Identification of pOENI-1 and Related Plasmids in Oenococcus oeni Strains Performing the Malolactic Fermentation in Wine

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Favier, Marion ^a,b   Bilhère, Eric ^a   Lonvaud Funel, Aline ^a   Moine, Virginie ^c   Lucas, Patrick M ^a  

^a UNIVERSITÉ DE BORDEAUX   (France)

^b SARCO   (France)

^c Laffort   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL SURVIVAL; CONTROLLED STUDY; FERMENTATION; MALOLACTIC FERMENTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OENOCOCCUS OENI; OYE GENE; PLASMID; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TAUE GENE; WINE;

BACTERIAL PROTEINS; FERMENTATION; GENE DOSAGE; GENES, BACTERIAL; KINETICS; LACTIC ACID; MALATES; MOLECULAR SEQUENCE DATA; OENOCOCCUS; OPEN READING FRAMES; PLASMIDS; POLYMERASE CHAIN REACTION; WINE;

OENOCOCCUS OENI;

EID: 84868354550     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049082     Document Type: Article

References (65)

1. Fleet GH, Lafon-Lafourcade S, Ribereau-Gayon P, (1984) Evolution of yeasts and lactic acid bacteria during fermentation and storage of Bordeaux wines. Appl Environ Microbiol 48: 1034-1038.
2. Lafon-Lafourcade S, Carre E, Ribereau-Gayon P, (1983) Occurrence of lactic acid bacteria during the different stages of vinification and conservation of wines. Appl Environ Microbiol 46: 874-880.
3. Lonvaud-Funel A, (1999) Lactic acid bacteria in the quality improvement and depreciation of wine. Antonie Van Leeuwenhoek 76: 317-331.
4. Davis CR, Wibowo D, Eschenbruch R, Lee TH, Fleet GH, (1985) Practical implications of malolactic fermentation: A Review. Am J Enol Vitic 36: 290-301.
5. Davis CR, Wibowo DJ, Lee TH, Fleet GH, (1986) Growth and metabolism of lactic acid bacteria during and after malolactic fermentation of wines at different pH. Appl Environ Microbiol 51: 539-545.
6. Henick-Kling T, Sandine WE, Heatherbell DA, (1989) Evaluation of malolactic bacteria isolated from Oregon wines. Appl Environ Microbiol 55: 2010-2016.
7. Garcia-Ruiz A, Moreno-Arribas MV, Martin-Alvarez PJ, Bartolome B, (2011) Comparative study of the inhibitory effects of wine polyphenols on the growth of enological lactic acid bacteria. Int J Food Microbiol 145: 426-431.
8. Ugliano M, Moio L, (2005) Changes in the concentration of yeast-derived volatile compounds of red wine during malolactic fermentation with four commercial starter cultures of Oenococcus oeni. J Agric Food Chem 53: 10134-10139.
9. Gagné S, Lucas PM, Perello MC, Claisse O, Lonvaud-Funel A, et al. (2010) Variety and variability of glycosidase activities in an Oenococcus oeni strain collection tested with synthetic and natural substrates. J Appl Microbiol 110: 218-228.
10. Torriani S, Felis GE, Fracchetti F, (2010) Selection criteria and tools for malolactic starters development: an update. Ann Microbiol 61: 33-39.
11. Jobin MP, Garmyn D, Divies C, Guzzo J, (1999) Expression of the Oenococcus oeni trxA gene is induced by hydrogen peroxide and heat shock. Microbiology 145: 1245-1251.
12. Grandvalet C, Assad-Garcia JS, Chu-Ky S, Tollot M, Guzzo J, et al. (2008) Changes in membrane lipid composition in ethanol- and acid-adapted Oenococcus oeni cells: characterization of the cfa gene by heterologous complementation. Microbiology 154: 2611-2619.
13. Coucheney F, Gal L, Beney L, Lherminier J, Gervais P, et al. (2005) A small HSP, Lo18, interacts with the cell membrane and modulates lipid physical state under heat shock conditions in a lactic acid bacterium. Biochim Biophys Acta 1720: 92-98.
14. Weidmann S, Rieu A, Rega M, Coucheney F, Guzzo J, (2010) Distinct amino acids of the Oenococcus oeni small heat shock protein Lo18 are essential for damaged protein protection and membrane stabilization. FEMS Microbiol Lett 309: 8-15.
15. Bourdineaud JP, Nehme B, Tesse S, Lonvaud-Funel A, (2003) The ftsH gene of the wine bacterium Oenococcus oeni is involved in protection against environmental stress. Appl Environ Microbiol 69: 2512-2520.
16. Bourdineaud JP, Nehme B, Tesse S, Lonvaud-Funel A, (2004) A bacterial gene homologous to ABC transporters protect Oenococcus oeni from ethanol and other stress factors in wine. Int J Food Microbiol 92: 1-14.
