noninducing conditions, the binding interface between ECFs and ASDIs is surprisingly variable between the published cocrystal structures. In this work, we provide a comprehensive computational analysis of the ASDI protein family and study the different contact themes between ECFs and ASDIs. To this end, we harness the coevolution of these diverse protein families and predict covarying amino acid residues as likely candidates of an interaction interface. As a result, we find two common binding interfaces linking the first alpha-helix of the ASDI to the DNA-binding region in the σ4 domain of the ECF, and the fourth alpha-helix of the ASDI to the RNA polymerase (RNAP)-binding region of the σ2 domain. The conservation of these two binding interfaces contrasts with the apparent quaternary structure diversity of the ECF/ASDI complexes, partially explaining the high specificity between cognate ECF and ASDI pairs. Furthermore, we suggest that the dual inhibition of RNAP- and DNA-binding interfaces is likely a universal feature of other ECF anti-σ factors, preventing the formation of nonfunctional trimeric complexes between σ/anti-σ factors and RNAP or DNA. IMPORTANCE In the bacterial world, extracytoplasmic function σ factors (ECFs) are the most widespread family of alternative σ factors, mediating many cellular responses to environmental cues, such as stress. This work uses a computational approach to investigate how these σ factors interact with class I anti-σ factors—the most abundant regulators of ECF activity. By comprehensively classifying the anti-σs into phylogenetic groups and by comparing this phylogeny to the one of the cognate ECFs, the study shows how these protein families have coevolved to maintain their interaction over evolutionary time. These results shed light on the common contact residues that link ECFs and anti-σs in different phylogenetic families and set the basis for the rational design of anti-σs to specifically target certain ECFs. This will help to prevent the cross talk between heterologous ECF/anti-σ pairs, allowing their use as orthogonal regulators for the construction of genetic circuits in synthetic biology.
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Lang, Claus, Melanie J. Barnett, Robert F. Fisher, Lucinda S. Smith, Michelle E. Diodati i Sharon R. Long. "MostSinorhizobium melilotiExtracytoplasmic Function Sigma Factors Control Accessory Functions". mSphere 3, nr 5 (10.10.2018). http://dx.doi.org/10.1128/mspheredirect.00454-18.
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ABSTRACTBacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF σs) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacteriumSinorhizobium meliloticarries genes for 11 ECF-like σs (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entireS. meliloticohort of ECF σs. We discovered new targets for individual σs, confirmed others by overexpressing individual ECF σs, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF σ gene and its demonstrated or putative anti-σ gene and also a strain in which all 11 ECF σ and anti-σ genes were deleted. This all-ECF σ deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF σs were required for symbiosis on the host plantsMedicago sativaandMedicago truncatula: the strain deleted for all ECF σ and anti-σ genes was symbiotically normal.IMPORTANCEFixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.
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Pinto, Daniela, i Rute R. da Fonseca. "Evolution of the extracytoplasmic function σ factor protein family". NAR Genomics and Bioinformatics 2, nr 1 (13.01.2020). http://dx.doi.org/10.1093/nargab/lqz026.
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Abstract Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF σ factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF σ factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF σ factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated σ factor. At last, we also demonstrate horizontal transfer of ECF σ factors between soil bacteria.
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Joshi, Anuja C., Prabhjot Kaur, Radhika K. Nair, Deepti S. Lele, Vinay Kumar Nandicoori i Balasubramanian Gopal. "Selectivity among Anti-σ Factors byMycobacterium tuberculosisClpX Influences Intracellular Levels of Extracytoplasmic Function σ Factors". Journal of Bacteriology 201, nr 6 (7.01.2019). http://dx.doi.org/10.1128/jb.00748-18.
