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Gallagher KA, Schumacher MA, Bush MJ, Bibb MJ, Chandra G, Holmes NA, Zeng W, Henderson M, Zhang H, Findlay KC, Brennan RG, Buttner MJ. c-di-GMP Arms an Anti-σ to Control Progression of Multicellular Differentiation in Streptomyces. Mol Cell 2020; 77:586-599.e6. [PMID: 31810759 PMCID: PMC7005675 DOI: 10.1016/j.molcel.2019.11.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022]
Abstract
Streptomyces are our primary source of antibiotics, produced concomitantly with the transition from vegetative growth to sporulation in a complex developmental life cycle. We previously showed that the signaling molecule c-di-GMP binds BldD, a master repressor, to control initiation of development. Here we demonstrate that c-di-GMP also intervenes later in development to control differentiation of the reproductive hyphae into spores by arming a novel anti-σ (RsiG) to bind and sequester a sporulation-specific σ factor (σWhiG). We present the structure of the RsiG-(c-di-GMP)2-σWhiG complex, revealing an unusual, partially intercalated c-di-GMP dimer bound at the RsiG-σWhiG interface. RsiG binds c-di-GMP in the absence of σWhiG, employing a novel E(X)3S(X)2R(X)3Q(X)3D motif repeated on each helix of a coiled coil. Further studies demonstrate that c-di-GMP is essential for RsiG to inhibit σWhiG. These findings reveal a newly described control mechanism for σ-anti-σ complex formation and establish c-di-GMP as the central integrator of Streptomyces development.
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Affiliation(s)
- Kelley A. Gallagher
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria A. Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA,Corresponding author
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maureen J. Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Wenjie Zeng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Max Henderson
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hengshan Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Richard G. Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK,Corresponding author
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2
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Structural basis for transcription activation by Crl through tethering of σ S and RNA polymerase. Proc Natl Acad Sci U S A 2019; 116:18923-18927. [PMID: 31484766 DOI: 10.1073/pnas.1910827116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti-σ-factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS-regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σS (σS 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β'-subunit that we call the β'-clamp-toe (β'CT). Deletion of the β'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β'CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS 2 and the β'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.
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3
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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4
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The stress sigma factor of RNA polymerase RpoS/σS is a solvent-exposed open molecule in solution. Biochem J 2018; 475:341-354. [DOI: 10.1042/bcj20170768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 11/17/2022]
Abstract
In bacteria, one primary and multiple alternative sigma (σ) factors associate with the RNA polymerase core enzyme (E) to form holoenzymes (Eσ) with different promoter recognition specificities. The alternative σ factor RpoS/σS is produced in stationary phase and under stress conditions and reprograms global gene expression to promote bacterial survival. To date, the three-dimensional structure of a full-length free σ factor remains elusive. The current model suggests that extensive interdomain contacts in a free σ factor result in a compact conformation that masks the DNA-binding determinants of σ, explaining why a free σ factor does not bind double-stranded promoter DNA efficiently. Here, we explored the solution conformation of σS using amide hydrogen/deuterium exchange coupled with mass spectrometry, NMR, analytical ultracentrifugation and molecular dynamics. Our data strongly argue against a compact conformation of free σS. Instead, we show that σS adopts an open conformation in solution in which the folded σ2 and σ4 domains are interspersed by domains with a high degree of disorder. These findings suggest that E binding induces major changes in both the folding and domain arrangement of σS and provide insights into the possible mechanisms of regulation of σS activity by its chaperone Crl.
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5
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Crystal structure of Aquifex aeolicus σ N bound to promoter DNA and the structure of σ N-holoenzyme. Proc Natl Acad Sci U S A 2017; 114:E1805-E1814. [PMID: 28223493 DOI: 10.1073/pnas.1619464114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σN fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σN that, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σN in blocking transcription activity and in maintaining the activator sensitivity of σN.
