RNA-Seq of Bacillus licheniformis: Active regulatory RNA features expressed within a productive fermentation

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Wiegand, Sandra ^a   Dietrich, Sascha ^a   Hertel, Robert ^a   Bongaerts, Johannes ^b   Evers, Stefan ^b   Volland, Sonja ^a   Daniel, Rolf ^a   Liesegang, Heiko ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b HENKEL KGAA   (Germany)

Author keywords

Antisense RNA; DRNA Seq; NcRNA; Operon prediction; Reannotation; RNA based regulation; SRNA; Subtilisin; Transcription start site; UTR

Indexed keywords

COMPLEMENTARY RNA; RNA 5S; SUBTILISIN; TRANSFER RNA; UNTRANSLATED RNA; 3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACTERIAL RNA; PEPTIDE HYDROLASE; TRANSCRIPTOME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACILLUS LICHENIFORMIS; BACTERIAL GENOME; BACTERIAL STRAIN; BASE PAIRING; FERMENTATION; GENE LOCUS; GENE MAPPING; NONHUMAN; OPEN READING FRAME; OPERON; PROCESS OPTIMIZATION; PROTEIN EXPRESSION; REGULATORY SEQUENCE; RIBOSWITCH; RNA SEQUENCE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION TERMINATION; UNTRANSLATED REGION; BACILLUS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SEQUENCE ANALYSIS;

BACILLUS (BACTERIUM); BACILLUS LICHENIFORMIS; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; BACILLUS; BASE SEQUENCE; CLUSTER ANALYSIS; FERMENTATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; OPERON; PEPTIDE HYDROLASES; RNA, ANTISENSE; RNA, BACTERIAL; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, RNA; SUBTILISIN; TRANSCRIPTION INITIATION SITE; TRANSCRIPTOME;

EID: 84884737727     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-667     Document Type: Article

References (88)

