Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing

mBio

Volumn 5, Issue 4, 2014, Pages

  Conway, Tyrrell ^a   Creecy, James P ^a   Maddox, Scott M ^a   Grissom, Joe E ^a   Conkle, Trevor L ^a   Shadid, Tyler M ^a   Teramoto, Jun ^b   Miguel, Phillip San ^c   Shimada, Tomohiro ^d,e   Ishihama, Akira ^d   Mori, Hirotada ^f   Wanner, Barry L ^b  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

^d HOSEI UNIVERSITY   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^f NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE; RNA; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; DNA MICROARRAY; ESCHERICHIA COLI K 12; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PROMOTER REGION; RNA SEQUENCE; STEADY STATE; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; PROCEDURES; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS);

ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; OPERON; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84908310507     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.01442-14     Document Type: Article

References (83)

1. Lederberg J, Tatum EL. 1946. Gene recombination in Escherichia coli. Nature 158:558. http://dx.doi.org/10.1038/158558c0.
2. Jacob F, Monod J. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:318-356. http://dx.doi.org/10.1016/S0022-2836(61)80072-7.
3. Lehman IR, Bessman MJ, Simms ES, Kornberg A. 1958. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J. Biol. Chem. 233: 163-170.
4. Lengyel P, Speyer JF, Ochoa S. 1961. Synthetic polynucleotides and the amino acid code. Proc. Natl. Acad. Sci. U. S. A. 47:1936-1942. http://dx.doi.org/10.1073/pnas.47.12.1936.
5. Luria SE, Delbrück M. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491-511.
6. Arber W, Dussoix D. 1962. Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J. Mol. Biol. 5:18-36. http://dx.doi.org/10.1016/S0022-2836(62)80058-8.
7. Mulligan RC, Berg P. 1980. Expression of a bacterial gene in mammalian cells. Science 209:1422-1427. http://dx.doi.org/10.1126/science.6251549.
8. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell 31:147-157. http://dx.doi.org/10.1016/0092-8674(82)90414-7.
9. Boyer PD, Cross RL, Momsen W. 1973. A new concept for energy coupling in oxidative phosphorylation based on a molecular explanation of the oxygen exchange reactions. Proc. Natl. Acad. Sci. U. S. A. 70: 2837-2839. http://dx.doi.org/10.1073/pnas.70.10.2837.
10. Chang CN, Model P, Blobel G. 1979. Membrane biogenesis: cotranslational integration of the bacteriophage f1 coat protein into an Escherichia coli membrane fraction. Proc. Natl. Acad. Sci. U. S. A. 76:1251-1255. http://dx.doi.org/10.1073/pnas.76.3.1251.
11. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462. http://dx.doi.org/10.1126/science.277.5331.1453.
12. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G III, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot—2005. Nucleic Acids Res. 34:1-9. http://dx.doi.org/10.1093/nar/gnj001.
13. Balázsi G, Barabási AL, Oltvai ZN. 2005. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 102:7841-7846. http://dx.doi.org/10.1073/pnas.0500365102.
14. Price MN, Arkin AP, Alm EJ. 2006. The life-cycle of operons. PLoS Genet. 2:e96. http://dx.doi.org/10.1371/journal.pgen.0020096.
15. Zhang H, Yin Y, Olman V, Xu Y. 2012. Genomic arrangement of regulons in bacterial genomes. PLoS One 7:e29496. http://dx.doi.org/10.1371/journal.pone.0029496.
16. Taylor K, Hradecna Z, Szybalski W. 1967. Asymmetric distribution of the transcribing regions on the complementary strands of coliphage lambda DNA. Proc. Natl. Acad. Sci. U. S. A. 57:1618-1625. http://dx.doi.org/10.1073/pnas.57.6.1618.
17. Piette J, Cunin R, Boyen A, Charlier D, Crabeel M, Van Vliet F, Glansdorff N, Squires C, Squires CL. 1982. The regulatory region of the divergent argECBH operon in Escherichia coli K-12. Nucleic Acids Res. 10:8031-8048. http://dx.doi.org/10.1093/nar/10.24.8031.