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6
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Binding interface between the Salmonella σ(S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl. Sci Rep 2015; 5:13564. [PMID: 26338235 PMCID: PMC4559669 DOI: 10.1038/srep13564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/30/2015] [Indexed: 01/30/2023] Open
Abstract
In many Gram-negative bacteria, including Salmonella enterica serovar Typhimurium (S. Typhimurium), the sigma factor RpoS/σS accumulates during stationary phase of growth, and associates with the core RNA polymerase enzyme (E) to promote transcription initiation of genes involved in general stress resistance and starvation survival. Whereas σ factors are usually inactivated upon interaction with anti-σ proteins, σS binding to the Crl protein increases σS activity by favouring its association to E. Taking advantage of evolution of the σS sequence in bacterial species that do not contain a crl gene, like Pseudomonas aeruginosa, we identified and assigned a critical arginine residue in σS to the S. Typhimurium σS-Crl binding interface. We solved the solution structure of S. Typhimurium Crl by NMR and used it for NMR binding assays with σS and to generate in silico models of the σS-Crl complex constrained by mutational analysis. The σS-Crl models suggest that the identified arginine in σS interacts with an aspartate of Crl that is required for σS binding and is located inside a cavity enclosed by flexible loops, which also contribute to the interface. This study provides the basis for further structural investigation of the σS-Crl complex.
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7
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Feklístov A, Sharon BD, Darst SA, Gross CA. Bacterial sigma factors: a historical, structural, and genomic perspective. Annu Rev Microbiol 2014; 68:357-76. [PMID: 25002089 DOI: 10.1146/annurev-micro-092412-155737] [Citation(s) in RCA: 327] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides of the transcript. Here we recount the key advances in σ biology, from their discovery 45 years ago to the most recent progress in understanding their structure and function at the atomic level. Recent data provide important structural insights into the mechanisms whereby σs initiate promoter opening. We discuss both the housekeeping σs, which govern transcription of the majority of cellular genes, and the alternative σs, which direct RNA polymerase to specialized operons in response to environmental and physiological cues. The review concludes with a genome-scale view of the extracytoplasmic function σs, the most abundant group of alternative σs.
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8
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Xue J, Burz DS, Shekhtman A. Segmental labeling to study multidomain proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:17-33. [PMID: 23076577 DOI: 10.1007/978-94-007-4954-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This chapter contains a review of methodologies and recent applications of segmental labeling for NMR structural studies of proteins and protein complexes. Segmental labeling is used to specifically label a segment of protein structure with NMR active nuclei, thus reducing NMR spectral complexity and greatly facilitating structural NMR studies of large multi-domain proteins. It can also be used to introduce a synthetic fragment into a protein structure to study post-translationally modified proteins. Detailed protocols describing segmental labeling techniques are also included.
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Affiliation(s)
- Jing Xue
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
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9
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DNA-binding properties of the Bacillus subtilis and Aeribacillus pallidus AC6 σ(D) proteins. J Bacteriol 2010; 193:575-9. [PMID: 21097624 DOI: 10.1128/jb.01193-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
σ(D) proteins from Aeribacillus pallidus AC6 and Bacillus subtilis bound specifically, albeit weakly, to promoter DNA even in the absence of core RNA polymerase. Binding required a conserved CG motif within the -10 element, and this motif is known to be recognized by σ region 2.4 and critical for promoter activity.
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10
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Raha P, Chattopadhyay S, Mukherjee S, Chattopadhyay R, Roy K, Roy S. Alternative Sigma Factors in the Free State Are Equilibrium Mixtures of Open and Compact Conformations. Biochemistry 2010; 49:9809-19. [DOI: 10.1021/bi1011173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paromita Raha
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | | | - Srijata Mukherjee
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Ruchira Chattopadhyay
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Koushik Roy
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Siddhartha Roy
- Department of Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
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11
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Identification of conserved amino acid residues of the Salmonella sigmaS chaperone Crl involved in Crl-sigmaS interactions. J Bacteriol 2009; 192:1075-87. [PMID: 20008066 DOI: 10.1128/jb.01197-09] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteins that bind sigma factors typically attenuate the function of the sigma factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor sigma(S) (RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of sigma(S)-dependent genes. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than rpoS. Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the crl gene from Salmonella enterica serovar Typhimurium and complementation of a Deltacrl mutant of Salmonella indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-sigma(S) interaction and that residues 1 to 71 in sigma(S) are dispensable for Crl binding. In Escherichia coli, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses crl transcription. However, the Salmonella Crl and Fur proteins did not interact in the BACTH system. In addition, a fur mutation did not have any significant effect on the expression level of Crl in Salmonella. These results suggest that the relationship between Crl and Fur is different in Salmonella and E. coli.