17. Beltramo C, Grandvalet C, Pierre F, Guzzo J, (2004) Evidence for multiple levels of regulation of Oenococcus oeni clpP-clpL locus expression in response to stress. J Bacteriol 186: 2200-2205.
18. Grandvalet C, Coucheney F, Beltramo C, Guzzo J, (2005) CtsR is the master regulator of stress response gene expression in Oenococcus oeni. J Bacteriol 187: 5614-5623.
19. Mills DA, Rawsthorne H, Parker C, Tamir D, Makarova K, (2005) Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking. FEMS Microbiol Rev 29: 465-475.
20. Athane A, Bilhere E, Bon E, Morel G, Lucas P, et al. (2008) Characterization of an acquired dps-containing gene island in the lactic acid bacterium Oenococcus oeni. J Appl Microbiol 105: 1866-1875.
21. Bon E, Delaherche A, Bilhere E, De Daruvar A, Lonvaud-Funel A, et al. (2009) Oenococcus oeni genome plasticity associated with fitness. Appl Environ Microbiol 75: 2079-2090.
22. Renouf V, Favier M, (2010) Genetic and physiological characterisation of Oenococcus oeni strains to perform malolactic fermentation in wines. S Afr J Enol Vitic 31: 75-81.
23. Wang TT, Lee BH, (1997) Plasmids in Lactobacillus. Crit Rev Biotechnol 17: 227-272.
24. Mills S, McAuliffe OE, Coffey A, Fitzgerald GF, Ross RP, (2006) Plasmids of lactococci - genetic accessories or genetic necessities? FEMS Microbiol Rev 30: 243-273.
25. Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, et al. (2005) Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71: 8371-8382.
26. Fremaux C, Aigle M, Lonvaud-Funel A, (1993) Sequence analysis of Leuconostoc oenos DNA: organization of pLo13, a cryptic plasmid. Plasmid 30: 212-223.
27. Zuniga M, Pardo I, Ferrer S, (1996) Nucleotide sequence of plasmid p4028, a cryptic plasmid from Leuconostoc oenos. Plasmid 36: 67-74.
28. Brito L, Vieira G, Santos MA, Paveia H, (1996) Nucleotide sequence analysis of pOg32, a cryptic plasmid from Leuconostoc oenos. Plasmid 36: 49-54.
29. Alegre MT, Rodriguez MC, Mesas JM, (1999) Nucleotide sequence analysis of pRS1, a cryptic plasmid from Oenococcus oeni. Plasmid 41: 128-134.
30. Mesas JM, Rodriguez MC, Alegre MT, (2001) Nucleotide sequence analysis of pRS2 and pRS3, two small cryptic plasmids from Oenococcus oeni. Plasmid 46: 149-151.
31. Lucas PM, Claisse O, Lonvaud-Funel A, (2008) High frequency of histamine-producing bacteria in the enological environment and instability of the histidine decarboxylase production phenotype. Appl Environ Microbiol 74: 811-817.
32. Brito L, Paveia H, (1999) Presence and analysis of large plasmids in Oenococcus oeni. Plasmid 41: 260-267.
33. Prevost H, Cavin JF, Lamoureux M, Divies C, (1995) Plasmid and chromosome characterization of Leuconostoc oenos strains. Am J Enol Vitic 46: 43-48.
34. Sgorbati B, Palenzona D, Sozzi T, (1985) Plasmidograms in some heterolactic bacteria from alcoholic beverages and their structural relatedness. Microbiol Alim Nutr 3: 21-34.
35. Sgorbati B, Palenzona D, Ercoli L (1987) Characterization of the pesticides-resistance plasmid pBL34 from Leuconostoc oenos. Microbiol Alim Nutr 5, 295-301.
36. Bilhere E, Lucas PM, Claisse O, Lonvaud-Funel A, (2009) Multilocus sequence typing of Oenococcus oeni: detection of two subpopulations shaped by intergenic recombination. Appl Environ Microbiol 75: 1291-1300.
37. Tamura K, Dudley J, Nei M, Kumar S, (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.
38. Lucas PM, Wolken WA, Claisse O, Lolkema JS, Lonvaud-Funel A, (2005) Histamine-producing pathway encoded on an unstable plasmid in Lactobacillus hilgardii 0006. Appl Environ Microbiol 71: 1417-1424.
39. Besemer J, Borodovsky M, (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
40. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL, (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Research 27: 4636-4641.
41. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40: D306-D312.
42. Zhang W, Yu D, Sun Z, Chen X, Bao Q, et al. (2008) Complete nucleotide sequence of plasmid plca36 isolated from Lactobacillus casei Zhang. Plasmid 60: 131-135.
