title: Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University, Schubertstrasse 81, Giessen, D-35392, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Hain
authors.forename: Rohit
authors.initials: R
authors.lastname: Ghai
authors.forename: André
authors.initials: A
authors.lastname: Billion
authors.forename: Carsten Tobias
authors.initials: CT
authors.lastname: Kuenne
authors.forename: Christiane
authors.initials: C
authors.lastname: Steinweg
authors.forename: Benjamin
authors.initials: B
authors.lastname: Izar
authors.forename: Walid
authors.initials: W
authors.lastname: Mohamed
authors.forename: Mobarak Abu
authors.initials: MA
authors.lastname: Mraheil
authors.forename: Eugen
authors.initials: E
authors.lastname: Domann
authors.forename: Silke
authors.initials: S
authors.lastname: Schaffrath
authors.forename: Uwe
authors.initials: U
authors.lastname: Kärst
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Sebastian
authors.initials: S
authors.lastname: Oehm
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Rainer
authors.initials: R
authors.lastname: Merkl
authors.forename: Sonja
authors.initials: S
authors.lastname: Vorwerk
authors.forename: Philippe
authors.initials: P
authors.lastname: Glaser
authors.forename: Patricia
authors.initials: P
authors.lastname: Garrido
authors.forename: Christophe
authors.initials: C
authors.lastname: Rusniok
authors.forename: Carmen
authors.initials: C
authors.lastname: Buchrieser
authors.forename: Werner
authors.initials: W
authors.lastname: Goebel
authors.forename: Trinad
authors.initials: T
authors.lastname: Chakraborty
mesh_terms: D000818:Animals; D001435:Bacteriophages / Q000235:genetics; D004195:Disease Models, Animal; D005408:Flagellin / Q000378:metabolism; D020440:Gene Duplication / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D022761:Gene Transfer, Horizontal / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D006801:Humans; D008089:Listeria monocytogenes / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity / Q000821:virology; D008088:Listeriosis / Q000382:microbiology; D008565:Membrane Proteins / Q000378:metabolism; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D009154:Mutation / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D014774:Virulence / Q000235:genetics
chemical_list: D008565:Membrane Proteins; D009711:Nucleotides; D005408:Flagellin