title: Gene expression diversity among Mycobacterium tuberculosis clinical isolates.
abstract: Intraspecies genetic diversity has been demonstrated to be important in the pathogenesis and epidemiology of several pathogens, such as HIV, influenza, Helicobacter and Salmonella. It is also important to consider strain-to-strain variation when identifying drug targets and vaccine antigens and developing tools for molecular diagnostics. Here, the authors present a description of the variability in gene expression patterns among ten clinical isolates of Mycobacterium tuberculosis, plus the laboratory strains H37Rv and H37Ra, growing in liquid culture. They identified 527 genes (15 % of those tested) that are variably expressed among the isolates studied. The remaining genes were divided into three categories based on their expression levels: unexpressed (38 %), low to undetectable expression (31 %) and consistently expressed (16 %). The expression categories were compared with functional categories and three biologically interesting gene lists: genes that are deleted among clinical isolates, T-cell antigens and essential genes. There were significant associations between expression variability and the classification of genes as T-cell antigens, involved in lipid metabolism, PE/PPE, insertion sequences and phages, and deleted among clinical isolates. This survey of mRNA expression among clinical isolates of M. tuberculosis demonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions.
authors.affiliation: Department of Medicine, Division of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Department of Medicine, Division of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA.
authors.forename: Katharine E
authors.initials: KE
authors.lastname: Kripke
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.
authors.forename: Alok J
authors.initials: AJ
authors.lastname: Saldanha
authors.affiliation: Department of Medicine, Division of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA.
authors.forename: Weihong
authors.initials: W
authors.lastname: Yan
authors.affiliation: Statistics Department, Sequoia Hall, Stanford, CA 94305, USA.
authors.forename: Susan
authors.initials: S
authors.lastname: Holmes
authors.affiliation: Department of Medicine, Division of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305-5107, USA.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Small
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D015870:Gene Expression; D020043:Genes, Essential; D014644:Genetic Variation; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics / Q000254:growth & development* / Q000472:pathogenicity; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011948:Receptors, Antigen, T-Cell / Q000235:genetics / Q000378:metabolism; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D011948:Receptors, Antigen, T-Cell