The transcriptionally active regions in the genome of Bacillus subtilis

Abstract

Summary The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand‐specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome‐wide expression during mid‐exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non‐coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22 , is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA . Through this work we have discovered a long conserved 3′ untranslated region (UTR) in a group of membrane‐associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN , which encodes a target of the twin‐arginine translocase (Tat) protein translocation system.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 78

1. 1.

   Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-410.

   Not in our library10.1016/s0022-2836(05)80360-2

2. 2.

   Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol. 1961;81:741-746.

   Not in our library10.1128/jb.81.5.741-746.1961

3. 3.

   Ando Y, Asari S, Suzuma S, Yamane K, Nakamura K. Expression of a small RNA, BS203 RNA, from the yocI–yocJ intergenic region of the Bacillus subtilis genome. FEMS Microbiol Lett. 2002;207:29-33.

   Not in our library10.1111/j.1574-6968.2002.tb11023.x

4. 4.

   Auchtung JM, Lee CA, Grossman AD. Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. J Bacteriol. 2006;188:5273-5285.

   Not in our library10.1128/jb.00300-06

5. 5.
   From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later · 2009

   No notice
6. 6.

   Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, et al. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004;306:2242-2246.

   Not in our library10.1126/science.1103388

7. 7.

   Burguière P, Auger S, Hullo MF, Danchin A, Martin-Verstraete I. Three different systems participate in l-cystine uptake in Bacillus subtilis. J Bacteriol. 2004;186:4875-4884.

   Not in our library10.1128/jb.186.15.4875-4884.2004

8. 8.

   Burkholder PR, Giles NH. Induced biochemical mutations in Bacillus subtilis. Am J Bot. 1947;34:345-348.

   Not in our library

9. 9.

   Cervantes C, Ji G, Ramirez J, Silver S. Resistance to arsenic compounds in microorganisms. FEMS Microbiol Rev. 1994;15:355-367.

   Not in our library10.1111/j.1574-6976.1994.tb00145.x

10. 10.

    Cohn F. Untersuchungen über Bakterien. Beitr Biol Pflanzen. 1872;1:127-224.

    Not in our library

11. 11.

    Cohn F. Untersuchungen über Bakterien, IV. Beiträge zur Biologie der Bacillen. Beitr Biol Pflanzen. 1876;2:249-277.

    Not in our library

12. 12.

    Conn HJ. The identity of Bacillus subtilis. J Infect Dis. 1930;46:341-350.

    Not in our library

13. 13.

    David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, et al. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA. 2006;103:5320-5325.

    Not in our library10.1073/pnas.0601091103

14. 14.

    DeLisa MP, Tullman D, Georgiou G. Folding quality control in the export of proteins by the bacterial twin-arginine translocation pathway. Proc Natl Acad Sci USA. 2003;100:6115-6120.

    Not in our library10.1073/pnas.0937838100

15. 15.

    Deutscher J, Galinier A, Martin-Verstraete I, Sonenshein AL, Hoch JA, Losick R. Carbohydrate uptake and metabolism. Bacillus subtilis and its closest relatives. 2002;129-150.

    Not in our library

16. 16.

    Dubey AK, Baker CS, Suzuki K, Jones AD, Pandit P, Romeo T, Babitzke P. CsrA regulates translation of the Escherichia coli carbon starvation gene, cstA, by blocking ribosome access to the cstA transcript. J Bacteriol. 2003;185:4450-4460.

    Not in our library10.1128/jb.185.15.4450-4460.2003

17. 17.

    Ehrenberg CG. Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes. Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833–1835. 1835;145-336.

    Not in our library

18. 18.

    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.

    Not in our library10.1128/jb.01530-08

19. 19.

    Fillinger S, Boschi-Muller S, Azza S, Dervyn E, Branlant G, Aymerich S. Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem. 2000;275:14031-14037.

    Not in our library10.1074/jbc.275.19.14031

20. 20.

    Gaballa A, Antelmann H, Aguilar C, Khakh SK, Kyung-Bok S, Smaldone GT, Helmann JD. The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small basic proteins. Proc Natl Acad Sci USA. 2008;105:11927-11932.

    Not in our library10.1073/pnas.0711752105

21. 21.