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ABSTRACTExtracytoplasmic function σ factors that are stress inducible are often sequestered in an inactive complex with a membrane-associated anti-σ factor.Mycobacterium tuberculosismembrane-associated anti-σ factors have a small, stable RNA gene A (ssrA)-like degron for targeted proteolysis. Interaction between the unfoldase, ClpX, and a substrate with an accessible degron initiates energy-dependent proteolysis. Four anti-σ factors with a mutation in the degron provided a set of natural substrates to evaluate the influence of the degron on degradation strength in ClpX-substrate processivity. We note that a point mutation in the degron (X-Ala-Ala) leads to an order-of-magnitude difference in the dwell time of the substrate on ClpX. Differences in ClpX/anti-σ interactions were correlated with changes in unfoldase activities. Green fluorescent protein (GFP) chimeras or polypeptides with a length identical to that of the anti-σ factor degron also demonstrate degron-dependent variation in ClpX activities. We show that degron-dependent ClpX activity leads to differences in anti-σ degradation, thereby regulating the release of free σ from the σ/anti-σ complex.M. tuberculosisClpX activity thus influences changes in gene expression by modulating the cellular abundance of ECF σ factors.IMPORTANCEThe ability ofMycobacterium tuberculosisto quickly adapt to changing environmental stimuli occurs by maintaining protein homeostasis. Extracytoplasmic function (ECF) σ factors play a significant role in coordinating the transcription profile to changes in environmental conditions. Release of the σ factor from the anti-σ is governed by the ClpXP2P1 assembly.M. tuberculosisECF anti-σ factors have anssrA-like degron for targeted degradation. A point mutation in the degron leads to differences in ClpX-mediated proteolysis and affects the cellular abundance of ECF σ factors. ClpX activity thus synchronizes changes in gene expression with environmental stimuli affectingM. tuberculosisphysiology.
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Grove, Anne. "Extracytoplasmic Function Sigma Factors Governing Production of the Primary Siderophores in Pathogenic Burkholderia Species". Frontiers in Microbiology 13 (24.02.2022). http://dx.doi.org/10.3389/fmicb.2022.851011.
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Bacteria respond to changing environments by modulating their gene expression programs. One of the mechanisms by which this may be accomplished is by substituting the primary σ factor with an alternative σ factor belonging to the family of extracytoplasmic function (ECF) σ factors. ECF σ factors are activated only in presence of specific signals, and they direct the RNA polymerase (RNAP) to transcribe a defined subset of genes. One condition, which may trigger the activation of an ECF σ factor, is iron limitation. To overcome iron starvation, bacteria produce and secrete siderophores, which chelate iron and facilitate its cellular uptake. In the genus Burkholderia, which includes several serious human pathogens, uptake of iron is critical for virulence, and expression of biosynthetic gene clusters encoding proteins involved in synthesis and transport of the primary siderophores are under control of an ECF σ factor. This review summarizes mechanisms involved in regulation of these gene clusters, including the role of global transcriptional regulators. Since siderophore-mediated iron acquisition is important for virulence, interference with this process constitutes a viable approach to the treatment of bacterial infections.
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Mascher, Thorsten. "Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction". Annual Review of Microbiology 77, nr 1 (12.07.2023). http://dx.doi.org/10.1146/annurev-micro-032221-024032.
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Responding to environmental cues is a prerequisite for survival in the microbial world. Extracytoplasmic function σ factors (ECFs) represent the third most abundant and by far the most diverse type of bacterial signal transduction. While archetypal ECFs are controlled by cognate anti-σ factors, comprehensive comparative genomics efforts have revealed a much higher abundance and regulatory diversity of ECF regulation than previously appreciated. They have also uncovered a diverse range of anti-σ factor–independent modes of controlling ECF activity, including fused regulatory domains and phosphorylation-dependent mechanisms. While our understanding of ECF diversity is comprehensive for well-represented and heavily studied bacterial phyla—such as Proteobacteria, Firmicutes, and Actinobacteria (phylum Actinomycetota)—our current knowledge about ECF-dependent signaling in the vast majority of underrepresented phyla is still far from complete. In particular, the dramatic extension of bacterial diversity in the course of metagenomic studies represents both a new challenge and an opportunity in expanding the world of ECF-dependent signal transduction. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Agnoli, Kirsty, Sayali S. Haldipurkar, Yingzhi Tang, Aaron T. Butt i Mark S. Thomas. "Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities". Journal of Bacteriology 201, nr 3 (19.11.2018). http://dx.doi.org/10.1128/jb.00507-18.
