Transcriptome Analysis of Lactococcus Lactis in Coculture with Saccharomyces Cerevisiae

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2007 Nov 13

PMID 17993564

Citations 21

Authors

Mathieu Maligoy

Myriam Mercade

Muriel Cocaign-Bousquet

Pascal Loubiere

Affiliations

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Abstract

The study of microbial interactions in mixed cultures remains an important conceptual and methodological challenge for which transcriptome analysis could prove to be the essential method for improving our understanding. However, the use of whole-genome DNA chips is often restricted to the pure culture of the species for which the chips were designed. In this study, massive cross-hybridization was observed between the foreign cDNA and the specific Lactococcus lactis DNA chip. A very simple method is proposed to considerably decrease this nonspecific hybridization, consisting of adding the microbial partner's DNA. A correlation was established between the resulting cross-hybridization and the phylogenetic distance between the microbial partners. The response of L. lactis to the presence of Saccharomyces cerevisiae was analyzed during the exponential growth phase in fermentors under defined growth conditions. Although no differences between growth kinetics were observed for the pure and the mixed cultures of L. lactis, the mRNA levels of 158 genes were significantly modified. More particularly, a strong reorientation of pyrimidine metabolism was observed when L. lactis was grown in mixed cultures. These changes in transcript abundance were demonstrated to be regulated by the ethanol produced by the yeast and were confirmed by an independent method (quantitative reverse transcription-PCR).

Citing Articles

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References

Patrignani F, Lanciotti R, Mathara J, Guerzoni M, Holzapfel W . Potential of functional strains, isolated from traditional Maasai milk, as starters for the production of fermented milks. Int J Food Microbiol. 2005; 107(1):1-11. DOI: 10.1016/j.ijfoodmicro.2005.08.004. View

Cocaign-Bousquet M, Garrigues C, Loubiere P, Lindley N . Physiology of pyruvate metabolism in Lactococcus lactis. Antonie Van Leeuwenhoek. 1996; 70(2-4):253-67. DOI: 10.1007/BF00395936. View

Sakala R, Hayashidani H, Kato Y, Hirata T, Makino Y, Fukushima A . Change in the composition of the microflora on vacuum-packaged beef during chiller storage. Int J Food Microbiol. 2002; 74(1-2):87-99. DOI: 10.1016/s0168-1605(01)00732-2. View

Arsene-Ploetze F, Kugler V, Martinussen J, Bringel F . Expression of the pyr operon of Lactobacillus plantarum is regulated by inorganic carbon availability through a second regulator, PyrR2, homologous to the pyrimidine-dependent regulator PyrR1. J Bacteriol. 2006; 188(24):8607-16. PMC: 1698236. DOI: 10.1128/JB.00985-06. View

Johnson M, Conners S, Montero C, Chou C, Shockley K, Kelly R . The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Appl Environ Microbiol. 2006; 72(1):811-8. PMC: 1352257. DOI: 10.1128/AEM.72.1.811-818.2006. View

Andersen P, Martinussen J, Hammer K . Sequence analysis and identification of the pyrKDbF operon from Lactococcus lactis including a novel gene, pyrK, involved in pyrimidine biosynthesis. J Bacteriol. 1996; 178(16):5005-12. PMC: 178286. DOI: 10.1128/jb.178.16.5005-5012.1996. View

Redon E, Loubiere P, Cocaign-Bousquet M . Transcriptome analysis of the progressive adaptation of Lactococcus lactis to carbon starvation. J Bacteriol. 2005; 187(10):3589-92. PMC: 1111995. DOI: 10.1128/JB.187.10.3589-3592.2005. View

Bodrossy L, Stralis-Pavese N, Konrad-Koszler M, Weilharter A, Reichenauer T, Schofer D . mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol. 2006; 72(2):1672-6. PMC: 1392935. DOI: 10.1128/AEM.72.2.1672-1676.2006. View

Visser W, Scheffers W, van Dijken J . Oxygen requirements of yeasts. Appl Environ Microbiol. 1990; 56(12):3785-92. PMC: 185068. DOI: 10.1128/aem.56.12.3785-3792.1990. View

10.

Cho J, Tiedje J . Quantitative detection of microbial genes by using DNA microarrays. Appl Environ Microbiol. 2002; 68(3):1425-30. PMC: 123775. DOI: 10.1128/AEM.68.3.1425-1430.2002. View

11.

Jorgensen C, Hammer K, Martinussen J . CTP limitation increases expression of CTP synthase in Lactococcus lactis. J Bacteriol. 2003; 185(22):6562-74. PMC: 262100. DOI: 10.1128/JB.185.22.6562-6574.2003. View

12.

Huser A, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J . Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source. J Biotechnol. 2003; 106(2-3):269-86. DOI: 10.1016/j.jbiotec.2003.08.006. View

13.

Martinussen J, Hammer K . The carB gene encoding the large subunit of carbamoylphosphate synthetase from Lactococcus lactis is transcribed monocistronically. J Bacteriol. 1998; 180(17):4380-6. PMC: 107444. DOI: 10.1128/JB.180.17.4380-4386.1998. View

14.

Thompson J, Higgins D, Gibson T . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22(22):4673-80. PMC: 308517. DOI: 10.1093/nar/22.22.4673. View

15.

Bolotin A, Wincker P, Mauger S, Jaillon O, Malarme K, Weissenbach J . The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 2001; 11(5):731-53. PMC: 311110. DOI: 10.1101/gr.gr-1697r. View

16.

Martinussen J, Hammer K . The pyrH gene of Lactococcus lactis subsp. cremoris encoding UMP kinase is transcribed as part of an operon including the frr1 gene encoding ribosomal recycling factor 1. Gene. 1999; 241(1):157-66. DOI: 10.1016/s0378-1119(99)00452-7. View

17.

Wu L, Liu X, Schadt C, Zhou J . Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol. 2006; 72(7):4931-41. PMC: 1489353. DOI: 10.1128/AEM.02738-05. View

18.

Zhou J . Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol. 2003; 6(3):288-94. DOI: 10.1016/s1369-5274(03)00052-3. View

19.

Rhee S, Liu X, Wu L, Chong S, Wan X, Zhou J . Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol. 2004; 70(7):4303-17. PMC: 444823. DOI: 10.1128/AEM.70.7.4303-4317.2004. View

20.

Moller K, Olsson L, Piskur J . Ability for anaerobic growth is not sufficient for development of the petite phenotype in Saccharomyces kluyveri. J Bacteriol. 2001; 183(8):2485-9. PMC: 95164. DOI: 10.1128/JB.183.8.2485-2489.2001. View