Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 23, 2015, Pages 7171-7176

  Hubin, Elizabeth A ^a   Tabib Salazar, Aline ^b,c   Humphrey, Laurence J ^b   Flack, Joshua E ^a,d   Olinares, Paul Dominic B ^a   Darst, Seth A ^a   Campbell, Elizabeth A ^a   Paget, Mark S ^b  

^a ROCKEFELLER UNIVERSITY   (United States)

^b UNIVERSITY OF SUSSEX   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Actinobacteria; Mycobacteria; RbpA; Transcription; X ray crystallography

Indexed keywords

ARGININE; SUMO PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR RBPA; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN;

ACTINOPHAGE; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANISOTROPY; ARTICLE; BACTERIAL GENETICS; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING; DNA CROSS LINKING; GEL PERMEATION CHROMATOGRAPHY; GENE FUNCTION; GENE FUSION; GENE IDENTIFICATION; GENE INTERACTION; GENE STRUCTURE; GENETIC ANALYSIS; HOUSEKEEPING GENE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MUTAGENESIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; STATIC ELECTRICITY; TRANSCRIPTION INITIATION; ACTINOBACTERIA; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ACTINOBACTERIA; CORYNEBACTERINEAE; MYCOBACTERIUM TUBERCULOSIS;

ACTINOBACTERIA; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DNA, BACTERIAL; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

EID: 84931291946     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1504942112     Document Type: Article

References (40)

1. Burgess RR, Travers AA, Dunn JJ, Bautz EK (1969) Factor stimulating transcription by RNA polymerase. Nature 221(5175):43-46.
2. Murakami KS, Darst SA (2003) Bacterial RNA polymerases: The wholo story. Curr Opin Struct Biol 13(1):31-39.
3. Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57:441-466.
4. Campbell EA, et al. (2002) Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol Cell 9(3):527-539.
5. Murakami KS, Masuda S, Darst SA (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296(5571):1280-1284.
6. Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA (2002) Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science 296(5571):1285-1290.
7. Vassylyev DG, et al. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417(6890):712-719.
8. Zhang Y, et al. (2012) Structural basis of transcription initiation. Science 338(6110): 1076-1080.
9. Lonetto M, Gribskov M, Gross CA (1992) The sigma 70 family: Sequence conservation and evolutionary relationships. J Bacteriol 174(12):3843-3849.
10. Stallings CL, et al. (2009) CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence. Cell 138(1):146-159.
11. Newell KV, Thomas DP, Brekasis D, Paget MSB (2006) The RNA polymerase-binding protein RbpA confers basal levels of rifampicin resistance on Streptomyces coelicolor. Mol Microbiol 60(3):687-696.
12. Forti F, Mauri V, Dehò G, Ghisotti D (2011) Isolation of conditional expression mutants in Mycobacterium tuberculosis by transposon mutagenesis. Tuberculosis (Edinb) 91(6): 569-578.
13. Srivastava DB, et al. (2013) Structure and function of CarD, an essential mycobacterial transcription factor. Proc Natl Acad Sci USA 110(31):12619-12624.
14. Davis E, Chen J, Leon K, Darst SA, Campbell EA (2015) Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Res 43(1):433-445.
15. Tabib-Salazar A, et al. (2013) The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase. Nucleic Acids Res 41(11):5679-5691.
16. Bortoluzzi A, et al. (2013) Mycobacterium tuberculosis RNA polymerase-binding protein A (RbpA) and its interactions with sigma factors. J Biol Chem 288(20):14438-14450.
17. Hu Y, Morichaud Z, Perumal AS, Roquet-Baneres F, Brodolin K (2014) Mycobacterium RbpA cooperates with the stress-response σB subunit of RNA polymerase in promoter DNA unwinding. Nucleic Acids Res 42(16):10399-10408.
18. Hu Y, Morichaud Z, Chen S, Leonetti JP, Brodolin K (2012) Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the σA-containing RNA polymerase holoenzyme. Nucleic Acids Res 40(14):6547-6557.
19. Cortes T, et al. (2013) Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Reports 5(4): 1121-1131.
20. Bao X, Nickels BE, Fan H (2012) Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66. Proc Natl Acad Sci USA 109(42):16870-16875.
21. Banta AB, et al. (2013) Key features of σS required for specific recognition by Crl, a transcription factor promoting assembly of RNA polymerase holoenzyme. Proc Natl Acad Sci USA 110(40):15955-15960.
22. Banta AB, et al. (2014) Structure of the RNA polymerase assembly factor Crl and identification of its interaction surface with sigma S. J Bacteriol 196(18):3279-3288.
23. Feklistov A, Darst SA (2011) Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit. Cell 147(6):1257-1269.
24. Brodolin K, Mustaev A, Severinov K, Nikiforov V (2000) Identification of RNA polymerase β' subunit segment contacting the melted region of the lacUV5 promoter. J Biol Chem 275(5):3661-3666.
25. Guo Y, Gralla JD (1998) Promoter opening via a DNA fork junction binding activity. Proc Natl Acad Sci USA 95(20):11655-11660.
26. Jameson DM, Seifried SE (1999) Quantification of protein-protein interactions using fluorescence polarization. Methods 19(2):222-233.
27. Dey A, Verma AK, Chatterji D (2011) Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA. Microbiology 157(Pt 7):2056-2071.
28. Dey A, Verma AK, Chatterji D (2010) Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology 156(Pt 3):873-883.
29. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood D (2000) Practical Streptomyces Genetics (The John Innes Foundation, Norwich, United Kingdom).
30. Cadene M, Chait BT (2000) A robust, detergent-friendly method for mass spectrometric analysis of integral membrane proteins. Anal Chem 72(22):5655-5658.
31. Fenyo D, et al. (2007) MALDI sample preparation: The ultra thin layer method. J Vis Exp 3(2007):192.
32. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology, eds Carter Jr, CW, Sweet RM (Academic, New York), Vol 276, pp 307-326.
33. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126-2132.
34. Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213-221.
35. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372(3):774-797.
36. Paget MS, Chamberlin L, Atrih A, Foster SJ, Buttner MJ (1999) Evidence that the extracytoplasmic function sigma factor σE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J Bacteriol 181(1):204-211.
37. Studier FW, Moffatt BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189(1):113-130.
38. Karimova G, Ullmann A, Ladant D (2001) Protein-protein interaction between Bacillus stearothermophilus tyrosyl-tRNA synthetase subdomains revealed by a bacterial twohybrid system. J Mol Microbiol Biotechnol 3(1):73-82.
39. Diederichs K, Karplus PA (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4(4):269-275.
40. Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336(6084):1030-1033.