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ABSTRACTOrbS and PvdS are extracytoplasmic function (ECF) σ factors that regulate transcription of operons required for the biosynthesis of the siderophores ornibactin and pyoverdine in theBurkholderia cepaciacomplex andPseudomonasspp., respectively. Here we show that promoter recognition by OrbS requires specific tetrameric −35 and −10 element sequences that are strikingly similar to those of the consensus PvdS-dependent promoter. However, whereasPseudomonas aeruginosaPvdS can serve OrbS-dependent promoters, OrbS cannot utilize PvdS-dependent promoters. To identify features present at OrbS-dependent promoters that facilitate recognition by OrbS, we carried out a detailed analysis of the nucleotide sequence requirements for promoter recognition by both OrbS and PvdS. This revealed that DNA sequence features located outside the sigma binding elements are required for efficient promoter utilization by OrbS. In particular, the presence of an A-tract extending downstream from the −35 element at OrbS-dependent promoters was shown to be an important contributor to OrbS specificity. Our observations demonstrate that the nature of the spacer sequence can have a major impact on promoter recognition by some ECF σ factors through modulation of the local DNA architecture.IMPORTANCEECF σ factors regulate subsets of bacterial genes in response to environmental stress signals by directing RNA polymerase to promoter sequences known as the −35 and −10 elements. In this work, we identify the −10 and −35 elements that are recognized by the ECF σ factor OrbS. Furthermore, we demonstrate that efficient promoter utilization by this σ factor also requires a polyadenine tract located downstream of the −35 region. We propose that the unique architecture of A-tract DNA imposes conformational features on the −35 element that facilitates efficient recognition by OrbS. Our results show that sequences located between the core promoter elements can make major contributions to promoter recognition by some ECF σ factors.
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Castro, Ana N., Lincoln T. Lewerke, Jessica L. Hastie i Craig D. Ellermeier. "Signal Peptidase Is Necessary and Sufficient for Site 1 Cleavage of RsiV inBacillus subtilisin Response to Lysozyme". Journal of Bacteriology 200, nr 11 (22.01.2018). http://dx.doi.org/10.1128/jb.00663-17.
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ABSTRACTExtracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that allow bacteria to sense and respond to changes in the environment. σVis an ECF σ factor found primarily in low-GC Gram-positive bacteria and is required for lysozyme resistance in several opportunistic pathogens. In the absence of lysozyme, σVis inhibited by the anti-σ factor RsiV. In response to lysozyme, RsiV is degraded via the process of regulated intramembrane proteolysis (RIP). RIP is initiated by cleavage of RsiV at site 1, which allows the intramembrane protease RasP to cleave RsiV within the transmembrane domain at site 2 and leads to activation of σV. Previous work suggested that RsiV is cleaved by signal peptidase at site 1. Here we demonstratein vitrothat signal peptidase is sufficient for cleavage of RsiV only in the presence of lysozyme and provide evidence that multipleBacillus subtilissignal peptidases can cleave RsiVin vitro. This cleavage is dependent upon the concentration of lysozyme, consistent with previous work that showed that binding to RsiV was required for σVactivation. We also show that signal peptidase activity is required for site 1 cleavage of RsiVin vivo. Thus, we demonstrate that signal peptidase is the site 1 protease for RsiV.IMPORTANCEExtracytoplasmic function (ECF) σ factors are a diverse family of alternative σ factors that respond to extracellular signals. The ECF σ factor σVis present in many low-GC Gram-positive bacteria and induces resistance to lysozyme, a component of the innate immune system. The anti-σ factor RsiV inhibits σVactivity in the absence of lysozyme. Lysozyme binds RsiV, which initiates a proteolytic cascade leading to destruction of RsiV and activation of σV. This proteolytic cascade is initiated by signal peptidase, a component of the general secretory system. We show that signal peptidase is necessary and sufficient for cleavage of RsiV at site 1 in the presence of lysozyme. This report describes a role for signal peptidase in controlling gene expression.
