Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, Izar B, Mohamed W, Mraheil M, Domann E, Schaffrath S, Kärst U, et al. (2012)
BMC Genomics 13(1): 144.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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ABSTRACT: BACKGROUND: Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. RESULTS: The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. CONCLUSION: Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
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BMC Genomics
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13
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1
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144
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Hain T, Ghai R, Billion A, et al. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics. 2012;13(1):144.
Hain, T., Ghai, R., Billion, A., Kuenne, C. T., Steinweg, C., Izar, B., Mohamed, W., et al. (2012). Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics, 13(1), 144. doi:10.1186/1471-2164-13-144
Hain, T., Ghai, R., Billion, A., Kuenne, C. T., Steinweg, C., Izar, B., Mohamed, W., Mraheil, M., Domann, E., Schaffrath, S., et al. (2012). Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics 13, 144.
Hain, T., et al., 2012. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics, 13(1), p 144.
T. Hain, et al., “Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes”, BMC Genomics, vol. 13, 2012, pp. 144.
Hain, T., Ghai, R., Billion, A., Kuenne, C.T., Steinweg, C., Izar, B., Mohamed, W., Mraheil, M., Domann, E., Schaffrath, S., Kärst, U., Goesmann, A., Oehm, S., Pühler, A., Merkl, R., Vorwerk, S., Glaser, P., Garrido, P., Rusniok, C., Buchrieser, C., Goebel, W., Chakraborty, T.: Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics. 13, 144 (2012).
Hain, Torsten, Ghai, Rohit, Billion, Andre, Kuenne, Carsten Tobias, Steinweg, Christiane, Izar, Benjamin, Mohamed, Walid, Mraheil, Mobarak, Domann, Eugen, Schaffrath, Silke, Kärst, Uwe, Goesmann, Alexander, Oehm, Sebastian, Pühler, Alfred, Merkl, Rainer, Vorwerk, Sonja, Glaser, Philippe, Garrido, Patricia, Rusniok, Christophe, Buchrieser, Carmen, Goebel, Werner, and Chakraborty, Trinad. “Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes”. BMC Genomics 13.1 (2012): 144.

29 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.
Kuenne C, Billion A, Mraheil MA, Strittmatter A, Daniel R, Goesmann A, Barbuddhe S, Hain T, Chakraborty T., BMC Genomics 14(), 2013
PMID: 23339658
Listeria phages: Genomes, evolution, and application.
Klumpp J, Loessner MJ., Bacteriophage 3(3), 2013
PMID: 24251077

90 References

Daten bereitgestellt von Europe PubMed Central.

Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM., Science 269(5223), 1995
PMID: 7542800
Cloning and assembly strategies in microbial genome projects.
Frangeul L, Nelson KE, Buchrieser C, Danchin A, Glaser P, Kunst F., Microbiology (Reading, Engl.) 145 ( Pt 10)(), 1999
PMID: 10537184
CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects.
Frangeul L, Glaser P, Rusniok C, Buchrieser C, Duchaud E, Dehoux P, Kunst F., Bioinformatics 20(5), 2004
PMID: 14752000
MAVID: constrained ancestral alignment of multiple sequences.
Bray N, Pachter L., Genome Res. 14(4), 2004
PMID: 15060012
VISTA: computational tools for comparative genomics.
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215394
GECO--linear visualization for comparative genomics.
Kuenne CT, Ghai R, Chakraborty T, Hain T., Bioinformatics 23(1), 2007
PMID: 17077098
PILER-CR: fast and accurate identification of CRISPR repeats
AUTHOR UNKNOWN, 2007
ACT: the Artemis Comparison Tool.
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J., Bioinformatics 21(16), 2005
PMID: 15976072
SIGI: score-based identification of genomic islands
AUTHOR UNKNOWN, 2004
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
AUTHOR UNKNOWN, 2006
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bolstad BM, Irizarry RA, Astrand M, Speed TP., Bioinformatics 19(2), 2003
PMID: 12538238
Significance analysis of microarrays applied to the ionizing radiation response.
Tusher VG, Tibshirani R, Chu G., Proc. Natl. Acad. Sci. U.S.A. 98(9), 2001
PMID: 11309499
Vector plasmid for insertional mutagenesis and directional cloning in Listeria spp.
Schaferkordt S, Chakraborty T., BioTechniques 19(5), 1995
PMID: 8588903
Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.
Billion A, Ghai R, Chakraborty T, Hain T., Bioinformatics 22(22), 2006
PMID: 16966358

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