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Structure of the bacterial RNA polymerase promoter specificity sigma subunit.

Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA
Mol Cell 9 527-39 (2002)
Related entries: 1ku2, 1ku3

Cited: 328 times
EuropePMC logo PMID: 11931761

Abstract

The sigma subunit is the key regulator of bacterial transcription. Proteolysis of Thermus aquaticus sigma(A), which occurred in situ during crystallization, reveals three domains, sigma(2), sigma(3), and sigma(4), connected by flexible linkers. Crystal structures of each domain were determined, as well as of sigma(4) complexed with -35 element DNA. Exposed surfaces of each domain are important for RNA polymerase binding. Universally conserved residues important for -10 element recognition and melting lie on one face of sigma(2), while residues important for extended -10 recognition lie on sigma(3). Genetic studies correctly predicted that a helix-turn-helix motif in sigma(4) recognizes the -35 element but not the details of the protein-DNA interactions. Positive control mutants in sigma(4) cluster in two regions, positioned to interact with activators bound just upstream or downstream of the -35 element.

Reviews - 1ku7 mentioned but not cited (5)

  1. Catabolite activator protein: DNA binding and transcription activation. Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, Ebright RH. Curr Opin Struct Biol 14 10-20 (2004)
  2. Structural biology of bacterial RNA polymerase. Murakami KS. Biomolecules 5 848-864 (2015)
  3. Transcriptional control in the prereplicative phase of T4 development. Hinton DM. Virol J 7 289 (2010)
  4. The Bordetella pertussis model of exquisite gene control by the global transcription factor BvgA. Decker KB, James TD, Stibitz S, Hinton DM. Microbiology (Reading) 158 1665-1676 (2012)
  5. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)

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  1. The structure of a transcription activation subcomplex reveals how σ(70) is recruited to PhoB promoters. Blanco AG, Canals A, Bernués J, Solà M, Coll M. EMBO J 30 3776-3785 (2011)
  2. FpvIR control of fpvA ferric pyoverdine receptor gene expression in Pseudomonas aeruginosa: demonstration of an interaction between FpvI and FpvR and identification of mutations in each compromising this interaction. Rédly GA, Poole K. J Bacteriol 187 5648-5657 (2005)
  3. Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to RPo. Kontur WS, Saecker RM, Davis CA, Capp MW, Record MT. Biochemistry 45 2161-2177 (2006)
  4. Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR. Wickstrum JR, Egan SM. J Bacteriol 186 6277-6285 (2004)
  5. Structural basis of DNA recognition by the alternative sigma-factor, sigma54. Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE. J Mol Biol 369 1070-1078 (2007)
  6. Mutational analysis of sigma70 region 4 needed for appropriation by the bacteriophage T4 transcription factors AsiA and MotA. Baxter K, Lee J, Minakhin L, Severinov K, Hinton DM. J Mol Biol 363 931-944 (2006)
  7. Interactions between the 2.4 and 4.2 regions of sigmaS, the stress-specific sigma factor of Escherichia coli, and the -10 and -35 promoter elements. Checroun C, Bordes P, Leroy O, Kolb A, Gutierrez C. Nucleic Acids Res 32 45-53 (2004)
  8. The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs. Burton SP, Burton ZF. Transcription 5 e967599 (2014)
  9. Phenotypic plasticity as an adaptation to a functional trade-off. Yi X, Dean AM. Elife 5 e19307 (2016)
  10. Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Osmundson J, Montero-Diez C, Westblade LF, Hochschild A, Darst SA. Cell 151 1005-1016 (2012)
  11. Different requirements for σ Region 4 in BvgA activation of the Bordetella pertussis promoters P(fim3) and P(fhaB). Decker KB, Chen Q, Hsieh ML, Boucher P, Stibitz S, Hinton DM. J Mol Biol 409 692-709 (2011)
  12. Surfaces of Spo0A and RNA polymerase sigma factor A that interact at the spoIIG promoter in Bacillus subtilis. Kumar A, Buckner Starke C, DeZalia M, Moran CP. J Bacteriol 186 200-206 (2004)
  13. The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL. Biochemistry 59 4523-4532 (2020)
  14. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Mol Cell 81 2887-2900.e5 (2021)
  15. High performance transcription factor-DNA docking with GPU computing. Wu J, Hong B, Takeda T, Guo JT. Proteome Sci 10 Suppl 1 S17 (2012)
  16. Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region. Couñago RM, Chen NH, Chang CW, Djoko KY, McEwan AG, Kobe B. Nucleic Acids Res 44 6981-6993 (2016)
  17. DNA-binding residues and binding mode prediction with binding-mechanism concerned models. Huang YF, Huang CC, Liu YC, Oyang YJ, Huang CK. BMC Genomics 10 Suppl 3 S23 (2009)
  18. Structural analysis of the recognition of the -35 promoter element by SigW from Bacillus subtilis. Kwon E, Devkota SR, Pathak D, Dahal P, Kim DY. PLoS One 14 e0221666 (2019)
  19. Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties. Wang CC, Chen CY. Proteome Sci 9 Suppl 1 S11 (2011)
  20. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Fernandez-Lopez R, Ruiz R, Del Campo I, Gonzalez-Montes L, Boer DR, de la Cruz F, Moncalian G. Nucleic Acids Res 50 11938-11947 (2022)


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  1. Multiple sigma subunits and the partitioning of bacterial transcription space. Gruber TM, Gross CA. Annu Rev Microbiol 57 441-466 (2003)
  2. The regulation of bacterial transcription initiation. Browning DF, Busby SJ. Nat Rev Microbiol 2 57-65 (2004)
  3. The many faces of the helix-turn-helix domain: transcription regulation and beyond. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. FEMS Microbiol Rev 29 231-262 (2005)
  4. Bacterial RNA polymerases: the wholo story. Murakami KS, Darst SA. Curr Opin Struct Biol 13 31-39 (2003)
  5. The sigma70 family of sigma factors. Paget MS, Helmann JD. Genome Biol 4 203 (2003)
  6. Bacterial sigma factors: a historical, structural, and genomic perspective. Feklístov A, Sharon BD, Darst SA, Gross CA. Annu Rev Microbiol 68 357-376 (2014)
  7. Evolution of multisubunit RNA polymerases in the three domains of life. Werner F, Grohmann D. Nat Rev Microbiol 9 85-98 (2011)
  8. Local and global regulation of transcription initiation in bacteria. Browning DF, Busby SJ. Nat Rev Microbiol 14 638-650 (2016)
  9. rRNA transcription in Escherichia coli. Paul BJ, Ross W, Gaal T, Gourse RL. Annu Rev Genet 38 749-770 (2004)
  10. Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Haugen SP, Ross W, Gourse RL. Nat Rev Microbiol 6 507-519 (2008)
  11. The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. Bush M, Dixon R. Microbiol Mol Biol Rev 76 497-529 (2012)
  12. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Paget MS. Biomolecules 5 1245-1265 (2015)
  13. Regulation of alternative sigma factor use. Österberg S, del Peso-Santos T, Shingler V. Annu Rev Microbiol 65 37-55 (2011)
  14. Sigma and RNA polymerase: an on-again, off-again relationship? Mooney RA, Darst SA, Landick R. Mol Cell 20 335-345 (2005)
  15. The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase. Typas A, Becker G, Hengge R. Mol Microbiol 63 1296-1306 (2007)