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Casas-Pastor, Delia, Raphael R. Müller, Sebastian Jaenicke, Karina Brinkrolf, Anke Becker, Mark J. Buttner, Carol A. Gross, Thorsten Mascher, Alexander Goesmann i Georg Fritz. "Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family". Nucleic Acids Research, 4.01.2021. http://dx.doi.org/10.1093/nar/gkaa1229.
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Abstract Extracytoplasmic function σ factors (ECFs) represent one of the major bacterial signal transduction mechanisms in terms of abundance, diversity and importance, particularly in mediating stress responses. Here, we performed a comprehensive phylogenetic analysis of this protein family by scrutinizing all proteins in the NCBI database. As a result, we identified an average of ∼10 ECFs per bacterial genome and 157 phylogenetic ECF groups that feature a conserved genetic neighborhood and a similar regulation mechanism. Our analysis expands previous classification efforts ∼50-fold, enriches many original ECF groups with previously unclassified proteins and identifies 22 entirely new ECF groups. The ECF groups are hierarchically related to each other and are further composed of subgroups with closely related sequences. This two-tiered classification allows for the accurate prediction of common promoter motifs and the inference of putative regulatory mechanisms across subgroups composing an ECF group. This comprehensive, high-resolution description of the phylogenetic distribution of the ECF family, together with the massive expansion of classified ECF sequences and an openly accessible data repository called ‘ECF Hub’ (https://www.computational.bio.uni-giessen.de/ecfhub), will serve as a powerful hypothesis-generator to guide future research in the field.
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Dubey, Ashutosh Prakash, Parul Pandey, Vijay Shankar Singh, Mukti Nath Mishra, Sudhir Singh, Rajeev Mishra i Anil Kumar Tripathi. "An ECF41 Family σ Factor Controls Motility and Biogenesis of Lateral Flagella in Azospirillum brasilense Sp245". Journal of Bacteriology 202, nr 16 (8.06.2020). http://dx.doi.org/10.1128/jb.00231-20.
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ABSTRACT ECF41 is a large family of bacterial extracytoplasmic function (ECF) σ factors. Their role in bacterial physiology or behavior, however, is not known. One of the 10 ECF σ factors encoded in the genome of Azospirillum brasilense Sp245, RpoE10, exhibits features characteristic of the typical ECF41-type σ factors. Inactivation of rpoE10 in A. brasilense Sp245 led to an increase in motility that could be complemented by the expression of rpoE10. By comparing the number of lateral flagella, transcriptome, and proteome of A. brasilense Sp245 with those of its rpoE10::km mutant, we show here that this ECF41-type σ factor is involved in the negative regulation of swimming motility and biogenesis of lateral flagella of A. brasilense Sp245. The genome of A. brasilense Sp245 also encodes two OmpR-type regulators (LafR1 and LafR2) and three flagellins, including Laf1, the major flagellin of lateral flagella. Elevated levels of laf1 transcripts and Laf1 protein in the rpoE10::km mutant indicated that RpoE10 negatively regulates the expression of Laf1. The elevated level of LafR1 in the rpoE10::km mutant indicated that LafR1 is also negatively regulated by RpoE10. The loss of motility and Laf1 in the lafR1::km mutant, complemented by lafR1 expression, showed that LafR1 is a positive regulator of Laf1 and motility in A. brasilense. In addition, upregulation of laf1::lacZ and lafR1::lacZ fusions by RpoE10 and downregulation of the laf1::lacZ fusion by LafR1 suggest that RpoE10 negatively regulates swimming motility and the expression of LafR1 and Laf1. However, LafR1 positively regulates the swimming motility and Laf1 expression. IMPORTANCE Among extracytoplasmic function (ECF) σ factors, ECF41-type σ factors are unique due to the presence of a large C-terminal extension in place of a cognate anti-σ factor, which regulates their activity. Despite their wide distribution and abundance in bacterial genomes, their physiological or behavioral roles are not known. We show here an indirect negative role of an ECF41-type of σ factor in the expression of lateral flagellar genes and motility in A. brasilense. This study suggests that the motility of A. brasilense might be controlled by a regulatory cascade involving RpoE10, an unknown repressor, LafR1, and lateral flagellar genes, including that encoding Laf1.