18. Wek RC, Hatfield GW. 1986. Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K-12. Transcription from divergent overlapping promoters. J. Biol. Chem. 261:2441-2450.
19. Nomura T, Aiba H, Ishihama A. 1985. Transcriptional organization of the convergent overlapping dnaQ-rnh genes of Escherichia coli. J. Biol. Chem. 260:7122-7125.
20. Sameshima JH, Wek RC, Hatfield GW. 1989. Overlapping transcription and termination of the convergent ilvA and ilvY genes of Escherichia coli. J. Biol. Chem. 264:1224-1231.
21. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. 2010. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250-255. http://dx.doi.org/10.1038/nature08756.
22. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18:1262-1268. http://dx.doi.org/10.1038/82367.
23. Dornenburg JE, Devita AM, Palumbo MJ, Wade JT. 2010. Widespread antisense transcription in Escherichia coli. mBio 1(1):e00024-10. http://dx.doi.org/10.1128/mBio.00024-10.
24. Wade JT, Dornenburg JE, Devita AM, Palumbo MJ. 2010. Reply to “Concerns about recently identified widespread antisense transcription in Escherichia coli.” mBio 1(2):e00119-10. http://dx.doi.org/10.1128/mBio.00119-10.
25. Raghavan R, Sloan DB, Ochman H. 2012. Antisense transcription is pervasive but rarely conserved in enteric bacteria. mBio 3(4):e00156-12. http://dx.doi.org/10.1128/mBio.00156-12.
26. Behrens S, Widder S, Mannala GK, Qing X, Madhugiri R, Kefer N, Mraheil MA, Rattei T, Hain T. 2014. Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs. PLoS One 9:e83979. http://dx.doi.org/10.1371/journal.pone.0083979.
27. Chatterjee A, Johnson CM, Shu CC, Kaznessis YN, Ramkrishna D, Dunny GM, Hu WS. 2011. Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation. Proc. Natl. Acad. Sci. U. S. A. 108:9721-9726. http://dx.doi.org/10.1073/pnas.1101569108.
28. Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. 2009. Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271. http://dx.doi.org/10.1126/science.1176951.
29. Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC. 2012. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc. Natl. Acad. Sci. U. S. A. 109:E1277-E1286. http://dx.doi.org/10.1073/pnas.1201061109.
30. Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penadés JR, Valle J, Solano C, Gingeras TR. 2011. Genome-wide antisense transcription drives mRNA processing in bacteria. Proc. Natl. Acad. Sci. U. S. A. 108: 20172-20177. http://dx.doi.org/10.1073/pnas.1113521108.
31. Passalacqua KD, Varadarajan A, Weist C, Ondov BD, Byrd B, Read TD, Bergman NH. 2012. Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis. PLoS One 7:e43350. http://dx.doi.org/10.1371/journal.pone.0043350.
32. Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, Bécavin C, Archambaud C, Cossart P, Sorek R. 2012. Comparative transcriptomics of pathogenic and nonpathogenic Listeria species. Mol. Syst. Biol. 8:583. http://dx.doi.org/10.1038/msb.2012.11.
33. Lybecker M, Zimmermann B, Bilusic I, Tukhtubaeva N, Schroeder R. 2014. The double-stranded transcriptome of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 111:3134-3139. http://dx.doi.org/10.1073/pnas.1315974111.
34. Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P. 2013. The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat. Rev. Microbiol. 11:75-82. http://dx.doi.org/10.1038/nrmicro2934.
35. Cho BK, Zengler K, Qiu Y, Park YS, Knight EM, Barrett CL, Gao Y, Palsson BØ. 2009. The transcription unit architecture of the Escherichia coli genome. Nat. Biotechnol. 27:1043-1049. http://dx.doi.org/10.1038/nbt.1582.
36. Kim D, Hong JS, Qiu Y, Nagarajan H, Seo JH, Cho BK, Tsai SF, Palsson BØ. 2012. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet. 8:e1002867. http://dx.doi.org/10.1371/journal.pgen.1002867.
37. Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E. 2009. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 4:e7526. http://dx.doi.org/10.1371/journal.pone.0007526.
38. Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J. 2013. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41: D203-D213. http://dx.doi.org/10.1093/nar/gkt1054.
39. Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J. 2012. How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics 13:734. http://dx.doi.org/10.1186/1471-2164-13-734.
40. Li S, Dong X, Su Z. 2013. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K-12 through accurate fulllength transcripts assembling. BMC Genomics 14:520. http://dx.doi.org/10.1186/1471-2164-14-520.
41. Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JC. 2013. An infection-relevant transcriptomic compendium for Salmonella enterica serovar Typhimurium. Cell Host Microbe 14:683-695. http://dx.doi.org/10.1016/j.chom.2013.11.010.
42. Fabich AJ, Jones SA, Chowdhury FZ, Cernosek A, Anderson A, Smalley D, McHargue JW, Hightower GA, Smith JT, Autieri SM, Leatham MP, Lins JJ, Allen RL, Laux DC, Cohen PS, Conway T. 2008. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect. Immun. 76:1143-1152. http://dx.doi.org/10.1128/IAI.01386-07.
43. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7:709-715. http://dx.doi.org/10.1038/nmeth.1491.
44. Richmond CS, Glasner JD, Mau R, Jin H, Blattner FR. 1999. Genomewide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27: 3821-3835. http://dx.doi.org/10.1093/nar/27.19.3821.
45. Tao H, Bausch C, Richmond C, Blattner FR, Conway T. 1999. Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181:6425-6440.
46. Reference deleted.
47. Lin YF, A DR, Guan S, Mamanova L, McDowall KJ. 2013. A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease. BMC Genomics 14:620. http://dx.doi.org/10.1186/1471-2164-14-620.
48. Wiegand S, Dietrich S, Hertel R, Bongaerts J, Evers S, Volland S, Daniel R, Liesegang H. 2013. RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 14:667. http://dx.doi.org/10.1186/1471-2164-14-667.
49. Balasubramanian D, Kumari H, Jaric M, Fernandez M, Turner KH, Dove SL, Narasimhan G, Lory S, Mathee K. 2014. Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. Nucleic Acids Res. 42:979-998. http://dx.doi.org/10.1093/nar/gkt942.
50. Bohannon DE, Connell N, Keener J, Tormo A, Espinosa-Urgel M, Zambrano MM, Kolter R. 1991. Stationary-phase-inducible “gearbox” promoters: differential effects of katF mutations and role of sigma 70. J. Bacteriol. 173:4482-4492.
51. Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloe D, Le Gall C, Schaeffer B, Le Crom S, Guedj M, Jaffrezic F. 2012. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief. Bioinform. 14:671-683. http://dx.doi.org/10.1093/bib/bbs046.
52. Egan SE, Fliege R, Tong S, Shibata A, Wolf RE, Jr, Conway T. 1992. Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon. J. Bacteriol. 174:4638-4646.
53. Deana A, Celesnik H, Belasco JG. 2008. The bacterial enzyme RppH triggers messenger RNA degradation by 5= pyrophosphate removal. Nature 451:355-358. http://dx.doi.org/10.1038/nature06475.
54. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. 2005. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23:137-144. http://dx.doi.org/10.1038/nbt1053.
55. Shimada T, Yamamoto K, Ishihama A. 2011. Novel members of the cra regulon involved in carbon metabolism in Escherichia coli. J. Bacteriol. 193:649-659. http://dx.doi.org/10.1128/JB.01214-10.
56. Thomason MK, Storz G. 2010. Bacterial antisense RNAs: how many are there, and what are they doing? Annu. Rev. Genet. 44:167-188. http://dx.doi.org/10.1146/annurev-genet-102209-163523.
57. Tuerk C, MacDougal S, Gold L. 1992. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. U. S. A. 89:6988-6992. http://dx.doi.org/10.1073/pnas.89.15.6988.
58. Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. Bioinformatics 27:-1017-1018. http://dx.doi.org/10.1093/bioinformatics/btr064.
59. Robison K, McGuire AM, Church GM. 1998. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284:241-254. http://dx.doi.org/10.1006/jmbi.1998.2160.