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12
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Banerjee P, Warf MB, Alexander R. Effect of a domain-spanning disulfide on aminoacyl-tRNA synthetase activity. Biochemistry 2009; 48:10113-9. [PMID: 19772352 DOI: 10.1021/bi9012275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes regulated by allostery undergo conformational rearrangement upon binding effector molecules. For modular proteins, a flexible interface may mediate reorientation of the protein domains and transmit binding events to activate catalysis at a distance. Aminoacyl-tRNA synthetases (aaRSs) that use tRNA anticodons as identity elements can be considered allosteric enzymes in which aminoacylation of the tRNA acceptor stem is enhanced upon anticodon binding. We reasoned that anticodon-triggered conformational change might be restricted upon introduction of a disulfide linkage near the core of an aaRS. Here we show that a double cysteine mutation engineered at the Escherichia coli MetRS domain interface spontaneously generates a disulfide linkage. This disulfide clamp has no effect on methionyl adenylate formation but reduces the level of tRNA(Met) aminoacylation approximately 2-fold. Activity is restored upon chemical reduction of the disulfide, demonstrating that E. coli MetRS requires a flexible interface domain for full catalytic efficiency.
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Affiliation(s)
- Papri Banerjee
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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13
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Koo BM, Rhodius VA, Nonaka G, deHaseth PL, Gross CA. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev 2009; 23:2426-36. [PMID: 19833768 DOI: 10.1101/gad.1843709] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In bacteria, multiple sigmas direct RNA polymerase to distinct sets of promoters. Housekeeping sigmas direct transcription from thousands of promoters, whereas most alternative sigmas are more selective, recognizing more highly conserved promoter motifs. For sigma(32) and sigma(28), two Escherichia coli Group 3 sigmas, altering a few residues in Region 2.3, the portion of sigma implicated in promoter melting, to those universally conserved in housekeeping sigmas relaxed their stringent promoter requirements and significantly enhanced melting of suboptimal promoters. All Group 3 sigmas and the more divergent Group 4 sigmas have nonconserved amino acids at these positions and rarely transcribe >100 promoters. We suggest that the balance of "melting" and "recognition" functions of sigmas is critical to setting the stringency of promoter recognition. Divergent sigmas may generally use a nonoptimal Region 2.3 to increase promoter stringency, enabling them to mount a focused response to altered conditions.
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Affiliation(s)
- Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California 94158, USA
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14
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Koo BM, Rhodius VA, Campbell EA, Gross CA. Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element. Mol Microbiol 2009; 72:830-43. [PMID: 19400790 PMCID: PMC2756079 DOI: 10.1111/j.1365-2958.2009.06691.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sigma28 controls the expression of flagella-related genes and is the most widely distributed alternative sigma factor, present in motile Gram-positive and Gram-negative bacteria. The distinguishing feature of sigma28 promoters is a long -10 region (GCCGATAA). Despite the fact that the upstream GC is highly conserved, previous studies have not indicated a functional role for this motif. Here we examine the functional relevance of the GCCG motif and determine which residues in sigma28 participate in its recognition. We find that the GCCG motif is a functionally important composite element. The upstream GC constitutes an extended -10 motif and is recognized by R91, a residue in Domain 3 of sigma28. The downstream CG is the upstream edge of -10 region of the promoter; two residues in Region 2.4, D81 and R84, participate in its recognition. Consistent with their role in base-specific recognition of the promoter, R91, D81 and D84 are universally conserved in sigma28 orthologues. Sigma28 is the second Group 3 sigma shown to use an extended -10 region in promoter recognition, raising the possibility that other Group 3 sigmas will do so as well.
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Affiliation(s)
- Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Virgil A. Rhodius
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth A. Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Carol A. Gross
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Cell and Tissue biology, University of California at San Francisco, San Francisco, CA 94158, USA
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15
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Schwartz EC, Shekhtman A, Dutta K, Pratt MR, Cowburn D, Darst S, Muir TW. A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. ACTA ACUST UNITED AC 2008; 15:1091-103. [PMID: 18940669 DOI: 10.1016/j.chembiol.2008.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/15/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
The sigma factors are the key regulators of bacterial transcription initiation. Through direct read-out of promoter DNA sequence, they recruit the core RNA polymerase to sites of initiation, thereby dictating the RNA polymerase promoter-specificity. The group 1 sigma factors, which direct the vast majority of transcription initiation during log phase growth and are essential for viability, are autoregulated by an N-terminal sequence known as sigma1.1. We report the solution structure of Thermotoga maritima sigmaA sigma1.1. We additionally demonstrate by using chemical crosslinking strategies that sigma1.1 is in close proximity to the promoter recognition domains of sigmaA. We therefore propose that sigma1.1 autoinhibits promoter DNA binding of free sigmaA by stabilizing a compact organization of the sigma factor domains that is unable to bind DNA.
