BMC Microbiology | |
Genome-wide identification of Bacillus subtilis Zur-binding sites associated with a Zur box expands its known regulatory network | |
Sandrine Auger1  Philippe Noirot1  Eric Prestel1  | |
[1] AgroParisTech, UMR Micalis, Jouy-en-Josas, F-78352, France | |
关键词: Disulfide stress; Zinc homeostasis; ChIP-on-chip; B. subtilis; Zur regulator; | |
Others : 1137579 DOI : 10.1186/s12866-015-0345-4 |
|
received in 2014-09-23, accepted in 2015-01-13, 发布年份 2015 | |
![]() |
【 摘 要 】
Background
The Bacillus subtilis Zur transcription factor recognizes a specific DNA motif, the Zur box, to repress expression of genes in response to zinc availability. Although several Zur-regulated genes are well characterized, a genome-wide mapping of Zur-binding sites is needed to define further the set of genes directly regulated by this protein.
Results
Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we reported the identification of 80 inter- and intragenic chromosomal sites bound by Zur. Seven Zur-binding regions constitute the Zur primary regulon while 35 newly identified targets were associated with a predicted Zur box. Using transcriptional fusions an intragenic Zur box was showed to promote a full Zur-mediated repression when placed within a promoter region. In addition, intragenic Zur boxes appeared to mediate a transcriptional cis-repressive effect (4- to 9-fold) but the function of Zur at these sites remains unclear. Zur binding to intragenic Zur boxes could prime an intricate mechanisms of regulation of the transcription elongation, possibly with other transcriptional factors. However, the disruption of zinc homeostasis in Δzur cells likely affects many cellular processes masking direct Zur-dependent effects. Finally, most Zur-binding sites were located near or within genes responsive to disulfide stress. These findings expand the potential Zur regulon and reveal unknown interconnections between zinc and redox homeostasis regulatory networks.
Conclusions
Our findings considerably expand the potential Zur regulon, and reveal a new level of complexity in Zur binding to its targets via a Zur box motif and via a yet unknown mechanism that remains to be characterized.
【 授权许可】
2015 Prestel et al.; licensee BioMed Central.
【 预 览 】
Files | Size | Format | View |
---|---|---|---|
20150317100655520.pdf | 1314KB | ![]() |
|
Figure 7. | 54KB | Image | ![]() |
Figure 6. | 49KB | Image | ![]() |
Figure 5. | 19KB | Image | ![]() |
Figure 4. | 22KB | Image | ![]() |
Figure 3. | 27KB | Image | ![]() |
Figure 2. | 53KB | Image | ![]() |
Figure 1. | 108KB | Image | ![]() |
【 图 表 】
Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
【 参考文献 】
- [1]McCall KA, Huang CC, Fierke CA: Function and Mechanism of Zinc Metalloenzymes. J Nutr 2000, 130(5):1437S-46.
- [2]Krishna SS, Majumdar I, Grishin NV: Structural classification of zinc fingers. Nucleic Acids Res 2003, 31(2):532-50.
- [3]McDevitt CA, Ogunniyi AD, Valkov E, Lawrence MC, Kobe B, McEwan AG, et al.: A molecular mechanism for bacterial susceptibility to zinc. PLoS Pathog 2011, 7(11):e1002357.
- [4]Blencowe DK, Morby AP: Zn(II) metabolism in prokaryotes. FEMS Microbiol Rev 2003, 27(2–3):291-311.
- [5]Moore CM, Gaballa A, Hui M, Ye RW, Helmann JD: Genetic and physiological responses of Bacillus subtilis to metal ion stress. Mol Microbiol 2005, 57(1):27-40.
- [6]Patzer SI, Hantke K: The ZnuABC high-affinity zinc uptake system and its regulator Zur in Escherichia coli. Mol Microbiol 1998, 28(6):1199-210.
- [7]Gaballa A, Helmann JD: Identification of a zinc-specific metalloregulatory protein, Zur, controlling zinc transport operons in Bacillus subtilis. J Bacteriol 1998, 180(22):5815-21.
- [8]Outten CE, Tobin DA, Penner-Hahn JE, O'Halloran TV: Characterization of the metal receptor sites in Escherichia coli Zur, an ultrasensitive zinc(II) metalloregulatory protein. Biochemistry 2001, 40(35):10417-23.
- [9]Lee JW, Helmann JD: Functional specialization within the Fur family of metalloregulators. Biometals 2007, 20(3–4):485-99. Epub 2007 Jan 2010
- [10]Gaballa A, Wang T, Ye RW, Helmann JD: Functional analysis of the Bacillus subtilis Zur regulon. J Bacteriol 2002, 184(23):6508-14.
- [11]Gabriel SE, Miyagi F, Gaballa A, Helmann JD: Regulation of the Bacillus subtilis yciC gene and insights into the DNA-binding specificity of the zinc-sensing metalloregulator Zur. J Bacteriol 2008, 190(10):3482-8.
- [12]Ma Z, Gabriel SE, Helmann JD: Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur. Nucleic Acids Res 2011, 39(21):9130-8.
- [13]Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, et al.: Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol 2009, 191(22):6936-49.
- [14]Nanamiya H, Akanuma G, Natori Y, Murayama R, Kosono S, Kudo T, et al.: Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Mol Microbiol 2004, 52(1):273-83.