    Gaidenko TA, Kim TJ, Weigel AL, Brody MS, Price CW. The blue-light receptor YtvA acts in the environmental stress signaling pathway of Bacillus subtilis. J Bacteriol. 2006;188:6387-6395.

    Not in our library10.1128/jb.00691-06

22. 22.

    Gardan R, Rapoport G, Débarbouille M. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol. 1995;249:843-856.

    Not in our library10.1006/jmbi.1995.0342

23. 23.

    Gollnick P, Babitzke P, Antson A, Yanofsky C. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu Rev Genet. 2005;39:47-68.

    Not in our library10.1146/annurev.genet.39.073003.093745

24. 24.

    Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA Web suite. Nucleic Acids Res. 2008;36:W70-W74.

    Not in our library10.1093/nar/gkn188

25. 25.

    Grundy FJ, Henkin TM. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram-positive bacteria. Mol Microbiol. 1998;30:737-774.

    Not in our library10.1046/j.1365-2958.1998.01105.x

26. 26.

    Haldenwang WG. The sigma factors of Bacillus subtilis. Microbiol Mol Biol Rev. 1995;59:1-30.

    Not in our library10.1128/mr.59.1.1-30.1995

27. 27.

    Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 2004;20:3682-3686.

    Not in our library10.1093/bioinformatics/bth423

28. 28.

    Helmann JD, Wu MF, Kobel PA, Gamo FJ, Wilson M, Morshedi MM, et al. Global transcriptional response of Bacillus subtilis to heat shock. J Bacteriol. 2001;183:7318-7328.

    Not in our library10.1128/jb.183.24.7318-7328.2001

29. 29.
    Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species · 2005

    No notice
30. 30.

    Huang JM, La Ragione RM, Nunez A, Cutting SM. Immunostimulatory activity of Bacillus spores. FEMS Immunol Med Microbiol. 2008;53:195-203.

    Not in our library10.1111/j.1574-695x.2008.00415.x

31. 31.

    Huber W, Toedling J, Steinmetz LM. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics. 2006;22:1963-1970.

    Not in our library10.1093/bioinformatics/btl289

32. 32.

    Jarmer H, Larsen TS, Krogh A, Saxild HH, Brunak S, Knudsen S. Sigma A recognition sites in the Bacillus subtilis genome. Microbiology. 2001;147:2417-2424.

    Not in our library10.1099/00221287-147-9-2417

33. 33.

    Jerga A, Lu YJ, Schujman GE, de Mendoza D, Rock CO. Identification of a soluble diacylglycerol kinase required for lipoteichoic acid production in Bacillus subtilis. J Biol Chem. 2007;282:21738-21745.

    Not in our library10.1074/jbc.m703536200

34. 34.

    Jongbloed JDH, Grieger U, Antelmann H, Hecker M, Nijland R, Bron S, van Dijl JM. Two minimal Tat translocases in Bacillus. Mol Microbiol. 2004;54:1319-1325.

    Not in our library10.1111/j.1365-2958.2004.04341.x

35. 35.

    Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480-D484.

    Not in our library10.1093/nar/gkm882

36. 36.

    Kawano M, Reynolds AA, Miranda-Rios J, Storz G. Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 2005;33:1040-1050.

    Not in our library10.1093/nar/gki256

37. 37.

    Kent WJ. blat– the blast-like alignment tool. Genome Res. 2002;12:656-664.

    Not in our library10.1101/gr.229202

38. 38.
    Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake · 2007

    No notice
39. 39.

    Krogh S, O'Reailly M, Nolan N, Devine KM. The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome are highly homologous. Microbiology. 1996;142:2031-2040.

    Not in our library10.1099/13500872-142-8-2031

40. 40.

    Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, et al. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature. 1997;390:249-256.

    Not in our library10.1038/36786

Cited by papers we hold 5

• Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions · 2016
  No notice
• Association of RNAs with Bacillus subtilis Hfq. · 2013
  Not checked
• Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of Bacillus subtilis mRNAs · 2012
  No notice
• Investigation of the Staphylococcus aureus GraSR Regulon Reveals Novel Links to Virulence, Stress Response and Cell Wall Signal Transduction Pathways · 2011
  No notice
• Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes · 2010
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.