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Affiliation(s)
- Edmund C Schwartz
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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16
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England P, Westblade LF, Karimova G, Robbe-Saule V, Norel F, Kolb A. Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery. J Biol Chem 2008; 283:33455-64. [PMID: 18818199 PMCID: PMC2586269 DOI: 10.1074/jbc.m807380200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Indexed: 11/06/2022] Open
Abstract
The small regulatory protein Crl binds to sigmaS, the RNA polymerase stationary phase sigma factor. Crl facilitates the formation of the sigmaS-associated holoenzyme (EsigmaS) and thereby activates sigmaS-dependent genes. Using a real time surface plasmon resonance biosensor, we characterized in greater detail the specificity and mode of action of Crl. Crl specifically forms a 1:1 complex with sigmaS, which results in an increase of the association rate of sigmaS to core RNA polymerase without any effect on the dissociation rate of EsigmaS. Crl is also able to associate with preformed EsigmaS with a higher affinity than with sigmaS alone. Furthermore, even at saturating sigmaS concentrations, Crl significantly increases EsigmaS association with the katN promoter and the productive isomerization of the EsigmaS-katN complex, supporting a direct role of Crl in transcription initiation. Finally, we show that Crl does not bind to sigma70 itself but is able at high concentrations to form a weak and transient 1:1 complex with both core RNA polymerase and the sigma70-associated holoenzyme, leaving open the possibility that Crl might also exert a side regulatory role in the transcriptional activity of additional non-sigmaS holoenzymes.
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Affiliation(s)
- Patrick England
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Paris, France.
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17
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Rodriguez F, Arsène-Ploetze F, Rist W, Rüdiger S, Schneider-Mergener J, Mayer MP, Bukau B. Molecular Basis for Regulation of the Heat Shock Transcription Factor σ32 by the DnaK and DnaJ Chaperones. Mol Cell 2008; 32:347-58. [DOI: 10.1016/j.molcel.2008.09.016] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 04/23/2008] [Accepted: 09/26/2008] [Indexed: 10/21/2022]
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18
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Lee SS, Lim J, Cha J, Tan S, Heath JR. Rapid microwave-assisted CNBr cleavage of bead-bound peptides. JOURNAL OF COMBINATORIAL CHEMISTRY 2008; 10:807-9. [PMID: 18811218 PMCID: PMC2720530 DOI: 10.1021/cc800113d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Junhoe Cha
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Sylvia Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - James R. Heath
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
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19
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Mutagenesis of region 4 of sigma 28 from Chlamydia trachomatis defines determinants for protein-protein and protein-DNA interactions. J Bacteriol 2008; 191:651-60. [PMID: 18978051 DOI: 10.1128/jb.01083-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription factor sigma(28) in Chlamydia trachomatis (sigma(28)(Ct)) plays a role in the regulation of genes that are important for late-stage morphological differentiation. In vitro mutational and genetic screening in Salmonella enterica serovar Typhimurium was performed in order to identify mutants with mutations in region 4 of sigma(28)(Ct) that were defective in sigma(28)-specific transcription. Specially, the previously undefined but important interactions between sigma(28)(Ct) region 4 and the flap domain of the RNA polymerase beta subunit (beta-flap) or the -35 element of the chlamydial hctB promoter were examined. Our results indicate that amino acid residues E206, Y214, and E222 of sigma(28)(Ct) contribute to an interaction with the beta-flap when sigma(28)(Ct) associates with the core RNA polymerase. These residues function in contacts with the beta-flap similarly to their counterpart residues in Escherichia coli sigma(70). Conversely, residue Q236 of sigma(28)(Ct) directly binds the chlamydial hctB -35 element. The conserved counterpart residue in E. coli sigma(70) has not been reported to interact with the -35 element of the sigma(70) promoter. Observed functional disparity between sigma(28)(Ct) and sigma(70) region 4 is consistent with their divergent properties in promoter recognition. This work provides new insight into understanding the molecular basis of gene regulation controlled by sigma(28)(Ct) in C. trachomatis.