1. Veith B, Herzberg C, Steckel S, Feesche J, Maurer K-H, Ehrenreich P, Bäumer S, Henne A, Liesegang H, Merkl R, Ehrenreich A, Gottschalk G. The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol 2004, 7:204-211. 10.1159/000079829, 15383718.
2. Schallmey M, Singh A, Ward O. Developments in the use of Bacillus species for industrial production. Can J Microbiol 2004, 50:1-17. 10.1139/w03-076, 15052317.
3. Maurer K-H. Detergent proteases. Curr Opin Biotechnol 2004, 15:330-334. 10.1016/j.copbio.2004.06.005, 15296930.
4. Çali{dotless}k P, Takac S, Çali{dotless}k G, Özdamar T. Serine alkaline protease overproduction capacity of Bacillus licheniformis. Enzyme Microb Tech 2000, 26:45-60.
5. Çali{dotless}k P, Çali{dotless}k G, Takaç S, Ozdamar TH. Metabolic flux analysis for serine alkaline protease fermentation by Bacillus licheniformis in a defined medium: effects of the oxygen transfer rate. Biotechnol Bioeng 1999, 64:151-167. 10.1002/(SICI)1097-0290(19990720)64:2<151::AID-BIT4>3.0.CO;2-U, 10397851.
6. Degering C, Eggert T, Puls M, Bongaerts J, Evers S, Maurer K-H, Jaeger K-E. Optimization of protease secretion in Bacillus subtilis and Bacillus licheniformis by screening of homologous and heterologous signal peptides. Appl Environ Microbiol 2010, 76:6370-6376. 10.1128/AEM.01146-10, 2950444, 20709850.
7. Gupta R, Beg QK, Lorenz P. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 2002, 59:15-32. 10.1007/s00253-002-0975-y, 12073127.
8. Nielsen AK, Breüner A, Krzystanek M, Andersen JT, Poulsen TA, Olsen PB, Mijakovic I, Rasmussen MD. Global transcriptional analysis of Bacillus licheniformis reveals an overlap between heat shock and iron limitation stimulon. J Mol Microbiol Biotechnol 2010, 18:162-173. 10.1159/000315457, 20530967.
9. Rey M, Ramaiya P, Nelson N, Brody-Karpin S. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol 2004, 5:R77. 10.1186/gb-2004-5-10-r77, 545597, 15461803.
10. Waschkau B, Waldeck J, Wieland S, Eichstädt R, Meinhardt F. Generation of readily transformable Bacillus licheniformis mutants. Appl Microbiol Biotechnol 2008, 78:181-188. 10.1007/s00253-007-1278-0, 18046550.
11. Nahrstedt H, Waldeck J, Gröne M, Eichstädt R, Feesche J, Meinhardt F. Strain development in Bacillus licheniformis: Construction of biologically contained mutants deficient in sporulation and DNA repair. J Biotechnol 2005, 119:245-254. 10.1016/j.jbiotec.2005.04.003, 15951041.
12. Madan Babu M, Teichmann SA, Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol 2006, 358:614-633. 10.1016/j.jmb.2006.02.019, 16530225.
13. Romby P, Charpentier E. An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol Life Sci 2010, 67:217-237. 10.1007/s00018-009-0162-8, 19859665.
14. Storz G, Vogel J, Wassarman KM. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011, 43:880-891. 10.1016/j.molcel.2011.08.022, 3176440, 21925377.
15. Gottesman S, Storz G. Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011, 3:a003798. 10.1101/cshperspect.a003798, 20980440.
16. Waters L, Storz G. Regulatory RNAs in bacteria. Cell 2009, 136:615-628. 10.1016/j.cell.2009.01.043, 3132550, 19239884.
17. Schmiedel JM, Axmann IM, Legewie S. Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One 2012, 7:e42296. 10.1371/journal.pone.0042296, 3424230, 22927924.
18. Georg J, Hess WR. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol R 2011, 75:286-300.
19. Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 2007, 10:102-109. 10.1016/j.mib.2007.03.012, 17387036.
20. Sesto N, Wurtzel O, Archambaud C, Sorek R, Cossart P. The excludon: a new concept in bacterial antisense RNA-mediated gene regulation. Nat Rev Microbiol 2013, 11:75-82.
21. Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010, 11:9-16.
22. Güell M, Yus E, Lluch-Senar M, Serrano L. Bacterial transcriptomics: what is beyond the RNA horiz-ome?. Nat Rev Microbiol 2011, 9:658-669. 10.1038/nrmicro2620, 21836626.
23. Breaker RR. Prospects for riboswitch discovery and analysis. Mol Cell 2011, 43:867-879. 10.1016/j.molcel.2011.08.024, 21925376.
24. Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LOF. Before It Gets Started: Regulating Translation at the 5' UTR. Comp Funct Genom 2012, 2012:475731.
25. Zoll J, Heus H, van Kuppeveld F, Melchers W. The structure-function relationship of the enterovirus 3'-UTR. Virus Res 2009, 139:209-216. 10.1016/j.virusres.2008.07.014, 18706945.
26. Kaberdin VR, Bläsi U. Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol Rev 2006, 30:967-979. 10.1111/j.1574-6976.2006.00043.x, 16989654.
27. Evguenieva-Hackenberg E, Klug G. New aspects of RNA processing in prokaryotes. Curr Opin Microbiol 2011, 14:587-592. 10.1016/j.mib.2011.07.025, 21945217.
28. Vivancos AP, Güell M, Dohm JC, Serrano L, Himmelbauer H. Strand-specific deep sequencing of the transcriptome. Genome Res 2010, 20:989-999. 10.1101/gr.094318.109, 2892100, 20519413.
29. Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB. Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathog 2011, 7:e1002342. 10.1371/journal.ppat.1002342, 3207917, 22072964.
30. Vockenhuber M-P, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 2011, 8:468-477. 10.4161/rna.8.3.14421, 3218513, 21521948.
31. Schlüter J-P, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 2010, 11:245. 10.1186/1471-2164-11-245, 2873474, 20398411.
32. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010, 464:250-255. 10.1038/nature08756, 20164839.
33. Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH. Structure and complexity of a bacterial transcriptome. J Bacteriol 2009, 191:3203-3211. 10.1128/JB.00122-09, 2687165, 19304856.
34. Dötsch A, Eckweiler D, Schniederjans M, Zimmermann A, Jensen V, Scharfe M, Geffers R, Häussler S. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS One 2012, 7:e31092. 10.1371/journal.pone.0031092, 3272035, 22319605.
35. Kristoffersen SM, Haase C, Weil MR, Passalacqua KD, Niazi F, Hutchison SK, Desany B, Kolsto A-B, Tourasse NJ, Read TD, Okstad OA. Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biol 2012, 13:R30. 10.1186/gb-2012-13-4-r30, 3446304, 22537947.
36. Wurtzel O, Sesto N, Mellin JR, Karunker I, Edelheit S, Bécavin C, Archambaud C, Cossart P, Sorek R. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 2012, 8:1-14.
37. Lemire S, Figueroa-Bossi N, Bossi L. Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors. PLoS Genet 2011, 7:e1002149. 10.1371/journal.pgen.1002149, 3121763, 21731505.
38. Zheng X, Hu G-Q, She Z-S, Zhu H. Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics 2011, 12:361. 10.1186/1471-2164-12-361, 3160421, 21749696.
39. Nakagawa S, Niimura Y, Miura K, Gojobori T. Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci U S A 2010, 107:6382-6387. 10.1073/pnas.1002036107, 2851962, 20308567.
40. Veening J-W, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, Kuipers OP. Transient heterogeneity in extracellular protease production by Bacillus subtilis. Mol Syst Biol 2008, 4:184. 2387230, 18414485.
41. Shank EA, Kolter R. Extracellular signaling and multicellularity in Bacillus subtilis. Curr Opin Microbiol 2011, 14:741-747. 10.1016/j.mib.2011.09.016, 3291330, 22024380.
42. Gunka K, Commichau FM. Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation. Mol Microbiol 2012, 85:213-224. 10.1111/j.1365-2958.2012.08105.x, 22625175.
43. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Hartig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, et al. Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis. Science 2012, 335:1103-1106. 10.1126/science.1206848, 22383849.
44. Brantl S. Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria. Future Microbiol 2012, 7:853-871. 10.2217/fmb.12.59, 22827307.
45. Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009, 25:2271-2278. 10.1093/bioinformatics/btp393, 19561336.
46. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2011, 39:D141-D145. 10.1093/nar/gkq1129, 3013711, 21062808.
47. Sherlock G. Analysis of large-scale gene expression data. Curr Opin Immunol 2000, 12:201-205. 10.1016/S0952-7915(99)00074-6, 10712947.
48. Pool MR. Signal recognition particles in chloroplasts, bacteria, yeast and mammals (Review). Mol Membr Biol 2005, 22:3-15. 10.1080/09687860400026348, 16092520.
49. Hardcastle TJ, Kelly KA. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010, 11:422. 10.1186/1471-2105-11-422, 2928208, 20698981.
50. Kiley Thomason M, Storz G. Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet 2010, 44:167-188. 10.1146/annurev-genet-102209-163523, 3030471, 20707673.
51. Levine E, Zhang Z, Kuhlman T, Hwa T. Quantitative characteristics of gene regulation by small RNA. PLoS Biol 2007, 5:e229. 10.1371/journal.pbio.0050229, 1994261, 17713988.
52. Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 2011, 108:1-6.
53. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons B, Sorek R. A single-base resolution map of an archaeal transcriptome. Genome Res 2010, 20:133-141. 10.1101/gr.100396.109, 2798825, 19884261.
54. Jäger D, Sharma C, Thomsen J, Ehlers C, Vogel J, Schmitz R. Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci U S A 2009, 106:21878-21882. 10.1073/pnas.0909051106, 2799843, 19996181.
55. Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Médigue C, Danchin A. From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 2009, 155:1758-1775. 10.1099/mic.0.027839-0, 2885750, 19383706.
56. Rasmussen S, Nielsen H, Jarmer H. The Transcriptionally Active Regions in the Genome of Bacillus subtilis. Mol Microbiol 2009, 73:1043-1057. 10.1111/j.1365-2958.2009.06830.x, 2784878, 19682248.
57. Irnov I, Sharma C, Vogel J, Winkler W. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010, 38:6637-6651. 10.1093/nar/gkq454, 2965217, 20525796.