  16. Initial events in bacterial transcription initiation. Ruff EF, Record MT, Artsimovitch I. Biomolecules 5 1035-1062 (2015)
  17. The sigma factors of Mycobacterium tuberculosis: regulation of the regulators. Sachdeva P, Misra R, Tyagi AK, Singh Y. FEBS J 277 605-626 (2010)
  18. Cell-surface signaling in Pseudomonas: stress responses, iron transport, and pathogenicity. Llamas MA, Imperi F, Visca P, Lamont IL. FEMS Microbiol Rev 38 569-597 (2014)
  19. Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective. Campbell EA, Westblade LF, Darst SA. Curr Opin Microbiol 11 121-127 (2008)
  20. Control of the alternative sigma factor sigmaE in Escherichia coli. Ades SE. Curr Opin Microbiol 7 157-162 (2004)
  21. Region 4 of sigma as a target for transcription regulation. Dove SL, Darst SA, Hochschild A. Mol Microbiol 48 863-874 (2003)
  22. RNA polymerase holoenzyme: structure, function and biological implications. Borukhov S, Nudler E. Curr Opin Microbiol 6 93-100 (2003)
  23. RNA polymerase: the vehicle of transcription. Borukhov S, Nudler E. Trends Microbiol 16 126-134 (2008)
  24. Views of transcription initiation. Young BA, Gruber TM, Gross CA. Cell 109 417-420 (2002)
  25. Transcription regulation at the core: similarities among bacterial, archaeal, and eukaryotic RNA polymerases. Decker KB, Hinton DM. Annu Rev Microbiol 67 113-139 (2013)
  26. Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology. Bervoets I, Charlier D. FEMS Microbiol Rev 43 304-339 (2019)
  27. Signaling mechanisms for activation of extracytoplasmic function (ECF) sigma factors. Brooks BE, Buchanan SK. Biochim Biophys Acta 1778 1930-1945 (2008)
  28. Control of rRNA expression in Escherichia coli. Schneider DA, Ross W, Gourse RL. Curr Opin Microbiol 6 151-156 (2003)
  29. The sigmaS subunit of RNA polymerase as a signal integrator and network master regulator in the general stress response in Escherichia coli. Klauck E, Typas A, Hengge R. Sci Prog 90 103-127 (2007)
  30. Mechanisms for activating bacterial RNA polymerase. Ghosh T, Bose D, Zhang X. FEMS Microbiol Rev 34 611-627 (2010)
  31. Bacteriophage-induced modifications of host RNA polymerase. Nechaev S, Severinov K. Annu Rev Microbiol 57 301-322 (2003)
  32. Plant sigma factors and their role in plastid transcription. Lysenko EA. Plant Cell Rep 26 845-859 (2007)
  33. The complex architecture of mycobacterial promoters. Newton-Foot M, Gey van Pittius NC. Tuberculosis (Edinb) 93 60-74 (2013)
  34. Diverse and unified mechanisms of transcription initiation in bacteria. Chen J, Boyaci H, Campbell EA. Nat Rev Microbiol 19 95-109 (2021)
  35. Role of the RNA polymerase sigma subunit in transcription initiation. Borukhov S, Severinov K. Res Microbiol 153 557-562 (2002)
  36. Engineering of transcriptional regulators enhances microbial stress tolerance. Lin Z, Zhang Y, Wang J. Biotechnol Adv 31 986-991 (2013)
  37. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. Mazumder A, Kapanidis AN. J Mol Biol 431 3947-3959 (2019)
  38. The essential activities of the bacterial sigma factor. Davis MC, Kesthely CA, Franklin EA, MacLellan SR. Can J Microbiol 63 89-99 (2017)
  39. Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action. Lee J, Borukhov S. Front Mol Biosci 3 73 (2016)
  40. RNA polymerase: in search of promoters. Feklistov A. Ann N Y Acad Sci 1293 25-32 (2013)
  41. The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. Jensen D, Galburt EA. J Bacteriol 203 e00512-20 (2021)
  42. RNA polymerase structure and function at lac operon. Borukhov S, Lee J. C R Biol 328 576-587 (2005)
  43. Base flipping in open complex formation at bacterial promoters. Karpen ME, deHaseth PL. Biomolecules 5 668-678 (2015)
  44. DNA bending and looping in the transcriptional control of bacteriophage phi29. Camacho A, Salas M. FEMS Microbiol Rev 34 828-841 (2010)
  45. Bacterial MerR family transcription regulators: activationby distortion. Fang C, Zhang Y. Acta Biochim Biophys Sin (Shanghai) 54 25-36 (2022)
  46. Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses. de Dios R, Santero E, Reyes-Ramírez F. Int J Mol Sci 22 3900 (2021)
  47. Transcription regulation by bacteriophage T4 AsiA. Minakhin L, Severinov K. Protein Expr Purif 41 1-8 (2005)
  48. Shedding light on a Group IV (ECF11) alternative σ factor. Donohue TJ. Mol Microbiol 112 374-384 (2019)
  49. σ70 and PhoB activator: getting a better grip. Canals A, Blanco AG, Coll M. Transcription 3 160-164 (2012)
  50. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Wood DM, Dobson RCJ, Horne CR. Biochem Soc Trans 49 2711-2726 (2021)

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  1. Conserved and variable functions of the sigmaE stress response in related genomes. Rhodius VA, Suh WC, Nonaka G, West J, Gross CA. PLoS Biol 4 e2 (2006)
  2. Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Liu Y, Zhou J, Omelchenko MV, Beliaev AS, Venkateswaran A, Stair J, Wu L, Thompson DK, Xu D, Rogozin IB, Gaidamakova EK, Zhai M, Makarova KS, Koonin EV, Daly MJ. Proc Natl Acad Sci U S A 100 4191-4196 (2003)
  3. Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit. Feklistov A, Darst SA. Cell 147 1257-1269 (2011)
  4. Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. Saecker RM, Record MT, Dehaseth PL. J Mol Biol 412 754-771 (2011)
  5. Elicitation of structure-specific antibodies by epitope scaffolds. Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, Wyatt R, Kwong PD. Proc Natl Acad Sci U S A 107 17880-17887 (2010)
  6. Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Campbell EA, Tupy JL, Gruber TM, Wang S, Sharp MM, Gross CA, Darst SA. Mol Cell 11 1067-1078 (2003)
  7. Crystal structures of the E. coli transcription initiation complexes with a complete bubble. Zuo Y, Steitz TA. Mol Cell 58 534-540 (2015)
  8. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Opalka N, Chlenov M, Chacon P, Rice WJ, Wriggers W, Darst SA. Cell 114 335-345 (2003)
  9. Structural basis of replication origin recognition by the DnaA protein. Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S. Nucleic Acids Res 31 2077-2086 (2003)
  10. Anatomy of Escherichia coli sigma70 promoters. Shultzaberger RK, Chen Z, Lewis KA, Schneider TD. Nucleic Acids Res 35 771-788 (2007)
  11. In situ proteolysis for protein crystallization and structure determination. Dong A, Xu X, Edwards AM, Midwest Center for Structural Genomics, Structural Genomics Consortium, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H. Nat Methods 4 1019-1021 (2007)
  12. X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme. Murakami KS. J Biol Chem 288 9126-9134 (2013)
  13. A chaperone network controls the heat shock response in E. coli. Guisbert E, Herman C, Lu CZ, Gross CA. Genes Dev 18 2812-2821 (2004)
  14. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Elife 4 (2015)
  15. Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Bae B, Davis E, Brown D, Campbell EA, Wigneshweraraj S, Darst SA. Proc Natl Acad Sci U S A 110 19772-19777 (2013)
  16. Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernández-Tornero C, Kulbachinskiy A, Murakami KS. J Biol Chem 289 24549-24559 (2014)
