title: Generation and phenotyping of a collection of sRNA gene deletion mutants of the haloarchaeon Haloferax volcanii.
abstract: The haloarchaeon Haloferax volcanii was shown to contain 145 intergenic and 45 antisense sRNAs. In a comprehensive approach to unravel various biological roles of haloarchaeal sRNAs in vivo, 27 sRNA genes were selected and deletion mutants were generated. The phenotypes of these mutants were compared to that of the parent strain under ten different conditions, i.e. growth on four different carbon sources, growth at three different salt concentrations, and application of four different stress conditions. In addition, cell morphologies in exponential and stationary phase were observed. Furthermore, swarming of 17 mutants was analyzed. 24 of the 27 mutants exhibited a difference from the parent strain under at least one condition, revealing that haloarchaeal sRNAs are involved in metabolic regulation, growth under extreme conditions, regulation of morphology and behavior, and stress adaptation. Notably, 7 deletion mutants showed a gain of function phenotype, which has not yet been described for any other prokaryotic sRNA gene deletion mutant. Comparison of the transcriptomes of one sRNA gene deletion mutant and the parent strain led to the identification of differentially expressed genes. Genes for flagellins and chemotaxis were up-regulated in the mutant, in accordance with its gain of function swarming phenotype. While the deletion mutant analysis underscored that haloarchaeal sRNAs are involved in many biological functions, the degree of conservation is extremely low. Only 3 of the 27 genes are conserved in more than 10 haloarchaeal species. 22 of the 27 genes are confined to H. volcanii, indicating a fast evolution of haloarchaeal sRNA genes.
authors.affiliation: Goethe-University, Institute for Molecular Biosciences, Frankfurt, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Jaschinski
authors.affiliation: Goethe-University, Institute for Molecular Biosciences, Frankfurt, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Babski
authors.affiliation: Goethe-University, Institute for Molecular Biosciences, Frankfurt, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Lehr
authors.affiliation: Goethe-University, Institute for Molecular Biosciences, Frankfurt, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Burmester
authors.affiliation: Biology II, Ulm University, Ulm, Germany.
authors.forename: Juliane
authors.initials: J
authors.lastname: Benz
authors.affiliation: Biology II, Ulm University, Ulm, Germany.
authors.forename: Ruth
authors.initials: R
authors.lastname: Heyer
authors.affiliation: Biology II, Ulm University, Ulm, Germany.
authors.forename: Marcella
authors.initials: M
authors.lastname: Dörr
authors.affiliation: Biology II, Ulm University, Ulm, Germany.
authors.forename: Anita
authors.initials: A
authors.lastname: Marchfelder
authors.affiliation: Goethe-University, Institute for Molecular Biosciences, Frankfurt, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Soppa
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D004734:Energy Metabolism; D019143:Evolution, Molecular; D017353:Gene Deletion; D020869:Gene Expression Profiling; D019766:Genes, Archaeal; D019622:Haloferax volcanii / Q000145:classification* / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010641:Phenotype; D019642:RNA, Archaeal; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D059467:Transcriptome
chemical_list: D019642:RNA, Archaeal; D012965:Sodium Chloride