58. Mäder U, Schmeisky AG, Flórez LA, Stülke J. SubtiWiki-a comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res 2012, 40:D1278-D1287. 10.1093/nar/gkr923, 3245094, 22096228.
59. Eiamphungporn W, Helmann JD. Extracytoplasmic function sigma factors regulate expression of the Bacillus subtilis yabE gene via a cis-acting antisense RNA. J Bacteriol 2009, 191:1101-1105. 10.1128/JB.01530-08, 2632094, 19047346.
60. Gimpel M, Heidrich N, Mäder U, Krügel H, Brantl S. A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon. Mol Microbiol 2010, 76:990-1009. 10.1111/j.1365-2958.2010.07158.x, 20444087.
61. Geissmann T, Chevalier C, Cros M-J, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P. A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res 2009, 37:7239-7257. 10.1093/nar/gkp668, 2790875, 19786493.
62. Marchais A, Duperrier S, Durand S, Gautheret D, Stragier P. CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers. RNA Biol 2011, 8:358-364. 10.4161/rna.8.3.14998, 3218505, 21532344.
63. Saito S, Kakeshita H, Nakamura K. Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis. Gene 2009, 428:2-8. 10.1016/j.gene.2008.09.024, 18948176.
64. Silvaggi J, Perkins J, Losick R. Genes for Small, Noncoding RNAs under Sporulation Control in Bacillus subtilis. J Bacteriol 2006, 188:532-541. 10.1128/JB.188.2.532-541.2006, 1347314, 16385044.
65. Jahn N, Preis H, Wiedemann C, Brantl S. BsrG/SR4 from Bacillus subtilis-the first temperature-dependent type I toxin-antitoxin system. Mol Microbiol 2012, 83:579-598. 10.1111/j.1365-2958.2011.07952.x, 22229825.
66. Feucht A, Evans L, Errington J. Identification of sporulation genes by genome-wide analysis of the σE regulon of Bacillus subtilis. J Mol Biol 2003, 149:3023-3034.
67. Wemhoff S. Deletionsmutagenese des yqfCD/phoH-Operons in Bacillus licheniformis - Untersuchungen zur Auswirkung auf die Sporulation 2008, Westfälische Wilhelms-Universität Münster, Institut für Molekulare Mikrobiologie und Biotechnologie, Master thesis.
68. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
69. Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. BMC Bioinformatics 2011, 12:480. 10.1186/1471-2105-12-480, 3315510, 22177264.
70. Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
71. The UniProt Consortium The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009, 37:D169-D174. 2686606, 18836194, The UniProt Consortium.
72. Mao F, Dam P, Chou J, Olman V, Xu Y. DOOR: a database for prokaryotic operons. Nucleic Acids Res 2009, 37:D459-D463. 10.1093/nar/gkn757, 2686520, 18988623.
73. Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res 2009, 37:D479-D482. 10.1093/nar/gkn784, 2686487, 18948284.
74. Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 2007, 8:R22. 10.1186/gb-2007-8-2-r22, 1852404, 17313685.
75. Overbeek R. The ERGOTM genome analysis and discovery system. Nucleic Acids Res 2003, 31:164-171. 10.1093/nar/gkg148, 165577, 12519973.
76. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 10.1093/bioinformatics/16.10.944, 11120685.
77. Bose M, Barber RD. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006, 6:223-227.
78. Casjens S. Prophages and bacterial genomics: what have we learned so far?. Mol Microbiol 2003, 49:277-300. 10.1046/j.1365-2958.2003.03580.x, 12886937.
79. Saeed A, Bhagabati N, Braisted J, Liang W, Sharov V, Howe E, Li J, Thiagarajan M, White J, Quackenbush J. TM4 microarray software suite. Methods Enzymol 2006, 411:134.
80. Koburger T, Weibezahn J, Bernhardt J, Homuth G, Hecker M. Genome-wide mRNA profiling in glucose starved Bacillus subtilis cells. Mol Genet Genomics 2005, 274:1-12. 10.1007/s00438-005-1119-8, 15809868.
81. Hahne H, Mäder U, Otto A, Bonn F, Steil L, Bremer E, Hecker M, Becher D. A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 2010, 192:870-882. 10.1128/JB.01106-09, 2812467, 19948795.
82. Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21:3422-3423. 10.1093/bioinformatics/bti553, 15976072.
83. Darling AE, Mau B, Perna NT. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5:e11147. 10.1371/journal.pone.0011147, 2892488, 20593022.
84. Marco-Sola S, Sammeth M, Guigó R, Ribeca P. The Gem mapper: fast, accurate and versatile alignment by filtration. Nat Methods 2012, 9:1186-1188.
85. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics 2009, 25:1335-1337. 10.1093/bioinformatics/btp157, 2732312, 19307242.
86. Martin J, Zhu W, Passalacqua K, Bergman N, Borodovsky M. Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 2010, 11:S10.
87. Schwarzer M. Physiologische Untersuchungen zur Regulation des Aminosäure-Stoffwechsels von Bacillus licheniformis DSM13 2010, Georg-August-Universität Göttingen, Institut für Mikrobiologie und Genetik, PhD thesis.
88. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning - A Laboratory Manual 1989, Cold Spring Harbor: Cold Spring Harbor Laboratory Press.