  17. A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria. Campbell EA, Greenwell R, Anthony JR, Wang S, Lim L, Das K, Sofia HJ, Donohue TJ, Darst SA. Mol Cell 27 793-805 (2007)
  18. The structural basis for promoter -35 element recognition by the group IV sigma factors. Lane WJ, Darst SA. PLoS Biol 4 e269 (2006)
  19. Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk. Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S. PLoS Pathog 11 e1004744 (2015)
  20. Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation. Sorenson MK, Ray SS, Darst SA. Mol Cell 14 127-138 (2004)
  21. TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Philips SJ, Canalizo-Hernandez M, Yildirim I, Schatz GC, Mondragón A, O'Halloran TV. Science 349 877-881 (2015)
  22. Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Camarero JA, Shekhtman A, Campbell EA, Chlenov M, Gruber TM, Bryant DA, Darst SA, Cowburn D, Muir TW. Proc Natl Acad Sci U S A 99 8536-8541 (2002)
  23. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. Hubin EA, Fay A, Xu C, Bean JM, Saecker RM, Glickman MS, Darst SA, Campbell EA. Elife 6 e22520 (2017)
  24. Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters. Hook-Barnard IG, Hinton DM. Gene Regul Syst Bio 1 275-293 (2007)
  25. Structure of a ternary transcription activation complex. Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. Mol Cell 13 45-53 (2004)
  26. Structure and function of CarD, an essential mycobacterial transcription factor. Srivastava DB, Leon K, Osmundson J, Garner AL, Weiss LA, Westblade LF, Glickman MS, Landick R, Darst SA, Stallings CL, Campbell EA. Proc Natl Acad Sci U S A 110 12619-12624 (2013)
  27. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Chung WH, Craighead JL, Chang WH, Ezeokonkwo C, Bareket-Samish A, Kornberg RD, Asturias FJ. Mol Cell 12 1003-1013 (2003)
  28. Analysis of promoter elements involved in the transcriptional initiation of RpoS-dependent Borrelia burgdorferi genes. Eggers CH, Caimano MJ, Radolf JD. J Bacteriol 186 7390-7402 (2004)
  29. Mitochondrial transcription is regulated via an ATP "sensing" mechanism that couples RNA abundance to respiration. Amiott EA, Jaehning JA. Mol Cell 22 329-338 (2006)
  30. T4 AsiA blocks DNA recognition by remodeling sigma70 region 4. Lambert LJ, Wei Y, Schirf V, Demeler B, Werner MH. EMBO J 23 2952-2962 (2004)
  31. The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. Shimada T, Yamazaki Y, Tanaka K, Ishihama A. PLoS One 9 e90447 (2014)
  32. Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambdacI. Nickels BE, Dove SL, Murakami KS, Darst SA, Hochschild A. J Mol Biol 324 17-34 (2002)
  33. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Cavanagh AT, Klocko AD, Liu X, Wassarman KM. Mol Microbiol 67 1242-1256 (2008)
  34. Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Tsuchiya Y, Kinoshita K, Nakamura H. Proteins 55 885-894 (2004)
  35. Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Sclavi B, Zaychikov E, Rogozina A, Walther F, Buckle M, Heumann H. Proc Natl Acad Sci U S A 102 4706-4711 (2005)
  36. An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Ross W, Schneider DA, Paul BJ, Mertens A, Gourse RL. Genes Dev 17 1293-1307 (2003)
  37. Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX. Stüdemann A, Noirclerc-Savoye M, Klauck E, Becker G, Schneider D, Hengge R. EMBO J 22 4111-4120 (2003)
  38. Stepwise Promoter Melting by Bacterial RNA Polymerase. Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA. Mol Cell 78 275-288.e6 (2020)
  39. Structural basis for -10 promoter element melting by environmentally induced sigma factors. Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH. Nat Struct Mol Biol 21 269-276 (2014)
  40. Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival. Wu Q, Pei J, Turse C, Ficht TA. BMC Microbiol 6 102 (2006)
  41. RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. Jeronimo C, Langelier MF, Zeghouf M, Cojocaru M, Bergeron D, Baali D, Forget D, Mnaimneh S, Davierwala AP, Pootoolal J, Chandy M, Canadien V, Beattie BK, Richards DP, Workman JL, Hughes TR, Greenblatt J, Coulombe B. Mol Cell Biol 24 7043-7058 (2004)
  42. Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription. Chen H, Tang H, Ebright RH. Mol Cell 11 1621-1633 (2003)
  43. Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase. Lerner E, Chung S, Allen BL, Wang S, Lee J, Lu SW, Grimaud LW, Ingargiola A, Michalet X, Alhadid Y, Borukhov S, Strick TR, Taatjes DJ, Weiss S. Proc Natl Acad Sci U S A 113 E6562-E6571 (2016)
  44. DNA gyrase genes in Mycobacterium tuberculosis: a single operon driven by multiple promoters. Unniraman S, Chatterji M, Nagaraja V. J Bacteriol 184 5449-5456 (2002)
  45. Interactions between the Rhodobacter sphaeroides ECF sigma factor, sigma(E), and its anti-sigma factor, ChrR. Anthony JR, Newman JD, Donohue TJ. J Mol Biol 341 345-360 (2004)
  46. Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Davis E, Chen J, Leon K, Darst SA, Campbell EA. Nucleic Acids Res 43 433-445 (2015)
  47. Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli. Typas A, Hengge R. Mol Microbiol 59 1037-1051 (2006)
  48. Photo-cross-linking of a purified preinitiation complex reveals central roles for the RNA polymerase II mobile clamp and TFIIE in initiation mechanisms. Forget D, Langelier MF, Thérien C, Trinh V, Coulombe B. Mol Cell Biol 24 1122-1131 (2004)
  49. Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Klein-Marcuschamer D, Stephanopoulos G. Proc Natl Acad Sci U S A 105 2319-2324 (2008)
  50. Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4. Patikoglou GA, Westblade LF, Campbell EA, Lamour V, Lane WJ, Darst SA. J Mol Biol 372 649-659 (2007)
  51. Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region. Singh SS, Typas A, Hengge R, Grainger DC. Nucleic Acids Res 39 5109-5118 (2011)
  52. The bacteriophage T4 transcription activator MotA interacts with the far-C-terminal region of the sigma70 subunit of Escherichia coli RNA polymerase. Pande S, Makela A, Dove SL, Nickels BE, Hochschild A, Hinton DM. J Bacteriol 184 3957-3964 (2002)
  53. YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity. Kim KS, Manasherob R, Cohen SN. Genes Dev 22 3497-3508 (2008)
  54. A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Schwartz EC, Shekhtman A, Dutta K, Pratt MR, Cowburn D, Darst S, Muir TW. Chem Biol 15 1091-1103 (2008)
  55. Identification and structure of the anti-sigma factor-binding domain of the disulphide-stress regulated sigma factor sigma(R) from Streptomyces coelicolor. Li W, Stevenson CE, Burton N, Jakimowicz P, Paget MS, Buttner MJ, Lawson DM, Kleanthous C. J Mol Biol 323 225-236 (2002)
  56. Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, Brodolin K. EMBO J 26 955-964 (2007)
  57. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Davis CA, Capp MW, Record MT, Saecker RM. Proc Natl Acad Sci U S A 102 285-290 (2005)
  58. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. Gregory BD, Nickels BE, Garrity SJ, Severinova E, Minakhin L, Urbauer RJ, Urbauer JL, Heyduk T, Severinov K, Hochschild A. Proc Natl Acad Sci U S A 101 4554-4559 (2004)
  59. An unusual primary sigma factor in the Bacteroidetes phylum. Vingadassalom D, Kolb A, Mayer C, Rybkine T, Collatz E, Podglajen I. Mol Microbiol 56 888-902 (2005)
