Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-Generation sequencing technologies

Applied and Environmental Microbiology

Volumn 78, Issue 12, 2012, Pages 4141-4148

  Leimena, Milkha M ^a,b   Wels, Michiel ^a,c   Bongers, Roger S ^c   Smid, Eddy J ^a,b   Zoetendal, Erwin G ^a,b   Kleerebezem, Michiel ^a,b,c  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c NIZO FOOD RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CDNA SYNTHESIS; COMPARATIVE ANALYSIS; DIFFERENTIALLY EXPRESSED GENE; DNA MICRO-ARRAY; LACTOBACILLUS PLANTARUM; MICROARRAY ANALYSIS; MODEL ORGANISMS; PREPARATION PROCEDURES; RELATIVE ABUNDANCE; RNA SEQUENCING; TRANSCRIPTION ANALYSIS; TRANSCRIPTOME ANALYSIS; TRANSCRIPTOMES; UNTRANSLATED REGIONS;

BIOASSAY; BIOCHIPS; GENES; MICROORGANISMS; TRANSCRIPTION;

RNA;

TRANSCRIPTOME;

ADVANCED TECHNOLOGY; COMPARATIVE STUDY; EUKARYOTE; GENE EXPRESSION; GENOME; LABORATORY METHOD; MITOCHONDRIAL DNA; MODEL VALIDATION; PROKARYOTE;

ARTICLE; COMPARATIVE STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; LACTOBACILLUS PLANTARUM; METHODOLOGY; MICROARRAY ANALYSIS; VALIDATION STUDY;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LACTOBACILLUS PLANTARUM; MICROARRAY ANALYSIS; TRANSCRIPTOME;

EUKARYOTA; LACTOBACILLUS PLANTARUM; PROKARYOTA;

EID: 84864094524     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00470-12     Document Type: Article

References (52)

1. Agarwal A, et al. 2010. Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics 11:383-399.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11:R106.
3. Baldi P, Long AD. 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509-519.
4. Bloom JS, Khan Z, Kruglyak L, Singh M, Caudy AA. 2009. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 10: 221-231.
5. Bolstad BM, Irizarry RA, Astrand M, Speed TP. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193.
6. Cloonan N, et al. 2008. Stem cell transcriptome profiling via massivescale mRNA sequencing. Nat. Methods 5:613-619.
7. de Hoon MJL, Makita Y, Nakai K, Miyano S. 2005. Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol. 1:e25.
8. De Man JC, Rogosa M, Sharpe ME. 1960. A medium for the cultivation of lactobacilli. J. Appl. Microbiol. 23:130-135.
9. Deutscher MP. 2006. Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res. 34:659-666.
10. Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:207-210.
11. Eveland AL, McCarty DR, Koch KE. 2008. Transcript profiling by 3=-untranslated region sequencing resolves expression of gene families. Plant Physiol. 146:32-44.
12. Everett KR, Rees-George J, Pushparajah IPS, Janssen BJ, Luo Z. 2010. Advantages and disadvantages of microarrays to study microbial population dynamics-a minireview. New Zealand Plant Protect. 63:1-6.
13. Frias-Lopez J, et al. 2008. Microbial community gene expression in ocean surface waters. Proc. Natl. Acad. Sci. U.S.A.105:3805-3810.
14. Garcia de la Nava J, Van Hijum S, Trelles O. 2004. Saturation and quantization reduction in microarray experiments using two scans at different sensitivities. Stat. Appl. Genet. Mol. Biol. 3:1-16.
15. Hardcastle TJ, Kelly KA. 2010. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11:422.
16. Irizarry RA, et al. 2005. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2:345-350.
17. Kang Y, et al. 2011. Transcript amplification from single bacterium for transcriptome analysis. Genome Res. 21:925-935.
18. Kilstrup M, Hammer K, Ruhdal Jensen P, Martinussen J. 2005. Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol. Rev. 29:555-590.
19. Kleerebezem M, et al. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U. S. A. 100:1990-1995.
20. Kozak M. 1983. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiol. Rev. 47:1-45.
21. Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010. RNA-seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493-500.
22. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. 2008. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18:1509-1517.
23. Meijerink M, et al. 2010. Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization. PLoS One 5:e10632.
24. Morozova O, Hirst M, Marra MA. 2009. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 10:135-151.
25. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5:621-628.
26. Nagalakshmi U, et al. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349.
27. Oshlack A, Robinson MD, Young MD. 2010. From RNA-seq reads to differential expression results. Genome Biol. 11:220.
28. Passalacqua KD, et al. 2009. Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191:3203-3211.
29. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
30. Serrano LM, et al. 2007. Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1. Microb. Cell Fact. 6:29.
31. Siezen RJ, Wilson G, Todt T. 2010. Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb. Biotechnol. 3:125-130.
32. Sorek R, Cossart P. 2010. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 11:9-16.
33. Stevens MJA, Molenaar D, de Jong A, De Vos WM, Kleerebezem M. 2010. Sigma54-mediated control of the mannose phosphotransferase system in Lactobacillus plantarum impacts on carbohydrate metabolism. Microbiology 156:695-707.
34. Stoughton RB. 2005. Applications of DNA microarrays in biology. Annu. Rev. Biochem. 74:53-82.
35. Sturn A, Quackenbush J, Trajanoski Z. 2002. Genesis: cluster analysis of microarray data. Bioinformatics 18:207-208.
36. Sultan M, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
37. Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. 2011. Differential expression in RNA-seq: a matter of depth. Genome Res. 21: 2213-2223.
38. Teusink B, et al. 2005. In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl. Environ. Microbiol. 71:7253-7262.
39. 't Hoen PA, et al. 2008. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 36:e141.
40. Trapnell C, et al. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7:562-578.
41. van Hijum SAFT, Garcia de la Nava J, Trelles O, Kok J, Kuipers OP. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.
42. van Vliet AH. 2010. Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol. Lett. 302:1-7.
43. Wang Z, Gerstein M, Snyder M. 2009. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63.
44. Warnecke F, Hess M. 2009. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J. Biotechnol. 142:91-95.
45. Wels MWW. 2008. Unraveling the regulatory network of Lactobacillus plantarum WCFS1. Wageningen University, Wageningen, the Netherlands.
46. Wilhelm BT, Landry JR. 2009. RNA-seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48: 249-257.
47. Willenbrock H, et al. 2009. Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing. RNA 15:2028-2034.
48. Wurtzel O, et al. 2010. A single-base resolution map of an archaeal transcriptome. Genome Res. 20:133-141.
49. Yang YH, et al. 2002. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:e15.
50. Yoder-Himes DR, et al. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A. 106:3976-3981.
51. Zhou J, Thompson DK. 2002. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13:204-207.
52. Zoetendal EG, et al. 2006. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat. Protoc. 1:954-959.