title: Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans.
abstract: We determined the effects of DNA damage caused by ultraviolet radiation on gene expression in Leptospira interrogans using DNA microarrays. These data were integrated with DNA binding in vivo of LexA1, a regulator of the DNA damage response, assessed by chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq). In response to DNA damage, Leptospira induced expression of genes involved in DNA metabolism, in mobile genetic elements and defective prophages. The DNA repair genes involved in removal of photo-damage (e.g. nucleotide excision repair uvrABC, recombinases recBCD and resolvases ruvABC) were not induced. Genes involved in various metabolic pathways were down regulated, including genes involved in cell growth, RNA metabolism and the tricarboxylic acid cycle. From ChIP-seq data, we observed 24 LexA1 binding sites located throughout chromosome 1 and one binding site in chromosome 2. Expression of many, but not all, genes near those sites was increased following DNA damage. Binding sites were found as far as 550 bp upstream from the start codon, or 1 kb into the coding sequence. Our findings indicate that there is a shift in gene expression following DNA damage that represses genes involved in cell growth and virulence, and induces genes involved in mutagenesis and recombination.
authors.affiliation: Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA.
authors.forename: Luciane
authors.initials: L
authors.lastname: Schons-Fonseca
authors.affiliation: Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil.
authors.forename: Josefa B
authors.initials: JB
authors.lastname: da Silva
authors.affiliation: Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
authors.forename: Juliana S
authors.initials: JS
authors.lastname: Milanez
authors.affiliation: Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil.
authors.forename: Renan H
authors.initials: RH
authors.lastname: Domingos
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA.
authors.forename: Janet L
authors.initials: JL
authors.lastname: Smith
authors.affiliation: Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
authors.forename: Helder I
authors.initials: HI
authors.lastname: Nakaya
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, MA 02139, USA.
authors.forename: Alan D
authors.identifier: http://orcid.org/0000-0002-8235-7227
authors.initials: AD
authors.lastname: Grossman
authors.affiliation: Centro de Biotecnologia, Instituto Butantan, São Paulo, São Paulo 05503-900, Brazil paulo.ho@butantan.gov.br.
authors.forename: Paulo L
authors.initials: PL
authors.lastname: Ho
authors.affiliation: Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210580, Brazil renata.costa@ufabc.edu.br.
authors.forename: Renata M A
authors.initials: RM
authors.lastname: da Costa
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D002455:Cell Division / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D002876:Chromosomes, Bacterial / Q000235:genetics; D004249:DNA Damage; D004260:DNA Repair / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics* / Q000528:radiation effects; D007921:Leptospira interrogans / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013014:SOS Response, Genetics / Q000235:genetics; D017422:Sequence Analysis, DNA; D012697:Serine Endopeptidases / Q000235:genetics* / Q000378:metabolism; D014466:Ultraviolet Rays; D000099160:LexA Repressor Protein
chemical_list: D001426:Bacterial Proteins; D012697:Serine Endopeptidases; D000099160:LexA Repressor Protein