  60. Structural basis for sigma factor mimicry in the general stress response of Alphaproteobacteria. Campagne S, Damberger FF, Kaczmarczyk A, Francez-Charlot A, Allain FH, Vorholt JA. Proc Natl Acad Sci U S A 109 E1405-14 (2012)
  61. Crosslink Mapping at Amino Acid-Base Resolution Reveals the Path of Scrunched DNA in Initial Transcribing Complexes. Winkelman JT, Winkelman BT, Boyce J, Maloney MF, Chen AY, Ross W, Gourse RL. Mol Cell 59 768-780 (2015)
  62. Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR. Chang CC, Lin LY, Zou XW, Huang CC, Chan NL. Nucleic Acids Res 43 7612-7623 (2015)
  63. The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase. Hook-Barnard IG, Hinton DM. Proc Natl Acad Sci U S A 106 737-742 (2009)
  64. Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase. Gleghorn ML, Davydova EK, Rothman-Denes LB, Murakami KS. Mol Cell 32 707-717 (2008)
  65. The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase. Tabib-Salazar A, Liu B, Doughty P, Lewis RA, Ghosh S, Parsy ML, Simpson PJ, O'Dwyer K, Matthews SJ, Paget MS. Nucleic Acids Res 41 5679-5691 (2013)
  66. AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact of cpCK2 phosphorylation. Schweer J, Türkeri H, Link B, Link G. Plant J 62 192-202 (2010)
  67. CorE from Myxococcus xanthus is a copper-dependent RNA polymerase sigma factor. Gómez-Santos N, Pérez J, Sánchez-Sutil MC, Moraleda-Muñoz A, Muñoz-Dorado J. PLoS Genet 7 e1002106 (2011)
  68. Structural basis for transcription initiation by bacterial ECF σ factors. Li L, Fang C, Zhuang N, Wang T, Zhang Y. Nat Commun 10 1153 (2019)
  69. Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA. Hubin EA, Tabib-Salazar A, Humphrey LJ, Flack JE, Olinares PD, Darst SA, Campbell EA, Paget MS. Proc Natl Acad Sci U S A 112 7171-7176 (2015)
  70. 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Klocko AD, Wassarman KM. Mol Microbiol 73 152-164 (2009)
  71. Novel architectural features of Bordetella pertussis fimbrial subunit promoters and their activation by the global virulence regulator BvgA. Chen Q, Decker KB, Boucher PE, Hinton D, Stibitz S. Mol Microbiol 77 1326-1340 (2010)
  72. Crystal structure of bacteriophage lambda cII and its DNA complex. Jain D, Kim Y, Maxwell KL, Beasley S, Zhang R, Gussin GN, Edwards AM, Darst SA. Mol Cell 19 259-269 (2005)
  73. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Hubin EA, Lilic M, Darst SA, Campbell EA. Nat Commun 8 16072 (2017)
  74. Substitutions in the Escherichia coli RNA polymerase sigma70 factor that affect recognition of extended -10 elements at promoters. Sanderson A, Mitchell JE, Minchin SD, Busby SJ. FEBS Lett 544 199-205 (2003)
  75. The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants. Thouvenot B, Charpentier B, Branlant C. Biochem J 383 371-382 (2004)
  76. Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. Irla M, Neshat A, Brautaset T, Rückert C, Kalinowski J, Wendisch VF. BMC Genomics 16 73 (2015)
  77. CueR activates transcription through a DNA distortion mechanism. Fang C, Philips SJ, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y, O'Halloran TV, Zhang Y. Nat Chem Biol 17 57-64 (2021)
  78. Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites. Typas A, Hengge R. Mol Microbiol 55 250-260 (2005)
  79. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Nat Commun 10 4828 (2019)
  80. Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element. Koo BM, Rhodius VA, Campbell EA, Gross CA. Mol Microbiol 72 815-829 (2009)
  81. Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli. Urtecho G, Tripp AD, Insigne KD, Kim H, Kosuri S. Biochemistry 58 1539-1551 (2019)
  82. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. Pineda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A, Miller ES, Hinton DM. J Mol Biol 344 1183-1197 (2004)
  83. AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. Yao J, Roy-Chowdhury S, Allison LA. Plant Physiol 132 739-747 (2003)
  84. RNA polymerase can track a DNA groove during promoter search. Sakata-Sogawa K, Shimamoto N. Proc Natl Acad Sci U S A 101 14731-14735 (2004)
  85. Redefining Escherichia coli σ(70) promoter elements: -15 motif as a complement of the -10 motif. Djordjevic M. J Bacteriol 193 6305-6314 (2011)
  86. The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species. Bleibtreu A, Clermont O, Darlu P, Glodt J, Branger C, Picard B, Denamur E. J Bacteriol 196 4276-4284 (2014)
  87. Interaction of Escherichia coli RNA polymerase σ70 subunit with promoter elements in the context of free σ70, RNA polymerase holoenzyme, and the β'-σ70 complex. Mekler V, Pavlova O, Severinov K. J Biol Chem 286 270-279 (2011)
  88. Structural and biochemical bases for the redox sensitivity of Mycobacterium tuberculosis RslA. Thakur KG, Praveena T, Gopal B. J Mol Biol 397 1199-1208 (2010)
  89. Studies of the Escherichia coli Rsd-sigma70 complex. Westblade LF, Ilag LL, Powell AK, Kolb A, Robinson CV, Busby SJ. J Mol Biol 335 685-692 (2004)
  90. The quorum-sensing transcription factor TraR decodes its DNA binding site by direct contacts with DNA bases and by detection of DNA flexibility. White CE, Winans SC. Mol Microbiol 64 245-256 (2007)
  91. General stress sigma factor RpoS influences time required to enter the viable but non-culturable state in Salmonella enterica. Kusumoto A, Asakura H, Kawamoto K. Microbiol Immunol 56 228-237 (2012)
  92. Structural basis of Q-dependent transcription antitermination. Shi J, Gao X, Tian T, Yu Z, Gao B, Wen A, You L, Chang S, Zhang X, Zhang Y, Feng Y. Nat Commun 10 2925 (2019)
  93. X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins. Molodtsov V, Nawarathne IN, Scharf NT, Kirchhoff PD, Showalter HD, Garcia GA, Murakami KS. J Med Chem 56 4758-4763 (2013)
  94. Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system. Aguilar C, Escalante A, Flores N, de Anda R, Riveros-McKay F, Gosset G, Morett E, Bolívar F. BMC Genomics 13 385 (2012)
  95. Insights from the architecture of the bacterial transcription apparatus. Iyer LM, Aravind L. J Struct Biol 179 299-319 (2012)
  96. Natural human isolates of Staphylococcus aureus selected for high production of proteases and alpha-hemolysin are sigmaB deficient. Karlsson-Kanth A, Tegmark-Wisell K, Arvidson S, Oscarsson J. Int J Med Microbiol 296 229-236 (2006)
  97. An extracytoplasmic function sigma factor controls beta-lactamase gene expression in Bacillus anthracis and other Bacillus cereus group species. Ross CL, Thomason KS, Koehler TM. J Bacteriol 191 6683-6693 (2009)
  98. Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. Onda Y, Yagi Y, Saito Y, Takenaka N, Toyoshima Y. Plant J 55 968-978 (2008)
  99. Mode of action of the TyrR protein: repression and activation of the tyrP promoter of Escherichia coli. Yang J, Hwang JS, Camakaris H, Irawaty W, Ishihama A, Pittard J. Mol Microbiol 52 243-256 (2004)
  100. 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. Koo BM, Rhodius VA, Campbell EA, Gross CA. Mol Microbiol 72 830-843 (2009)
  101. Systematic prediction of control proteins and their DNA binding sites. Sorokin V, Severinov K, Gelfand MS. Nucleic Acids Res 37 441-451 (2009)