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Li, Lingting, Chengli Fang, Ningning Zhuang, Tiantian Wang i Yu Zhang. "Structural basis for transcription initiation by bacterial ECF σ factors". Nature Communications 10, nr 1 (11.03.2019). http://dx.doi.org/10.1038/s41467-019-09096-y.
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Oliveira, Rute, Matthew J. Bush, Sílvia Pires, Govind Chandra, Delia Casas-Pastor, Georg Fritz i Marta V. Mendes. "The novel ECF56 SigG1-RsfG system modulates morphological differentiation and metal-ion homeostasis in Streptomyces tsukubaensis". Scientific Reports 10, nr 1 (grudzień 2020). http://dx.doi.org/10.1038/s41598-020-78520-x.
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AbstractExtracytoplasmic function (ECF) sigma factors are key transcriptional regulators that prokaryotes have evolved to respond to environmental challenges. Streptomyces tsukubaensis harbours 42 ECFs to reprogram stress-responsive gene expression. Among them, SigG1 features a minimal conserved ECF σ2–σ4 architecture and an additional C-terminal extension that encodes a SnoaL_2 domain, which is characteristic for ECF σ factors of group ECF56. Although proteins with such domain organisation are widely found among Actinobacteria, the functional role of ECFs with a fused SnoaL_2 domain remains unknown. Our results show that in addition to predicted self-regulatory intramolecular amino acid interactions between the SnoaL_2 domain and the ECF core, SigG1 activity is controlled by the cognate anti-sigma protein RsfG, encoded by a co-transcribed sigG1-neighbouring gene. Characterisation of ∆sigG1 and ∆rsfG strains combined with RNA-seq and ChIP-seq experiments, suggests the involvement of SigG1 in the morphological differentiation programme of S. tsukubaensis. SigG1 regulates the expression of alanine dehydrogenase, ald and the WhiB-like regulator, wblC required for differentiation, in addition to iron and copper trafficking systems. Overall, our work establishes a model in which the activity of a σ factor of group ECF56, regulates morphogenesis and metal-ions homeostasis during development to ensure the timely progression of multicellular differentiation.
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Bilyk, Bohdan, Sora Kim, Asif Fazal, Tania A. Baker i Ryan F. Seipke. "Regulation of Antimycin Biosynthesis Is Controlled by the ClpXP Protease". mSphere 5, nr 2 (8.04.2020). http://dx.doi.org/10.1128/msphere.00144-20.
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ABSTRACT The survival of any microbe relies on its ability to respond to environmental change. Use of extracytoplasmic function (ECF) RNA polymerase sigma (σ) factors is a major strategy enabling dynamic responses to extracellular signals. Streptomyces species harbor a large number of ECF σ factors, nearly all of which are uncharacterized, but those that have been characterized generally regulate genes required for morphological differentiation and/or response to environmental stress, except for σAntA, which regulates starter-unit biosynthesis in the production of antimycin, an anticancer compound. Unlike a canonical ECF σ factor, whose activity is regulated by a cognate anti-σ factor, σAntA is an orphan, raising intriguing questions about how its activity may be controlled. Here, we reconstituted in vitro ClpXP proteolysis of σAntA but not of a variant lacking a C-terminal di-alanine motif. Furthermore, we show that the abundance of σAntA in vivo was enhanced by removal of the ClpXP recognition sequence and that levels of the protein rose when cellular ClpXP protease activity was abolished. These data establish direct proteolysis as an alternative and, thus far, unique control strategy for an ECF RNA polymerase σ factor and expands the paradigmatic understanding of microbial signal transduction regulation. IMPORTANCE Natural products produced by Streptomyces species underpin many industrially and medically important compounds. However, the majority of the ∼30 biosynthetic pathways harbored by an average species are not expressed in the laboratory. This unrevealed biochemical diversity is believed to comprise an untapped resource for natural product drug discovery. Major roadblocks preventing the exploitation of unexpressed biosynthetic pathways are a lack of insight into their regulation and limited technology for activating their expression. Our findings reveal that the abundance of σAntA, which is the cluster-situated regulator of antimycin biosynthesis, is controlled by the ClpXP protease. These data link proteolysis to the regulation of natural product biosynthesis for the first time to our knowledge, and we anticipate that this will emerge as a major strategy by which actinobacteria regulate production of their natural products. Further study of this process will advance understanding of how expression of secondary metabolism is controlled and will aid pursuit of activating unexpressed biosynthetic pathways.
