Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus.
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.
Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
Ningning
N
Song
Trong
T
Nguyen Duc
Liesbeth
L
van Oeffelen
Serge
S
Muyldermans
Eveline
E
Peeters
Daniel
D
Charlier
D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology; D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D016384:Consensus Sequence; D018983:DNA Footprinting; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D019848:Gene Expression Regulation, Archaeal; D020745:Genome, Archaeal; D008239:Lysine / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D009875:Operator Regions, Genetic; D011485:Protein Binding; D016945:Sulfolobus acidocaldarius / Q000235:genetics; D048229:Sulfolobus solfataricus / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology; D024363:Transcription Initiation Site
D019843:Archaeal Proteins; D019641:DNA, Archaeal; D014157:Transcription Factors; D008239:Lysine