  102. Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif. Hook-Barnard I, Johnson XB, Hinton DM. J Bacteriol 188 8352-8359 (2006)
  103. Mitochondrial transcription factor Mtf1 traps the unwound non-template strand to facilitate open complex formation. Paratkar S, Patel SS. J Biol Chem 285 3949-3956 (2010)
  104. Phylogenetic and functional features of the plastid transcription kinase cpCK2 from Arabidopsis signify a role of cysteinyl SH-groups in regulatory phosphorylation of plastid sigma factors. Türkeri H, Schweer J, Link G. FEBS J 279 395-409 (2012)
  105. The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Nechaev S, Kamali-Moghaddam M, André E, Léonetti JP, Geiduschek EP. Proc Natl Acad Sci U S A 101 17365-17370 (2004)
  106. The crystal structure of the anti-σ factor CnrY in complex with the σ factor CnrH shows a new structural class of anti-σ factors targeting extracytoplasmic function σ factors. Maillard AP, Girard E, Ziani W, Petit-Härtlein I, Kahn R, Covès J. J Mol Biol 426 2313-2327 (2014)
  107. Analysis of promoters recognized by HrpL, an alternative sigma-factor protein from Pantoea agglomerans pv. gypsophilae. Nissan G, Manulis S, Weinthal DM, Sessa G, Barash I. Mol Plant Microbe Interact 18 634-643 (2005)
  108. Mutational analysis of an extracytoplasmic-function sigma factor to investigate its interactions with RNA polymerase and DNA. Wilson MJ, Lamont IL. J Bacteriol 188 1935-1942 (2006)
  109. Analysis of regions within the bacteriophage T4 AsiA protein involved in its binding to the sigma70 subunit of E. coli RNA polymerase and its role as a transcriptional inhibitor and co-activator. Pal D, Vuthoori M, Pande S, Wheeler D, Hinton DM. J Mol Biol 325 827-841 (2003)
  110. The Rhizobium etli sigma70 (SigA) factor recognizes a lax consensus promoter. Ramírez-Romero MA, Masulis I, Cevallos MA, González V, Dávila G. Nucleic Acids Res 34 1470-1480 (2006)
  111. A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription. Bonocora RP, Caignan G, Woodrell C, Werner MH, Hinton DM. Mol Microbiol 69 331-343 (2008)
  112. The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription. Fang C, Li L, Zhao Y, Wu X, Philips SJ, You L, Zhong M, Shi X, O'Halloran TV, Li Q, Zhang Y. Nat Commun 11 6284 (2020)
  113. Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with its DNA target site and with domain 4 of the RNA polymerase sigma subunit. Grainger DC, Webster CL, Belyaeva TA, Hyde EI, Busby SJ. Mol Microbiol 51 1297-1309 (2004)
  114. Dual promoters control expression of the Bacillus anthracis virulence factor AtxA. Bongiorni C, Fukushima T, Wilson AC, Chiang C, Mansilla MC, Hoch JA, Perego M. J Bacteriol 190 6483-6492 (2008)
  115. Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS). Rosenthal AZ, Hu M, Gralla JD. Mol Microbiol 59 1052-1061 (2006)
  116. Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery. England P, Westblade LF, Karimova G, Robbe-Saule V, Norel F, Kolb A. J Biol Chem 283 33455-33464 (2008)
  117. Binding sites of VanRB and sigma70 RNA polymerase in the vanB vancomycin resistance operon of Enterococcus faecium BM4524. Depardieu F, Courvalin P, Kolb A. Mol Microbiol 57 550-564 (2005)
  118. Involvement of region 4 of the sigma70 subunit of RNA polymerase in transcriptional activation of the lux operon during quorum sensing. Johnson DC, Ishihama A, Stevens AM. FEMS Microbiol Lett 228 193-201 (2003)
  119. Structural basis for the redox sensitivity of the Mycobacterium tuberculosis SigK-RskA σ-anti-σ complex. Shukla J, Gupta R, Thakur KG, Gokhale R, Gopal B. Acta Crystallogr D Biol Crystallogr 70 1026-1036 (2014)
  120. The -11A of promoter DNA and two conserved amino acids in the melting region of sigma70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact. Schroeder LA, Choi AJ, DeHaseth PL. Nucleic Acids Res 35 4141-4153 (2007)
  121. An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo. Gregory BD, Nickels BE, Darst SA, Hochschild A. Mol Microbiol 56 1208-1219 (2005)
  122. Interaction of T4 AsiA with its target sites in the RNA polymerase sigma70 subunit leads to distinct and opposite effects on transcription. Minakhin L, Niedziela-Majka A, Kuznedelov K, Adelman K, Urbauer JL, Heyduk T, Severinov K. J Mol Biol 326 679-690 (2003)
  123. Multispot single-molecule FRET: High-throughput analysis of freely diffusing molecules. Ingargiola A, Lerner E, Chung S, Panzeri F, Gulinatti A, Rech I, Ghioni M, Weiss S, Michalet X. PLoS One 12 e0175766 (2017)
  124. Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(C) from Mycobacterium tuberculosis. Thakur KG, Joshi AM, Gopal B. J Biol Chem 282 4711-4718 (2007)
  125. Structural basis for promoter specificity switching of RNA polymerase by a phage factor. Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S. Genes Dev 28 521-531 (2014)
  126. The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure. Nasim MT, Eperon IC, Wilkins BM, Brammar WJ. Mol Microbiol 53 405-417 (2004)
  127. The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase. Yuan AH, Nickels BE, Hochschild A. Proc Natl Acad Sci U S A 106 6597-6602 (2009)
  128. Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition. Kourennaia OV, Tsujikawa L, Dehaseth PL. J Bacteriol 187 6762-6769 (2005)
  129. Structure of the RNA polymerase core-binding domain of sigma(54) reveals a likely conformational fracture point. Hong E, Doucleff M, Wemmer DE. J Mol Biol 390 70-82 (2009)
  130. Disulfide cross-linking indicates that FlgM-bound and free sigma28 adopt similar conformations. Sorenson MK, Darst SA. Proc Natl Acad Sci U S A 103 16722-16727 (2006)
  131. In vitro properties of RpoS (sigma(S)) mutants of Escherichia coli with postulated N-terminal subregion 1.1 or C-terminal region 4 deleted. Gowrishankar J, Yamamoto K, Subbarayan PR, Ishihama A. J Bacteriol 185 2673-2679 (2003)
  132. The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes. Ni L, Jensen SO, Ky Tonthat N, Berg T, Kwong SM, Guan FH, Brown MH, Skurray RA, Firth N, Schumacher MA. Nucleic Acids Res 37 6970-6983 (2009)
  133. Sigma factors in a thousand E. coli genomes. Cook H, Ussery DW. Environ Microbiol 15 3121-3129 (2013)
  134. Structural basis of transcriptional activation by the Mycobacterium tuberculosis intrinsic antibiotic-resistance transcription factor WhiB7. Lilic M, Darst SA, Campbell EA. Mol Cell 81 2875-2886.e5 (2021)
  135. Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW. Devkota SR, Kwon E, Ha SC, Chang HW, Kim DY. PLoS One 12 e0174284 (2017)
  136. Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B. Nat Commun 12 2702 (2021)
  137. Substrate requirements for regulated intramembrane proteolysis of Bacillus subtilis pro-sigmaK. Prince H, Zhou R, Kroos L. J Bacteriol 187 961-971 (2005)
  138. A mutation in the yeast mitochondrial core RNA polymerase, Rpo41, confers defects in both specificity factor interaction and promoter utilization. Matsunaga M, Jaehning JA. J Biol Chem 279 2012-2019 (2004)
  139. Crl binds to domain 2 of σ(S) and confers a competitive advantage on a natural rpoS mutant of Salmonella enterica serovar Typhi. Monteil V, Kolb A, Mayer C, Hoos S, England P, Norel F. J Bacteriol 192 6401-6410 (2010)