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Lima, Lídia dos Passos, Juliana Biar Pereira, Anthony Jhoao Fasabi Flores, Alan Péricles Rodrigues Lorenzetti, Ana Laura Boechat, Maria Claudia Pereda, Sophia Gualtieri i in. "An Extracytoplasmic Function Sigma Factor Required for Full Virulence in Xanthomonas citri pv. citri". Journal of Bacteriology, 21.04.2022. http://dx.doi.org/10.1128/jb.00624-21.
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The Xanthomonas genus comprises a large number of phytopathogenic species that infect a wide variety of economically important plants worldwide. Bacterial adaptation to the plant and soil environment relies on their repertoire of signal transduction pathways, including alternative sigma factors of the extracytoplasmic function family (σ ECF ).
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Ho, Theresa D., Kelsie M. Nauta, Ute Müh i Craig D. Ellermeier. "Activation of the Extracytoplasmic Function σ Factor σP by β-Lactams in Bacillus thuringiensis Requires the Site-2 Protease RasP". mSphere 4, nr 4 (7.08.2019). http://dx.doi.org/10.1128/msphere.00511-19.
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ABSTRACT Bacteria can utilize alternative σ factors to regulate sets of genes in response to changes in the environment. The largest and most diverse group of alternative σ factors are the extracytoplasmic function (ECF) σ factors. σP is an ECF σ factor found in Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Previous work showed that σP is induced by ampicillin, a β-lactam antibiotic, and required for resistance to ampicillin. However, it was not known how activation of σP is controlled or what other antibiotics may activate σP. Here, we report that activation of σP is specific to a subset of β-lactams and that σP is required for resistance to these β-lactams. We demonstrate that activation of σP is controlled by the proteolytic destruction of the anti-σ factor RsiP and that degradation of RsiP requires multiple proteases. Upon exposure to β-lactams, the extracellular domain of RsiP is cleaved by an unknown protease, which we predict cleaves at site-1. Following cleavage by the unknown protease, the N terminus of RsiP is further degraded by the site-2 intramembrane protease RasP. Our data indicate that RasP cleavage of RsiP is not the rate-limiting step in σP activation. This proteolytic cascade leads to activation of σP, which induces resistance to β-lactams likely via increased expression of β-lactamases. IMPORTANCE The discovery of antibiotics to treat bacterial infections has had a dramatic and positive impact on human health. However, shortly after the introduction of a new antibiotic, bacteria often develop resistance. The bacterial cell envelope is essential for cell viability and is the target of many of the most commonly used antibiotics, including β-lactam antibiotics. Resistance to β-lactams is often dependent upon β-lactamases. In B. cereus, B. thuringiensis, and some B. anthracis strains, the expression of some β-lactamases is inducible. This inducible β-lactamase expression is controlled by activation of an alternative σ factor called σP. Here, we show that β-lactam antibiotics induce σP activation by degradation of the anti-σ factor RsiP.
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Guzina, Jelena, i Marko Djordjevic. "Mix-and-matching as a promoter recognition mechanism by ECF σ factors". BMC Evolutionary Biology 17, S1 (luty 2017). http://dx.doi.org/10.1186/s12862-016-0865-z.
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Herrou, Julien, Jonathan W. Willett i Sean Crosson. "Structured and Dynamic Disordered Domains Regulate the Activity of a Multifunctional Anti-σ Factor". mBio 6, nr 4 (28.07.2015). http://dx.doi.org/10.1128/mbio.00910-15.