60. Mitchell JE, Zheng D, Busby SJ, Minchin SD. 2003. Identification and analysis of “extended_10” promoters in Escherichia coli. Nucleic Acids Res. 31:4689-4695. http://dx.doi.org/10.1093/nar/gkg694.
61. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. 2009. JBrowse: a next-generation genome browser. Genome Res. 19:-1630-1638. http://dx.doi.org/10.1101/gr.094607.109.
62. Bernstein JA, Khodursky AB, Lin PH, Lin-Chao S, Cohen SN. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. U. S. A. 99:9697-9702. http://dx.doi.org/10.1073/pnas.112318199.
63. Kingsford CL, Ayanbule K, Salzberg SL. 2007. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 8:R22. http://dx.doi.org/10.1186/gb-2007-8-2-r22.
64. Potrykus K, Murphy H, Chen X, Epstein JA, Cashel M. 2010. Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res. 38:1636-1651. http://dx.doi.org/10.1093/nar/gkp1150.
65. Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2014. GenBank. Nucleic Acids Res. 42:D32-D37. http://dx.doi.org/10.1093/nar/gkt1030.
66. Cole ST, Honoré N. 1989. Transcription of the sulA-ompA region of Escherichia coli during the SOS response and the role of an antisense RNA molecule. Mol. Microbiol. 3:715-722. http://dx.doi.org/10.1111/j.1365-2958.1989.tb00220.x.
67. Michán C, Manchado M, Dorado G, Pueyo C. 1999. In vivo transcription of the Escherichia coli oxyR regulon as a function of growth phase and in response to oxidative stress. J. Bacteriol. 181:2759-2764.
68. Vecerek B, Moll I, Bläsi U. 2007. Control of fur synthesis by the noncoding RNA RyhB and iron-responsive decoding. EMBO J. 26:965-975. http://dx.doi.org/10.1038/sj.emboj.7601553.
69. Cunningham L, Guest JR. 1998. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 144(Part 8):2113-2123. http://dx.doi.org/10.1099/00221287-144-8-2113.
70. Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136:629-641. http://dx.doi.org/10.1016/j.cell.2009.02.006.
71. Chen YJ, Liu P, Nielsen AA, Brophy JA, Clancy K, Peterson T, Voigt CA. 2013. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat. Methods 10:659-664. http://dx.doi.org/10.1038/nmeth.2515.
72. Georg J, Hess WR. 2011. Cis-antisense RNA, another level of gene regulation in bacteria. Microbiol. Mol. Biol. Rev. 75:286-300. http://dx.doi.org/10.1128/MMBR.00032-10.
73. Juneau K, Miranda M, Hillenmeyer ME, Nislow C, Davis RW. 2006. Introns regulate RNA and protein abundance in yeast. Genetics 174: 511-518. http://dx.doi.org/10.1534/genetics.106.058560.
74. Koralewski TE, Krutovsky KV. 2011. Evolution of exon-intron structure and alternative splicing. PLoS One 6:e18055. http://dx.doi.org/10.1371/journal.pone.0018055.
75. Carmel L, Rogozin IB, Wolf YI, Koonin EV. 2007. Patterns of intron gain and conservation in eukaryotic genes. BMC Evol. Biol. 7:192. http://dx.doi.org/10.1186/1471-2148-7-192.
76. Rocha EP. 2008. The organization of the bacterial genome. Annu. Rev. Genet. 42:211-233. doi:http://dx.doi.org/10.1146/annurev.genet.42.110807.091653.
77. Neidhardt FC, Bloch PL, Smith DF. 1974. Culture medium for enterobacteria. J. Bacteriol. 119:736-747.
78. Wilmes-Riesenberg MR, Wanner BL. 1992. TnphoA and TnphoA’ elements for making and switching fusions for study of transcription, translation, and cell surface localization. J. Bacteriol. 174:4558-4575.
79. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. http://dx.doi.org/10.1186/gb-2009-10-3-r25.
80. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
81. Shimada T, Fujita N, Maeda M, Ishihama A. 2005. Systematic search for the cra-binding promoters using genomic SELEX system. Genes Cells 10: 907-918. http://dx.doi.org/10.1111/j.1365-2443.2005.00888.x.
82. Jishage M, Ishihama A. 1995. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38. J. Bacteriol. 177:6832-6835.
83. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R. 2010. A single-base resolution map of an archaeal transcriptome. Genome Res. 20:133-141.