  140. Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1. Wang Y, Sima L, Lv J, Huang S, Liu Y, Wang J, Krupovic M, Chen X. J Bacteriol 198 1952-1964 (2016)
  141. Structural basis of bacterial σ28 -mediated transcription reveals roles of the RNA polymerase zinc-binding domain. Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B. EMBO J 39 e104389 (2020)
  142. Structure-function studies of Escherichia coli RpoH (sigma32) by in vitro linker insertion mutagenesis. Narberhaus F, Balsiger S. J Bacteriol 185 2731-2738 (2003)
  143. Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile. Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA. Nature 604 541-545 (2022)
  144. Competence for genetic transformation in Streptococcus pneumoniae: mutations in σA bypass the comW requirement. Tovpeko Y, Morrison DA. J Bacteriol 196 3724-3734 (2014)
  145. Crystal structure of the bacteriophage T4 late-transcription coactivator gp33 with the β-subunit flap domain of Escherichia coli RNA polymerase. Twist KA, Campbell EA, Deighan P, Nechaev S, Jain V, Geiduschek EP, Hochschild A, Darst SA. Proc Natl Acad Sci U S A 108 19961-19966 (2011)
  146. The cross-species prediction of bacterial promoters using a support vector machine. Towsey M, Timms P, Hogan J, Mathews SA. Comput Biol Chem 32 359-366 (2008)
  147. Construction of Escherichia coli-Arthrobacter-Rhodococcus shuttle vectors based on a cryptic plasmid from Arthrobacter rhombi and investigation of their application for functional screening. Stanislauskiene R, Gasparaviciute R, Vaitekunas J, Meskiene R, Rutkiene R, Casaite V, Meskys R. FEMS Microbiol Lett 327 78-86 (2012)
  148. ExsA recruits RNA polymerase to an extended -10 promoter by contacting region 4.2 of sigma-70. Vakulskas CA, Brutinel ED, Yahr TL. J Bacteriol 192 3597-3607 (2010)
  149. Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases. Raindlová V, Janoušková M, Slavíčková M, Perlíková P, Boháčová S, Milisavljevič N, Šanderová H, Benda M, Barvík I, Krásný L, Hocek M. Nucleic Acids Res 44 3000-3012 (2016)
  150. Interactions among CII protein, RNA polymerase and the lambda PRE promoter: contacts between RNA polymerase and the -35 region of PRE are identical in the presence and absence of CII protein. Marr MT, Roberts JW, Brown SE, Klee M, Gussin GN. Nucleic Acids Res 32 1083-1090 (2004)
  151. Mapping the spatial neighborhood of the regulatory 6S RNA bound to Escherichia coli RNA polymerase holoenzyme. Steuten B, Setny P, Zacharias M, Wagner R. J Mol Biol 425 3649-3661 (2013)
  152. Regulation of RNA polymerase promoter selectivity by covalent modification of DNA. Zakharova M, Minakhin L, Solonin A, Severinov K. J Mol Biol 335 103-111 (2004)
  153. Structural Basis for Virulence Activation of Francisella tularensis. Travis BA, Ramsey KM, Prezioso SM, Tallo T, Wandzilak JM, Hsu A, Borgnia M, Bartesaghi A, Dove SL, Brennan RG, Schumacher MA. Mol Cell 81 139-152.e10 (2021)
  154. A gene located downstream of the clavulanic acid gene cluster in Streptomyces clavuligerus ATCC 27064 encodes a putative response regulator that affects clavulanic acid production. Song JY, Kim ES, Kim DW, Jensen SE, Lee KJ. J Ind Microbiol Biotechnol 36 301-311 (2009)
  155. A two-subunit bacterial sigma-factor activates transcription in Bacillus subtilis. MacLellan SR, Guariglia-Oropeza V, Gaballa A, Helmann JD. Proc Natl Acad Sci U S A 106 21323-21328 (2009)
  156. Crystal structure of Aquifex aeolicus σN bound to promoter DNA and the structure of σN-holoenzyme. Campbell EA, Kamath S, Rajashankar KR, Wu M, Darst SA. Proc Natl Acad Sci U S A 114 E1805-E1814 (2017)
  157. Effect of DNA bases and backbone on sigma70 holoenzyme binding and isomerization using fork junction probes. Fenton MS, Gralla JD. Nucleic Acids Res 31 2745-2750 (2003)
  158. Experimental Evolution of Escherichia coli K-12 at High pH and with RpoS Induction. Hamdallah I, Torok N, Bischof KM, Majdalani N, Chadalavada S, Mdluli N, Creamer KE, Clark M, Holdener C, Basting PJ, Gottesman S, Slonczewski JL. Appl Environ Microbiol 84 e00520-18 (2018)
  159. Extended -10 motif is critical for activity of the cspA promoter but does not contribute to low-temperature transcription. Phadtare S, Severinov K. J Bacteriol 187 6584-6589 (2005)
  160. Regulatory elements involved in the expression of competence genes in naturally transformable Vibrio cholerae. Lo Scrudato M, Borgeaud S, Blokesch M. BMC Microbiol 14 327 (2014)
  161. Structural origins of Escherichia coli RNA polymerase open promoter complex stability. Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA. Proc Natl Acad Sci U S A 118 e2112877118 (2021)
  162. Co-evolution of specific amino acid in sigma 1.2 region and nucleotide base in the discriminator to act as sensors of small molecule effectors of transcription initiation in mycobacteria. Tare P, Mallick B, Nagaraja V. Mol Microbiol 90 569-583 (2013)
  163. Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators. Kumaraswami M, Howe MM, Park HW. J Biol Chem 279 16581-16590 (2004)
  164. Genetic evidence for a novel interaction between transcriptional activator SoxS and region 4 of the σ(70) subunit of RNA polymerase at class II SoxS-dependent promoters in Escherichia coli. Zafar MA, Sanchez-Alberola N, Wolf RE. J Mol Biol 407 333-353 (2011)
  165. Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization. Datta AB, Panjikar S, Weiss MS, Chakrabarti P, Parrack P. Proc Natl Acad Sci U S A 102 11242-11247 (2005)
  166. The fused SnoaL_2 domain in the Mycobacterium tuberculosis sigma factor σJ modulates promoter recognition. Goutam K, Gupta AK, Gopal B. Nucleic Acids Res 45 9760-9772 (2017)
  167. Altering the interaction between sigma70 and RNA polymerase generates complexes with distinct transcription-elongation properties. Berghöfer-Hochheimer Y, Lu CZ, Gross CA. Proc Natl Acad Sci U S A 102 1157-1162 (2005)
  168. Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation. Miropolskaya N, Ignatov A, Bass I, Zhilina E, Pupov D, Kulbachinskiy A. J Biol Chem 287 23779-23789 (2012)
  169. Identification of a novel anti-sigmaE factor in Neisseria meningitidis. Hopman CT, Speijer D, van der Ende A, Pannekoek Y. BMC Microbiol 10 164 (2010)
  170. Mechanistic studies of the T4 DNA (gp41) replication helicase: functional interactions of the C-terminal Tails of the helicase subunits with the T4 (gp59) helicase loader protein. Delagoutte E, von Hippel PH. J Mol Biol 347 257-275 (2005)
  171. Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters. Weindl J, Hanus P, Dawy Z, Zech J, Hagenauer J, Mueller JC. Nucleic Acids Res 35 7003-7010 (2007)
  172. Promoter recognition by bacterial alternative sigma factors: the price of high selectivity? Feklistov A, Darst SA. Genes Dev 23 2371-2375 (2009)
  173. RNA polymerase-promoter interactions determining different stability of the Escherichia coli and Thermus aquaticus transcription initiation complexes. Mekler V, Minakhin L, Kuznedelov K, Mukhamedyarov D, Severinov K. Nucleic Acids Res 40 11352-11362 (2012)
  174. The secret to 6S: regulating RNA polymerase by ribo-sequestration. Decker KB, Hinton DM. Mol Microbiol 73 137-140 (2009)
  175. Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. Dekhtyar M, Morin A, Sakanyan V. BMC Bioinformatics 9 233 (2008)