43. Ito Y, Kawai Y, Arakawa K, Honme Y, Sasaki T, et al. (2009) Conjugative plasmid from Lactobacillus gasseri LA39 that carries genes for production of and immunity to the circular bacteriocin gassericin A. Appl Environ Microbiol. 75: 6340-6351.
44. Fang F, Flynn S, Li Y, Claesson MJ, van Pijkeren JP, et al. (2008) Characterization of endogenous plasmids from Lactobacillus salivarius UCC118. Appl Environ Microbiol 74: 3216-3228.
45. Chattoraj DK, (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 37: 467-476.
46. Rajewska M, Wegrzyn K, Konieczny I, (2012) AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 36: 408-434.
47. Ruckert C, Koch D, Rey D, Albersmeier A, Mormann S, et al. (2005) Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction. BMC Genomics 6: 121.
48. Weinitschke S, Denger K, Cook AM, Smits THM, (2007) The DUF81 protein TauE in Cupriavidus necator H16, a sulfite exporter in the metabolism of C2 sulfonates. Microbiology 153: 3055-3060.
49. Parreira R, Sao-Jose C, Isidro A, Domingues S, Vieira G, et al. (1999) Gene organization in a central DNA fragment of Oenococcus oeni bacteriophage fOg44 encoding lytic, integrative and non-essential functions. Gene 226: 83-93.
50. Fitzpatrick TB, Amrhein N, Macheroux P, (2003) Characterization of YqjM, an Old Yellow Enzyme homolog from Bacillus subtilis involved in the oxidative stress response. J Biol Chem 278: 19891-19897.
51. van den Hemel D, Brige A, Savvides SN, Van Beeumen J, (2006) Ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding. J Biol Chem 281: 28152-28161.
52. Brige A, Van den Hemel D, Carpentier W, De Smet L, Van Beeumen JJ, (2006) Comparative characterization and expression analysis of the four Old Yellow Enzyme homologues from Shewanella oneidensis indicate differences in physiological function. Biochem J 394: 335-344.
53. Bon E, Delaherche A, Bilhere E, De Daruvar A, Lonvaud-Funel A, et al. (2009) Oenococcus oeni genome plasticity associated with fitness. Appl Environ Microbiol 75: 2079-2090.
54. Bridier J, Claisse O, Coton M, Coton E, Lonvaud-Funel A, (2010) Evidence of distinct populations and specific subpopulations within the species Oenococcus oeni. Appl Environ Microbiol 76: 7754-7764.
55. Borneman A, McCarthy J, Chambers P, Bartowsky E, (2012) Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways. BMC Genomics 13: 373.
56. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, et al. (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103: 15611-15616.
57. Krejčík Z, Denger K, Weinitschke S, Hollemeyer K, Pačes V, et al. (2008) Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch of Microbiol 190: 159-168.
58. Carrete R, Vidal MT, Bordons A, Constanti M, (2002) Inhibitory effect of sulfur dioxide and other stress compounds in wine on the ATPase activity of Oenococcus oeni. FEMS Microbiol Lett 211: 155-159.
59. Blehert DS, Fox BG, Chambliss GH, (1999) Cloning and sequence analysis of two Pseudomonas flavoprotein xenobiotic reductases. J Bacteriol 181: 6254-6263.
60. Odat O, Matta S, Khalil H, Kampranis SC, Pfau R, et al. (2007) Old yellow enzymes, highly homologous FMN oxidoreductases with modulating roles in oxidative stress and programmed cell death in yeast. Journal Biol Chem 282: 36010-36023.
61. Reekmans R, Smet KD, Chen C, Hummelen PV, Contreras R, (2005) Old yellow enzyme interferes with Bax-induced NADPH loss and lipid peroxidation in yeast. FEMS Yeast Research 5: 711-725.
62. Trotter EW, Collinson EJ, Dawes IW, Grant CM, (2006) Old yellow enzymes protect against acrolein toxicity in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 72: 4885-4892.
63. Williams RE, Rathbone DA, Scrutton NS, Bruce NC, (2004) Biotransformation of explosives by the old yellow enzyme family of flavoproteins. Appl Environ Microbiol 70: 3566-3574.
64. Yin B, Yang X, Wei G, Ma Y, Wei D, (2008) Expression of two old yellow enzyme homologues from Gluconobacter oxydans and identification of their citral hydrogenation abilities. Mol Biotechnol 38: 241-245.
65. Kitko RD, Cleeton RL, Armentrout EI, Lee GE, Noguchi K, et al. (2009) Cytoplasmic acidification and the benzoate transcriptome in Bacillus subtilis. PLoS One 4: e8255.