Alternative sigma factor σ h activates competence gene expression in Lactobacillus sakei

BMC Microbiology

Volumn 12, Issue , 2012, Pages

  Schmid, Solveig ^a,b,d   Bevilacqua, Claudia ^c   Crutz Le Coq, Anne Marie ^a  

^a UMR1319 MICALIS   (France)

^b AGROPARISTECH   (France)

^c UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^d NONE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALERNATIVE SIGMA FACTOR H; SIGMA FACTOR; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; SIGH PROTEIN, BACTERIA; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENOME; BACTERIUM COMPETENCE; CONTROLLED STUDY; FIRMICUTES; GENE EXPRESSION PROFILING; LACTOBACILLUS SAKEI; NONHUMAN; PROTEIN FUNCTION; SPOROGENESIS; TRANSCRIPTOMICS; BACTERIUM TRANSFORMATION; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; LACTOBACILLUS; METABOLISM; MICROBIAL VIABILITY; NUCLEOTIDE SEQUENCE;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); FIRMICUTES; LACTOBACILLUS SAKEI;

BACTERIAL PROTEINS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; LACTOBACILLUS; MICROBIAL VIABILITY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGMA FACTOR; TRANSCRIPTION, GENETIC; TRANSCRIPTOME; TRANSFORMATION, BACTERIAL;

EID: 84857955907     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-12-32     Document Type: Article

References (58)