  176. Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism. Pannekoek Y, Huis In 't Veld RA, Schipper K, Bovenkerk S, Kramer G, Brouwer MC, van de Beek D, Speijer D, van der Ende A. mBio 8 e02293-16 (2017)
  177. Promoter activation by repositioning of RNA polymerase. Kumar A, Moran CP. J Bacteriol 190 3110-3117 (2008)
  178. Relationship between promoter sequence and its strength in gene expression. Li J, Zhang Y. Eur Phys J E Soft Matter 37 44 (2014)
  179. Structural basis of non-canonical transcriptional regulation by the σA-bound iron-sulfur protein WhiB1 in M. tuberculosis. Wan T, Li S, Beltran DG, Schacht A, Zhang L, Becker DF, Zhang L. Nucleic Acids Res 48 501-516 (2020)
  180. Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation. Devi PG, Campbell EA, Darst SA, Nickels BE. Mol Microbiol 75 607-622 (2010)
  181. A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation. Del Peso-Santos T, Bernardo LM, Skärfstad E, Holmfeldt L, Togneri P, Shingler V. Nucleic Acids Res 39 5853-5865 (2011)
  182. Bacillus subtilis RNA polymerase recruits the transcription factor Spo0A approximately P to stabilize a closed complex during transcription initiation. Seredick SD, Spiegelman GB. J Mol Biol 366 19-35 (2007)
  183. Efficient transcription initiation in bacteria: an interplay of protein-DNA interaction parameters. Djordjevic M. Integr Biol (Camb) 5 796-806 (2013)
  184. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Binder SC, Eckweiler D, Schulz S, Bielecka A, Nicolai T, Franke R, Häussler S, Meyer-Hermann M. Sci Rep 6 22212 (2016)
  185. RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase. Sudalaiyadum Perumal A, Vishwakarma RK, Hu Y, Morichaud Z, Brodolin K. Nucleic Acids Res 46 10106-10118 (2018)
  186. Structure-based functional inference of hypothetical proteins from Mycoplasma hyopneumoniae. da Fonsêca MM, Zaha A, Caffarena ER, Vasconcelos AT. J Mol Model 18 1917-1925 (2012)
  187. The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution. Sukackaite R, Grazulis S, Bochtler M, Siksnys V. J Mol Biol 378 1084-1093 (2008)
  188. Cloning, identification, and characterization of the rpoS-like sigma factor rpoX from Vibrio alginolyticus. Zhao JJ, Chen C, Zhang LP, Hu CQ. J Biomed Biotechnol 2009 126986 (2009)
  189. Mutagenesis of region 4 of sigma 28 from Chlamydia trachomatis defines determinants for protein-protein and protein-DNA interactions. Hua Z, Rao X, Feng X, Luo X, Liang Y, Shen L. J Bacteriol 191 651-660 (2009)
  190. Re-visiting protein-centric two-tier classification of existing DNA-protein complexes. Malhotra S, Sowdhamini R. BMC Bioinformatics 13 165 (2012)
  191. Structure of a Core Promoter in Bifidobacterium longum NCC2705. Kozakai T, Izumi A, Horigome A, Odamaki T, Xiao JZ, Nomura I, Suzuki T. J Bacteriol 202 e00540-19 (2020)
  192. The crystal structure of the RsbN-σBldN complex from Streptomyces venezuelae defines a new structural class of anti-σ factor. Schumacher MA, Bush MJ, Bibb MJ, Ramos-León F, Chandra G, Zeng W, Buttner MJ. Nucleic Acids Res 46 7405-7417 (2018)
  193. The pneumococcal σX activator, ComW, is a DNA-binding protein critical for natural transformation. Inniss NL, Prehna G, Morrison DA. J Biol Chem 294 11101-11118 (2019)
  194. Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity. Forrest D, Warman EA, Erkelens AM, Dame RT, Grainger DC. Nat Commun 13 1149 (2022)
  195. Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme. Bell N, Lee JJ, Summers ML. Mol Microbiol 104 179-194 (2017)
  196. Molecular modeling of RecX reveals its mode of interaction with RecA. Mishra S, Mazumdar PA, Dey J, Das AK. Biochem Biophys Res Commun 312 615-622 (2003)
  197. Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system. Montero-Diez C, Deighan P, Osmundson J, Darst SA, Hochschild A. J Bacteriol 195 3621-3628 (2013)
  198. Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable -10 element. Del Peso-Santos T, Landfors M, Skärfstad E, Ryden P, Shingler V. Nucleic Acids Res 40 11308-11320 (2012)
  199. Promoter activation by CII, a potent transcriptional activator from bacteriophage 186. Murchland I, Ahlgren-Berg A, Priest DG, Dodd IB, Shearwin KE. J Biol Chem 289 32094-32108 (2014)
  200. Structural and binding studies of the C-terminal domains of yeast TFIIF subunits Tfg1 and Tfg2. Kilpatrick AM, Koharudin LM, Calero GA, Gronenborn AM. Proteins 80 519-529 (2012)
  201. Visualizing the phage T4 activated transcription complex of DNA and E. coli RNA polymerase. James TD, Cardozo T, Abell LE, Hsieh ML, Jenkins LM, Jha SS, Hinton DM. Nucleic Acids Res 44 7974-7988 (2016)
  202. A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation. Ooi WY, Murayama Y, Mekler V, Minakhin L, Severinov K, Yokoyama S, Sekine SI. Nucleic Acids Res 46 431-441 (2018)
  203. An amino acid substitution at position 740 in sigma70 of Ralstonia solanacearum strain OE1-1 affects its in planta growth. Kanda A, Tsuneishi K, Mori A, Ohnishi K, Kiba A, Hikichi Y. Appl Environ Microbiol 74 5841-5844 (2008)
  204. An artificial activator that contacts a normally occluded surface of the RNA polymerase holoenzyme. Gregory BD, Deighan P, Hochschild A. J Mol Biol 353 497-506 (2005)
  205. Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast. Wang L, Wang X, He ZQ, Zhou SJ, Xu L, Tan XY, Xu T, Li BZ, Yuan YJ. Biotechnol Biofuels 13 193 (2020)
  206. Insights into Transcriptional Repression of the Homologous Toxin-Antitoxin Cassettes yefM-yoeB and axe-txe. Kędzierska B, Potrykus K, Szalewska-Pałasz A, Wodzikowska B. Int J Mol Sci 21 E9062 (2020)
  207. Molecular gymnastics: distortion of an RNA polymerase sigma factor. Hinton DM. Trends Microbiol 13 140-143 (2005)
  208. Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum. Ruwe M, Persicke M, Busche T, Müller B, Kalinowski J. Front Microbiol 10 2769 (2019)
  209. Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa. Myers KS, Noguera DR, Donohue TJ. mSystems 6 e0052621 (2021)
  210. Properties of Bacillus subtilis sigma A factors with region 1.1 and the conserved Arg-103 at the N terminus of region 1.2 deleted. Hsu HH, Huang WC, Chen JP, Huang LY, Wu CF, Chang BY. J Bacteriol 186 2366-2375 (2004)
  211. Role of the σ54 Activator Interacting Domain in Bacterial Transcription Initiation. Siegel AR, Wemmer DE. J Mol Biol 428 4669-4685 (2016)
  212. Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding. Chen B, Himes P, Liu Y, Zhang Y, Lu Z, Liu A, Yan H, Kroos L. J Bacteriol 196 2131-2142 (2014)
  213. Transcriptional control of mycobacterial DNA damage response by sigma adaptation. Müller AU, Kummer E, Schilling CM, Ban N, Weber-Ban E. Sci Adv 7 eabl4064 (2021)
  214. A Novel Function of δ Factor from Bacillus subtilis as a Transcriptional Repressor. Prajapati RK, Sur R, Mukhopadhyay J. J Biol Chem 291 24029-24035 (2016)
  215. Analysis of the Bombyx mori nucleopolyhedrovirus ie-1 promoter in insect, mammalian, plant, and bacterial cells. Fujita R, Ono C, Ono I, Asano SI, Bando H. Biochem Biophys Res Commun 464 1297-1301 (2015)
  216. Characteristics of σ-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus. Zhilina EV, Miropolskaya NA, Bass IA, Brodolin KL, Kulbachinskiy AV. Biochemistry (Mosc) 76 1098-1106 (2011)
