title: Genome wide identification of DNA binding motifs of NodD-factor in Sinorhizobium meliloti and Mesorhizobium loti.
abstract: NodD transcription factor is a regulatory protein of nitrogen fixing bacteria, which activates expression of nod genes participating in nodulation during interaction with its symbiont legumes. It's DNA binding motifs have been characterized and reported in Sinorhizobium meliloti and this pattern information has been used in our theoretical analyses to detect its novel regulated genes in genomes of S. meliloti and Mesorhizobium loti. M. loti, a symbiont to model legume plant Lotus japonicus, showed presence of these regulatory motifs in upstream sequences of nod and other functionally related genes. The methodology involved comparative potential weight matrix construction through GIBBS SAMPLER (RSAT) and MEME tools, using information of conserved upstream sequences of nine genes including nod and neighboring genes of both genomes possessing nod-box like motif. The resultant DNA consensus sequence had highly conserved nod-box like 17 bp long motif consensus sequence pattern for binding of detected NodD transcription factors as analyzed by homologous clustering method and therefore the genome wide predictions were considered highly accurate since confirmed by operon delineation method and the described methodology can be used in other nitrogen fixing bacteria to pursue the study in detail.
authors.affiliation: Department of Biotechnology, Institute of Engineering & Technology, UP Technical University, Lucknow, UP, India. ferozkhan306@rediffmail.com
authors.forename: Feroz
authors.initials: F
authors.lastname: Khan
authors.forename: Shipra
authors.initials: S
authors.lastname: Agarwal
authors.forename: B N
authors.initials: BN
authors.lastname: Mishra
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D011485:Protein Binding; D012231:Rhizobium / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C060773:NodD protein, Bacteria