1. Multiple sigma subunits and the partitioning of bacterial transcription space. Gruber TM, Gross CA, Annu Rev Microbiol 2003 57 441 466 10.1146/annurev.micro.57.030502.090913 14527287 (Pubitemid 37392951)
2. The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Staron A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T, Mol Microbiol 2009 74 3 557 581 10.1111/j.1365-2958.2009.06870.x 19737356
3. The sigma 70 family: sequence conservation and evolutionary relationships. Lonetto M, Gribskov M, Gross CA, J Bacteriol 1992 174 12 3843 3849 1597408
4. The sigma70 family of sigma factors. Paget MS, Helmann JD, Genome Biol 2003 4 1 203 10.1186/gb-2003-4-1-203 12540296 (Pubitemid 36181897)
5. Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis. Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD, J Bacteriol 2002 184 17 4881 4890 10.1128/JB.184.17.4881-4890.2002 12169614
6. Compartmentalization of gene expression during Bacillus subtilis spore formation. Hilbert DW, Piggot PJ, Microbiol Mol Biol Rev 2004 68 2 234 262 10.1128/MMBR.68.2.234-262.2004 15187183 (Pubitemid 38756864)
7. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Grossman AD, Annu Rev Genet 1995 29 477 508 10.1146/annurev.ge.29.120195.002401 8825484 (Pubitemid 26006321)
8. An autoregulatory circuit affecting peptide signaling in Bacillus subtilis. Lazazzera BA, Kurtser IG, McQuade RS, Grossman AD, J Bacteriol 1999 181 17 5193 5200 10464187 (Pubitemid 29416336)
9. Expression of competence genes in Bacillus subtilis. Albano M, Hahn J, Dubnau D, J Bacteriol 1987 169 7 3110 3117 3110135 (Pubitemid 17106334)
10. Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Schultz D, Wolynes PG, Ben Jacob E, Onuchic JN, Proc Natl Acad Sci USA 2009 106 50 21027 21034 10.1073/pnas.0912185106 19995980
11. Incidence and function of sigma factors in Ralstonia metallidurans and other bacteria. Nies DH, Arch Microbiol 2004 18 4 255 268 (Pubitemid 38471469)
12. A new staphylococcal sigma factor in the conserved gene cassette: functional significance and implication for the evolutionary processes. Morikawa K, Inose Y, Okamura H, Maruyama A, Hayashi H, Takeyasu K, Ohta T, Genes Cells 2003 8 8 699 712 10.1046/j.1365-2443.2003.00668.x 12875655 (Pubitemid 36974698)
13. Bacterial "competence" genes: signatures of active transformation, or only remnants? Claverys JP, Martin B, Trends Microbiol 2003 11 4 161 165 10.1016/S0966-842X(03)00064-7 12706993 (Pubitemid 36428829)
14. Ubiquitous late competence genes in Bacillus species indicate the presence of functional DNA uptake machineries. Kovacs AT, Smits WK, Mironczuk AM, Kuipers OP, Environ Microbiol 2009 11 8 1911 1922 10.1111/j.1462-2920.2009. 01937.x 19453701
15. Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae. Luo P, Morrison DA, J Bacteriol 2003 185 1 349 358 10.1128/JB.185.1.349-358.2003 12486073 (Pubitemid 36008854)
16. The complete genome sequence of the meat-borne lactic acid bacterium Lactobacillus sakei 23 K. Chaillou S, Champomier-Vergès MC, Cornet M, Crutz-Le Coq AM, Dudez AM, Martin V, Beaufils S, Darbon-Rongère E, Bossy R, Loux V, et al. Nat Biotechnol 2005 23 12 1527 1533 10.1038/nbt1160 16273110 (Pubitemid 41752930)
17. Evaluation of stored lamb bio-preserved using a three-strain cocktail of Lactobacillus sakei. Jones RJ, Wiklund E, Zagorec M, Tagg JR, Meat Sci 2010 86 4 955 959 10.1016/j.meatsci.2010.07.023 20800371
18. Evaluation of meat born lactic acid bacteria as protective cultures for the biopreservation of cooked meat products. Vermeiren L, Devlieghere F, Debevere J, Int J Food Microbiol 2004 96 2 149 164 10.1016/j.ijfoodmicro.2004. 03.016 15364469 (Pubitemid 39208843)
19. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Plewniak F, Jeanmougin F, Higgins DG, Thompson JD, Gibson TJ, Nucleic Acids Res 1997 25 24 4876 4882 10.1093/nar/25.24.4876 9396791 (Pubitemid 28022245)
20. Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei. Chaillou S, Daty M, Baraige F, Dudez AM, Anglade P, Jones R, Alpert CA, Champomier-Vergès MC, Zagorec M, Appl Environ Microbiol 2009 75 4 970 980 10.1128/AEM.01721-08 19114527