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20
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Campbell EA, Westblade LF, Darst SA. Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective. Curr Opin Microbiol 2008; 11:121-7. [PMID: 18375176 DOI: 10.1016/j.mib.2008.02.016] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 02/14/2008] [Accepted: 02/21/2008] [Indexed: 12/16/2022]
Abstract
In bacteria, sigma factors are essential for the promoter DNA-binding specificity of RNA polymerase. The sigma factors themselves are regulated by anti-sigma factors that bind and inhibit their cognate sigma factor, and 'appropriators' that deploy a particular sigma-associated RNA polymerase to a specific promoter class. Adding to the complexity is the regulation of anti-sigma factors by both anti-anti-sigma factors, which turn on sigma factor activity, and co-anti-sigma factors that act in concert with their partner anti-sigma factor to inhibit or redirect sigma activity. While sigma factor structure and function are highly conserved, recent results highlight the diversity of structures and mechanisms that bacteria use to regulate sigma factor activity, reflecting the diversity of environmental cues that the bacterial transcription system has evolved to respond.
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Affiliation(s)
- Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Sevostyanova A, Feklistov A, Barinova N, Heyduk E, Bass I, Klimasauskas S, Heyduk T, Kulbachinskiy A. Specific Recognition of the -10 Promoter Element by the Free RNA Polymerase σ Subunit. J Biol Chem 2007; 282:22033-9. [PMID: 17535803 DOI: 10.1074/jbc.m702495200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial RNA polymerase holoenzyme relies on its sigma subunit for promoter recognition and opening. In the holoenzyme, regions 2 and 4 of the sigma subunit are positioned at an optimal distance to allow specific recognition of the -10 and -35 promoter elements, respectively. In free sigma, the promoter binding regions are positioned closer to each other and are masked for interactions with the promoter, with sigma region 1 playing a role in the masking. To analyze the DNA-binding properties of the free sigma, we selected single-stranded DNA aptamers that are specific to primary sigma subunits from several bacterial species, including Escherichia coli and Thermus aquaticus. The aptamers share a consensus motif, TGTAGAAT, that is similar to the extended -10 promoter. We demonstrate that recognition of this motif by sigma region 2 occurs without major structural rearrangements of sigma observed upon the holoenzyme formation and is not inhibited by sigma regions 1 and 4. Thus, the complex process of the -10 element recognition by RNA polymerase holoenzyme can be reduced to a simple system consisting of an isolated sigma subunit and a short aptamer oligonucleotide.
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Affiliation(s)
- Anastasiya Sevostyanova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq, 2, Moscow, Russia
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Barembruch C, Hengge R. Cellular levels and activity of the flagellar sigma factor FliA of Escherichia coli are controlled by FlgM-modulated proteolysis. Mol Microbiol 2007; 65:76-89. [PMID: 17537210 DOI: 10.1111/j.1365-2958.2007.05770.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Escherichia coli the flagellar regulon consists of more than 60 genes organized in three hierarchically and temporally regulated transcriptional classes. The flagellar sigma factor FliA (sigma(28)) is responsible for class 3 expression and, in the early phase of flagellar assembly, is inhibited by its anti-sigma factor FlgM. The flagellar hook basal body forms a type III secretion system capable of secreting both flagellar subunits and FlgM. This results in release and therefore activation of FliA and class 3 expression. Here we demonstrate that FliA is also subject to proteolysis which mainly depends on Lon protease. FlgM not only acts as an anti-sigma factor but also protects FliA from being degraded. Based on quantitative measurements over time upon experimental induction of the flagellar cascade as well as during the growth cycle of a motile strain, we show that FliA proteolysis increases in parallel to class 3 expression, i.e. correlates with FlgM secretion and the phase of highest activity of FliA. Thus, when FlgM is not available due to secretion or mutation, and with RNA polymerase interaction being only transient during the transcription initiation cycle, the proteases can degrade FliA. Experiments with a lon mutant indicate that Lon protease and FliA degradation maintain appropriate FliA : FlgM stoichiometry upon induction of the flagellar system and thereby contribute to timely shut-off of this system.
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Affiliation(s)
- Claudia Barembruch
- Institut für Biologie - Mikrobiologie, Freie Universität Berlin, 14195 Berlin, Germany
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