  217. Inactivation and destruction by KMnO4 of Escherichia coli RNA polymerase open transcription complex: recommendations for footprinting experiments. Loziński T, Wierzchowski KL. Anal Biochem 320 239-251 (2003)
  218. Macromolecular structure and interaction studies of SigF and Usfx in Mycobacterium tuberculosis. Mustyala KK, Malkhed V, Potlapally SR, Chittireddy VR, Vuruputuri U. J Recept Signal Transduct Res 34 162-173 (2014)
  219. TFIIB is only ∼9 Å away from the 5'-end of a trimeric RNA primer in a functional RNA polymerase II preinitiation complex. Bick MJ, Malik S, Mustaev A, Darst SA. PLoS One 10 e0119007 (2015)
  220. Backbone dynamics of TFE-induced native-like fold of region 4 of Escherichia coli RNA polymerase sigma70 subunit. Kaczka P, Polkowska-Nowakowska A, Bolewska K, Zhukov I, Poznański J, Wierzchowski KL. Proteins 78 754-768 (2010)
  221. Chemogenomic Screen for Imipenem Resistance in Gram-Negative Bacteria. El Khoury JY, Maure A, Gingras H, Leprohon P, Ouellette M. mSystems 4 e00465-19 (2019)
  222. Contribution of bacterial promoter elements to transcription start site detection accuracy. Nikolic M, Stankovic T, Djordjevic M. J Bioinform Comput Biol 15 1650038 (2017)
  223. Evolutionary link between the mycobacterial plasmid pAL5000 replication protein RepB and the extracytoplasmic function family of σ factors. Basu A, Chatterjee S, Chatterjee S, Das Gupta SK. J Bacteriol 194 1331-1341 (2012)
  224. GPI0363 inhibits the interaction of RNA polymerase with DNA in Staphylococcus aureus. Paudel A, Panthee S, Hamamoto H, Sekimizu K. RSC Adv 9 37889-37894 (2019)
  225. Implication from the predicted docked interaction of sigma H and exploration of its interaction with RNA polymerase in Mycobacterium tuberculosis. Gupta AM, Bhattacharya S, Bagchi A, Mandal S. Bioinformation 11 296-301 (2015)
  226. NusA directly interacts with antitermination factor Q from phage λ. Dudenhoeffer BR, Borggraefe J, Schweimer K, Knauer SH. Sci Rep 10 6607 (2020)
  227. Plastid Gene Transcription: An Update on Promoters and RNA Polymerases. Ortelt J, Link G. Methods Mol Biol 2317 49-76 (2021)
  228. Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription. Brodolin K, Morichaud Z. J Biol Chem 296 100253 (2021)
  229. The Burkholderia cenocepacia iron starvation σ factor, OrbS, possesses an on-board iron sensor. Butt AT, Banyard CD, Haldipurkar SS, Agnoli K, Mohsin MI, Vitovski S, Paleja A, Tang Y, Lomax R, Ye F, Green J, Thomas MS. Nucleic Acids Res 50 3709-3726 (2022)
  230. The TFE-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of Escherichia coli RNA polymerase. Kaczka P, Winiewska M, Zhukov I, Rempoła B, Bolewska K, Łoziński T, Ejchart A, Poznańska A, Wierzchowski KL, Poznański J. Eur Biophys J 43 581-594 (2014)
  231. A mutant of Salmonella enterica serovar Typhimurium RNA polymerase extracytoplasmic stress response sigma factor sigma(E) with altered promoter specificity. Rezuchova B, Skovierova H, Homerova D, Roberts M, Kormanec J. Mol Genet Genomics 282 119-129 (2009)
  232. Characterisation and Mutagenesis Study of An Alternative Sigma Factor Gene (hrpL) from Erwinia mallotivora Reveal Its Central Role in Papaya Dieback Disease. Tamizi AA, Abu-Bakar N, Samsuddin AF, Rozano L, Ahmad-Redzuan R, Abdul-Murad AM. Biology (Basel) 9 E323 (2020)
  233. Crystallization and preliminary X-ray diffraction studies of two domains of a bilobed extra-cytoplasmic function sigma factor SigC from Mycobacterium tuberculosis. Thakur KG, Gopal B. Acta Crystallogr Sect F Struct Biol Cryst Commun 61 779-781 (2005)
  234. Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence. Berezhnoy AY, Shckorbatov YG. J Zhejiang Univ Sci B 6 1063-1068 (2005)
  235. Genetic analysis of phage Mu Mor protein amino acids involved in DNA minor groove binding and conformational changes. Kumaraswami M, Avanigadda L, Rai R, Park HW, Howe MM. J Biol Chem 286 35852-35862 (2011)
  236. Hydrogel for the Controlled Delivery of Bioactive Components from Extracts of Eupatorium glutinosum Lam. Leaves. Zamora-Mendoza L, Vispo SN, De Lima L, Mora JR, Machado A, Alexis F. Molecules 28 1591 (2023)
  237. Minor Alterations in Core Promoter Element Positioning Reveal Functional Plasticity of a Bacterial Transcription Factor. Chowdhury WP, Satyshur KA, Keck JL, Kiley PJ. mBio 12 e0275321 (2021)
  238. More pieces in the promoter jigsaw: recognition of -10 regions by alternative sigma factors. Busby SJ. Mol Microbiol 72 809-811 (2009)
  239. Residual Helicity at the Active Site of the Histidine Phosphocarrier, HPr, Modulates Binding Affinity to Its Natural Partners. Neira JL, Ortega-Alarcón D, Rizzuti B, Palomino-Schätzlein M, Velázquez-Campoy A, Falcó A. Int J Mol Sci 22 10805 (2021)
  240. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Proc Natl Acad Sci U S A 120 e2220785120 (2023)
  241. Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG. Nat Commun 13 3526 (2022)
  242. Systematic dissection of σ70 sequence diversity and function in bacteria. Park J, Wang HH. Cell Rep 36 109590 (2021)
  243. The core-independent promoter-specific binding of Bacillus subtilis σB. Kuo HH, Huang WC, Lin TF, Yeh HY, Liou KM, Chang BY. FEBS J 282 1307-1318 (2015)
  244. Toward a Universal Structural and Energetic Model for Prokaryotic Promoters. Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Biophys J 115 1180-1189 (2018)
  245. Universal functions of the σ finger in alternative σ factors during transcription initiation by bacterial RNA polymerase. Oguienko A, Petushkov I, Pupov D, Esyunina D, Kulbachinskiy A. RNA Biol 18 2028-2037 (2021)
  246. Alteration of the -35 and -10 sequences and deletion the upstream sequence of the -35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions with E. coli RNA polymerase to the transcription initiation process. Turecka K, Firczuk M, Werel W. Front Mol Biosci 10 1335409 (2023)
  247. An archaeal transcription factor EnfR with a novel 'eighth note' fold controls hydrogen production of a hyperthermophilic archaeon Thermococcus onnurineus NA1. Bae DW, Lee SH, Park JH, Son SY, Lin Y, Lee JH, Jang BR, Lee KH, Lee YH, Lee HS, Kang SG, Kim BS, Cha SS. Nucleic Acids Res 51 10026-10040 (2023)
  248. Evolving Escherichia coli Host Strains for Efficient Deuterium Labeling of Recombinant Proteins Using Sodium Pyruvate-d3. Kelpšas V, Leung A, von Wachenfeldt C. Int J Mol Sci 22 9678 (2021)
  249. In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices. Zhang Y, Wang S, Jia Z. Int J Mol Sci 21 E308 (2020)
  250. Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli. Santillán O, Ramírez-Romero MA, Lozano L, Checa A, Encarnación SM, Dávila G. Front Microbiol 7 1078 (2016)
  251. Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis. Wan T, Horová M, Khetrapal V, Li S, Jones C, Schacht A, Sun X, Zhang L. J Biol Chem 299 104777 (2023)
  252. The origin of genetic and metabolic systems: Evolutionary structuralinsights. Deng S. Heliyon 9 e14466 (2023)
  253. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. Zhu DX, Stallings CL. J Biol Chem 299 104724 (2023)


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