- [15]Akanuma G, Nanamiya H, Natori Y, Nomura N, Kawamura F: Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis. J Bacteriol 2006, 188(7):2715-20.
- [16]Nanamiya H, Kawamura F: Towards an elucidation of the roles of the ribosome during different growth phases in Bacillus subtilis. Biosci Biotechnol Biochem 2010, 74(3):451-61.
- [17]Gabriel SE, Helmann JD: Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions. J Bacteriol 2009, 191(19):6116-22.
- [18]Natori Y, Nanamiya H, Akanuma G, Kosono S, Kudo T, Ochi K, et al.: A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis. Mol Microbiol 2007, 63(1):294-307.
- [19]Gaballa A, Helmann JD: A peroxide-induced zinc uptake system plays an important role in protection against oxidative stress in Bacillus subtilis. Mol Microbiol 2002, 45(4):997-1005.
- [20]Ogura M: ZnuABC and ZosA zinc transporters are differently involved in competence development in Bacillus subtilis. J Biochem 2011, 150(6):615-25.
- [21]Moore CM, Helmann JD: Metal ion homeostasis in Bacillus subtilis. Curr Opin Microbiol 2005, 8(2):188-95.
- [22]Michna RH, Commichau FM, Todter D, Zschiedrich CP, Stulke J: SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. Nucleic Acids Res 2013, 42:D692-8.
- [23]Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, et al.: Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 2012, 335:1099-103.
- [24]Rochat T, Nicolas P, Delumeau O, Rabatinova A, Korelusova J, Leduc A, et al.: Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis. Nucleic Acids Res 2012, 40(19):9571-83.
- [25]Panina EM, Mironov AA, Gelfand MS: Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. Proc Natl Acad Sci 2003, 100(17):9912-7.
- [26]Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, et al.: Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 2012, 335:1103-6.
- [27]Baichoo N, Wang T, Ye R, Helmann JD: Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon. Mol Microbiol 2002, 45(6):1613-29.
- [28]Fillat MF: The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators. Arch Biochem Biophys 2014, 546:41-52.
- [29]Fuangthong M, Helmann JD: Recognition of DNA by three ferric uptake regulator (Fur) homologs in Bacillus subtilis. J Bacteriol 2003, 185(21):6348-57.
- [30]Bailey TL, Williams N, Misleh C, Li WW: MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34:W369-73.
- [31]Grant CE, Bailey TL, Noble WS: FIMO: scanning for occurrences of a given motif. Bioinformatics 2011, 27(7):1017-8.
- [32]Choi SK, Saier MH Jr: Regulation of sigL expression by the catabolite control protein CcpA involves a roadblock mechanism in Bacillus subtilis: potential connection between carbon and nitrogen metabolism. J Bacteriol 2005, 187(19):6856-61.
- [33]Belitsky BR, Sonenshein AL: Roadblock repression of transcription by Bacillus subtilis CodY. J Mol Biol 2011, 411:729-43.
- [34]Nakano S, Erwin KN, Ralle M, Zuber P: Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator, Spx. Mol Microbiol 2005, 55(2):498-510.
- [35]Zhang Y, Zuber P: Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide stress on ClpXP activity. J Bacteriol 2007, 189(21):7669-80.
- [36]Owen GA, Pascoe B, Kallifidas D, Paget MS: Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and sigmaR. J Bacteriol 2007, 189(11):4078-86.
- [37]Molecular cloning: a laboratory manual. Cold Spring Harbor Press, Cold Spring Harbor; 1989.
- [38]Kunst F, Rapoport G: Salt stress is an environmental signal affecting degradative enzyme synthesis in Bacillus subtilis. J Bacteriol 1995, 177(9):2403-7.
- [39]Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, et al.: Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 2005, 433(7025):531-7.
- [40]Zeghouf M, Li J, Butland G, Borkowska A, Canadien V, Richards D, et al.: Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J Proteome Res 2004, 3(3):463-8.
- [41]Lecointe F, Serena C, Velten M, Costes A, McGovern S, Meile JC, et al.: Anticipating chromosomal replication fork arrest: SSB targets repair DNA helicases to active forks. Embo J 2007, 26(19):4239-51.
- [42]Wach A: PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 1996, 12(3):259-65.
- [43]Stülke J, Martin-Verstraete I, Zagorec M, Rose M, Klier A, Rapoport G: Induction of the Bacillus subtilis ptsGHI operon by glucose is controlled by a novel antiterminator, GlcT. Mol Microbiol 1997, 25(1):65-78.
- [44]Miller JH: Assay of B-galactosidase. Cold Spring Harbor Laboratory, Cold Spring Harbor; 1972.
- [45]Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO: Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 2009, 6(5):343-5.
- [46]Mirouze N, Prepiak P, Dubnau D: Fluctuations in spo0A transcription control rare developmental transitions in Bacillus subtilis. PLoS Genet 2011, 7(4):e1002048.
- [47]Rasmussen S, Nielsen HB, Jarmer H: The transcriptionally active regions in the genome of Bacillus subtilis. Mol Microbiol 2009, 73:1043-57.
- [48]Reppas NB, Wade JT, Church GM, Struhl K: The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 2006, 24:747-57.