21. Conservation of key elements of natural competence in Lactococcus lactis ssp. Wydau S, Dervyn R, Anba J, Dusko Ehrlich S, Maguin E, FEMS Microbiol Lett 2006 257 1 32 42 10.1111/j.1574-6968.2006.00141.x 16553829
22. The sigH gene sequence can subspeciate staphylococci. Morikawa K, Ohniwa RL, Kumano M, Okamura H, Saito S, Ohta T, Diagn Microbiol Infect Dis 2008 61 4 373 380 10.1016/j.diagmicrobio.2008.03.015 18486401 (Pubitemid 351970644)
23. Development of genetic tools for Lactobacillus sakei: disruption of the -galactosidase gene and use of lacZ as a reporter gene to study regulation of the putative copper ATPase, AtkB. Stentz R, Loizel C, Malleret C, Zagorec M, Appl Environ Microbiol 2000 66 10 4272 4278 10.1128/AEM.66.10.4272-4278.2000 11010870
24. Regulation of spo0H, a gene coding for the Bacillus subtilis sigma H factor. Weir J, Predich M, Dubnau E, Nair G, Smith I, J Bacteriol 1991 173 2 521 529 1898930
25. Determination of an internal control to apply reverse transcription quantitative PCR to study stress response in the lactic acid bacterium Oenococcus oeni. Desroche N, Beltramo C, Guzzo J, J Microbiol Methods 2005 60 3 325 333 10.1016/j.mimet.2004.10.010 15649534 (Pubitemid 40093058)
26. Alternative sigma factor sigmaH modulates prophage integration and excision in Staphylococcus aureus. Tao L, Wu X, Sun B, PLoS Pathog 2010 6 5 1000888 10.1371/journal.ppat.1000888 20485515
27. Vectors for lactobacilli and other Gram-positive bacteria based on the minimal replicon of pRV500 from Lactobacillus sakei. Crutz-Le Coq AM, Zagorec M, Plasmid 2008 60 3 212 220 10.1016/j.plasmid.2008.08.002 18789962
28. DNA uptake during bacterial transformation. Chen I, Dubnau D, Nat Rev Microbiol 2004 2 3 241 249 10.1038/nrmicro844 15083159 (Pubitemid 39490085)
29. The sigma factors of Bacillus subtilis. Haldenwang WG, Microbiol Rev 1995 59 1 1 30 7708009
30. Natural genetic transformation: A novel tool for efficient genetic engineering of the dairy bacterium Streptococcus thermophilus. Blomqvist T, Steinmoen H, Havarstein LS, Appl Environ Microbiol 2006 72 10 6751 6756 10.1128/AEM.01156-06 17021227 (Pubitemid 44582918)
31. ClpC acts as a negative regulator of competence in Streptococcus thermophilus. Biornstad TJ, Havarstein LS, Microbiology 2011 157 Pt 6 1676 1684 21436217
32. Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, Cui X, Sloma A, Widner W, Dubnau D, Mol Microbiol 2002 43 5 1331 1345 10.1046/j.1365-2958.2002.02833.x 11918817 (Pubitemid 34304547)
33. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Mortier-Barriere I, Velten M, Dupaigne P, Mirouze N, Pietrement O, McGovern S, Fichant G, Martin B, Noirot P, Le Cam E, et al. Cell 2007 130 5 824 836 10.1016/j.cell.2007.07.038 17803906 (Pubitemid 47337112)
34. The MerR family of transcriptional regulators. Brown NL, Stoyanov JV, Kidd SP, Hobman JL, FEMS Microbiol Rev 2003 27 2-3 145 163 10.1016/S0168- 6445(03)00051-2 12829265 (Pubitemid 36694653)
35. Gene expression analysis of the Streptococcus pneumoniae competence regulons by use of DNA microarrays. Peterson S, Cline RT, Tettelin H, Sharov V, Morrison DA, J Bacteriol 2000 182 21 6192 6202 10.1128/JB.182.21.6192-6202.2000 11029442
36. The genetic transformation machinery: composition, localization, and mechanism. Claverys JP, Martin B, Polard P, FEMS Microbiol Rev 2009 33 3 643 656 10.1111/j.1574-6976.2009.00164.x 19228200
37. Differential expression of two paralogous genes of Bacillus subtilis encoding single-stranded DNA binding protein. Lindner C, Nijland R, van Hartskamp M, Bron S, Hamoen LW, Kuipers OP, J Bacteriol 2004 186 4 1097 1105 10.1128/JB.186.4.1097-1105.2004 14762004 (Pubitemid 38209469)
38. The oligopeptide transport system is essential for the development of natural competence in Streptococcus thermophilus strain LMD-9. Gardan R, Besset C, Guillot A, Gitton C, Monnet V, J Bacteriol 2009 191 14 4647 4655 10.1128/JB.00257-09 19447907
