Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus.

TitleExpanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus.
Publication TypeJournal Article
Year of Publication2013
AuthorsSong, N., T. Nguyen Duc, L. van Oeffelen, S. Muyldermans, E. Peeters, and D. Charlier
JournalNucleic Acids Res
Volume41
Issue5
Pagination2932-49
Date Published2013 Mar 1
ISSN1362-4962
KeywordsArchaeal Proteins, Base Sequence, Binding Sites, Chromatin Immunoprecipitation, Chromosome Mapping, Consensus Sequence, DNA Footprinting, DNA, Archaeal, Electrophoretic Mobility Shift Assay, Gene Expression Regulation, Archaeal, Genome, Archaeal, Lysine, Metabolic Networks and Pathways, Molecular Sequence Data, Operator Regions, Genetic, Protein Binding, Sulfolobus acidocaldarius, Sulfolobus solfataricus, Transcription Factors, Transcription Initiation Site
Abstract

Previously, Lrp-like transcriptional regulator LysM from the hyperthermoacidophilic crenarchaeon Sulfolobus solfataricus was proposed to have a single target, the lysWXJK operon of lysine biosynthesis, and a single effector molecule, l-lysine. Here we identify ∼70 novel binding sites for LysM in the S. solfataricus genome with a LysM-specific nanobody-based chromatin immunoprecipitation assay coupled to microarray hybridization (ChIP-chip) and in silico target site prediction using an energy-based position weight matrix, and validate these findings with in vitro binding. LysM binds to intergenic and coding regions, including promoters of various amino acid biosynthesis and transport genes. We confirm that l-lysine is the most potent effector molecule that reduces, but does not completely abolish, LysM binding, and show that several other amino acids and derivatives, including d-lysine, l-arginine, l-homoarginine, l-glutamine and l-methionine and branched-chain amino acids l-leucine, l-isoleucine and l-valine, significantly affect DNA-binding properties of LysM. Therefore, it appears from this study that LysM is a much more versatile regulator than previously thought, and that it uses a variety of amino acids to sense nutritional quality of the environment and to modulate expression of the metabolic machinery of Sulfolobus accordingly.

DOI10.1093/nar/gkt021
Alternate JournalNucleic Acids Res.
PubMed ID23355617
PubMed Central IDPMC3597687