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ABSTRACT The anti-σ factor NepR plays a central role in regulation of the general stress response (GSR) in alphaproteobacteria. This small protein has two known interaction partners: its cognate extracytoplasmic function (ECF) σ factor and the anti-anti-σ factor, PhyR. Stress-dependent phosphorylation of PhyR initiates a protein partner switch that promotes phospho-PhyR binding to NepR, which frees ECF σ to activate transcription of genes required for cell survival under adverse or fluctuating conditions. We have defined key functional roles for structured and intrinsically disordered domains of Caulobacter crescentus NepR in partner binding and activation of GSR transcription. We further demonstrate that NepR strongly stimulates the rate of PhyR phosphorylation in vitro and that this effect requires the structured and disordered domains of NepR. This result provides evidence for an additional layer of GSR regulation in which NepR directly influences activation of its binding partner, PhyR, as an anti-anti-σ factor. We conclude that structured and intrinsically disordered domains of NepR coordinately control multiple functions in the GSR signaling pathway, including core protein partner switch interactions and pathway activation by phosphorylation. IMPORTANCE Anti-σ factors are key molecular participants in a range of adaptive responses in bacteria. The anti-σ factor NepR plays a vital role in a multiprotein partner switch that governs general stress response (GSR) transcription in alphaproteobacteria. We have defined conserved and unconserved features of NepR structure that determine its function as an anti-σ factor and uncovered a functional role for intrinsically disordered regions of NepR in partner binding events required for GSR activation. We further demonstrate a novel function for NepR as an enhancer of PhyR phosphorylation; this activity also requires the disordered domains of NepR. Our results provide evidence for a new layer of GSR regulatory control in which NepR directly modulates PhyR phosphorylation and, hence, activation of the GSR.
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Liu, Qiang, Daniela Pinto i Thorsten Mascher. "Characterization of the Widely Distributed Novel ECF42 Group of Extracytoplasmic Function σ Factors inStreptomyces venezuelae". Journal of Bacteriology 200, nr 21 (20.08.2018). http://dx.doi.org/10.1128/jb.00437-18.
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ABSTRACTExtracytoplasmic function σ factors (ECFs) represent the third most abundant fundamental principle of bacterial signal transduction, outranked only by one- and two-component systems. A recent census of ECFs revealed a large number of novel groups whose functions and regulatory mechanisms have not yet been elucidated. Here, we report the characterization of members of the novel group ECF42. ECF42 is a highly abundant and widely distributed ECF group that is present in 11 phyla but is predominantly found inActinobacteria. Analysis of the genomic context conservation did not identify a putative anti-σ factor. Instead, ECF42 genes are cotranscribed with genes encoding a conserved DGPF protein. We have experimentally verified the target promoter of these ECFs (TGTCGA in the −35 region and CGA/TC in the −10 region), which was found upstream of the ECF42-encoding operons inStreptomyces venezuelae, suggesting that ECF42s are positively autoregulated. RNA sequencing (RNA-seq) was performed to define the regulons of the three ECF42 proteins inS. venezuelae, which identified mostly genes encoding DGPF proteins. In contrast to typical ECFs, ECF42 proteins harbor a long C-terminal extension, which is crucial for their activity. Our work provides the first analysis of the function and regulatory mechanism of this novel ECF group that contains a regulatory C-terminal extension.IMPORTANCEIn contrast to the one- and two-component signal transduction systems in bacteria, the importance and diversity of ECFs have only recently been recognized in the course of comprehensive phylogenetic and comparative genomics studies. Thus, most of the ECFs still have not been experimentally characterized regarding their physiological functions and regulation mechanisms so far. The physiological roles, target promoter, and target regulons of a novel group of ECFs, ECF42, inS. venezuelaehave been investigated in this work. More importantly, members of this group are characterized by a C-terminal extension, which has been verified to harbor a regulatory role in ECF42s. Hence, our work provides an important source for further research on such C-terminal extension containing ECFs.
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de Dios, Rubén, Elena Rivas-Marin, Eduardo Santero i Francisca Reyes-Ramírez. "Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA". Scientific Reports 10, nr 1 (20.03.2020). http://dx.doi.org/10.1038/s41598-020-62101-z.
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