39. Tracing the evolution of competence in Haemophilus influenzae. Maughan H, Redfield RJ, PLoS ONE 2009 4 6 5854 10.1371/journal.pone.0005854 19516897
40. Natural genetic transformation: prevalence, mechanisms and function. Johnsborg O, Eldholm V, Havarstein LS, Res Microbiol 2007 158 10 767 778 10.1016/j.resmic.2007.09.004 17997281 (Pubitemid 350235180)
41. Transfer of lactose-fermenting ability in Lactobacillus lactis. Hofer F, New Zealand Journal of Dairy Science and Technology 1985 20 3 179 183
42. Chitin induces natural competence in Vibrio cholerae. Meibom KL, Blokesch M, Dolganov NA, Wu CY, Schoolnik GK, Science 2005 310 5755 1824 1827 10.1126/science.1120096 16357262 (Pubitemid 41814384)
43. Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Shaw AJ, Hogsett DA, Lynd LR, Appl Environ Microbiol 2010 76 14 4713 4719 10.1128/AEM.00402-10 20472726
44. Transformation of environmental Bacillus subtilis isolates by transiently inducing genetic competence. Nijland R, Burgess JG, Errington J, Veening JW, PLoS ONE 2010 5 3 9724 10.1371/journal.pone.0009724 20300532
45. Sigma X induces competence gene expression in Streptococcus pyogenes. Woodbury RL, Wang X, Moran CP Jr, Res Microbiol 2006 157 9 851 856 10.1016/j.resmic.2006.07.002 16963231 (Pubitemid 44528977)
46. A novel double-tryptophan peptide pheromone controls competence in Streptococcus spp. via an Rgg regulator. Mashburn-Warren L, Morrison DA, Federle MJ, Mol Microbiol 2010 78 3 589 606 10.1111/j.1365-2958.2010.07361.x 20969646
47. Sensitivity of oral bacteria to 254 nm ultraviolet light. Metzger Z, Dotan M, Better H, Abramovitz I, Int Endod J 2007 40 2 120 127 10.1111/j.1365-2591.2006.01191.x 17229117
48. Bacillus subtilis sporulation and stationary phase gene expression. Phillips ZE, Strauch MA, Cell Mol Life Sci 2002 59 3 392 402 10.1007/s00018-002-8431-9 11964117 (Pubitemid 34267379)
49. A medium for the cultivation of lactobacilli. De Man JC, Rogosa M, Sharpe ME, J Appl Bacteriol 1960 23 130 135 10.1111/j.1365-2672.1960.tb00188.x
50. Carbohydrate utilization in Lactobacillus sake. Lauret R, Morel-Deville F, Berthier F, Champomier-Vergès M, Postma P, Ehrlich SD, Zagorec M, Appl Environ Microbiol 1996 62 6 1922 1927 16535331 (Pubitemid 26168982)
51. A roll tube method for the cultivation of strict anaerobes. Hungate RE, Methods in Microbiology London: Academic Press, Norris JR, Robbons DW, 1969 3B 117 132
52. Characterization of a theta-type plasmid from Lactobacillus sakei: a potential basis for low-copy-number vectors in lactobacilli. Alpert CA, Crutz-Le Coq AM, Malleret C, Zagorec M, Appl Environ Microbiol 2003 69 9 5574 5584 10.1128/AEM.69.9.5574-5584.2003 12957947 (Pubitemid 37150783)
53. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
54. Physiology of Streptococcus thermophilus during the late stage of milk fermentation with special regard to sulfur amino-acid metabolism. Herve-Jimenez L, Guillouard I, Guedon E, Gautier C, Boudebbouze S, Hols P, Monnet V, Rul F, Maguin E, Proteomics 2008 8 20 4273 4286 10.1002/pmic.200700489 18814336
55. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2-CT Method. Livak KJ, Schmittgen TD, Methods 2001 25 4 402 408 10.1006/meth.2001.1262 11846609 (Pubitemid 34164012)
56. Disruption of the sole ldh gene in Lactobacillus sakei prevents the production of both L- and D-lactate. Malleret C, Lauret R, Ehrlich SD, Morel-Deville F, Zagorec M, Microbiology 1998 144 3327 3333 10.1099/00221287- 144-12-3327 9884224 (Pubitemid 29011962)
57. Special-purpose vectors for lactococci. Kok J, Genetics and molecular biology of streptococci, lactococci and enterococci Washington, D.C.: American Society for Microbiology, Dunny GM, Cleary PP, McKay LL, 1991 97 102
58. High-frequency transformation of Lactobacillus sake by electroporation. Berthier F, Zagorec M, Champomier-Vergès M, Ehrlich SD, Morel-Deville F, Microbiology 1996 142 1273 1279 10.1099/13500872-142-5-1273 (Pubitemid 26154938)