GENOME WIDE IDENTIFICATION OF DNA BINDING MOTIFS OF NodD-FACTOR IN SINORHIZOBIUM MELILOTI AND MESORHIZOBIUM LOTI

2005 ◽  
Vol 03 (04) ◽  
pp. 773-801 ◽  
Author(s):  
FEROZ KHAN ◽  
SHIPRA AGARWAL ◽  
B. N. MISHRA
Keyword(s):  
Dna Binding ◽  
Sinorhizobium Meliloti ◽  
Consensus Sequence ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Model Legume ◽  
Binding Motifs ◽  
Mesorhizobium Loti ◽  
Genome Wide ◽  
Dna Binding Motifs

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.

scholarly journals RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach

2020 ◽  
Vol 11 ◽  
Author(s):  
Hermenegildo Taboada-Castro ◽  
Jaime Abraham Castro-Mondragón ◽  
Alejandro Aguilar-Vera ◽  
Alfredo José Hernández-Álvarez ◽  
Jacques van Helden ◽  
...  
Keyword(s):  
Dna Binding ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Binding Motifs ◽  
Dna Binding Motifs

scholarly journals Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice

Planta ◽  
2021 ◽  
Vol 253 (2) ◽  
Author(s):  
Joung Sug Kim ◽  
SongHwa Chae ◽  
Kyong Mi Jun ◽  
Gang-Seob Lee ◽  
Jong-Seong Jeon ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Binding ◽  
Gene Networks ◽  
Upstream Region ◽  
Transcriptional Level ◽  
Cis Elements ◽  
Promoter Regions ◽  
Entire Genome ◽  
Binding Motifs ◽  
Dna Binding Motifs

Abstract Main conclusion The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Abstract Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5′ upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear receptors

Cell ◽  
1991 ◽  
Vol 65 (7) ◽  
pp. 1267-1279 ◽  
Author(s):  
Anders M. Näär ◽  
Jean-Marle Boutin ◽  
Steven M. Lipkin ◽  
Victor C. Yu ◽  
Jeffrey M. Holloway ◽  
...  
Keyword(s):  
Dna Binding ◽  
Nuclear Receptors ◽  
Transcriptional Responses ◽  
Binding Motifs ◽  
Dna Binding Motifs

Polyamine biosynthesis and biological roles in rhizobia

2019 ◽  
Vol 366 (7) ◽  
Author(s):  
Victor A Becerra-Rivera ◽  
Michael F Dunn
Keyword(s):  
Stress Resistance ◽  
Biofilm Formation ◽  
Sinorhizobium Meliloti ◽  
Growth Stress ◽  
Nitrogen Fixing ◽  
Amino Groups ◽  
Nitrogen Fixing Bacteria ◽  
Polyamine Biosynthesis ◽  
Exopolysaccharide Production

ABSTRACTPolyamines are ubiquitous molecules containing two or more amino groups that fulfill varied and often essential physiological and regulatory roles in all organisms. In the symbiotic nitrogen-fixing bacteria known as rhizobia, putrescine and homospermidine are invariably produced while spermidine and norspermidine synthesis appears to be restricted to the alfalfa microsymbiont Sinorhizobium meliloti. Studies with rhizobial mutants deficient in the synthesis of one or more polyamines have shown that these compounds are important for growth, stress resistance, motility, exopolysaccharide production and biofilm formation. In this review, we describe these studies and examine how polyamines are synthesized and regulated in rhizobia.

ChemInform Abstract: Novel Class of DNA Binding Motifs Based on Bistetrahydrofuran and Bisfuran Skeleton with Long Alkyl Chains

ChemInform ◽  
2010 ◽  
Vol 32 (47) ◽  
pp. no-no
Author(s):  
Shigeki Sasaki ◽  
Takayuki Shibata ◽  
Hidemine Torigoe ◽  
Yosinori Shibata ◽  
Minoru Maeda
Keyword(s):  
Dna Binding ◽  
Binding Motifs ◽  
Alkyl Chains ◽  
Dna Binding Motifs

scholarly journals Improvement of  29 DNA polymerase amplification performance by fusion of DNA binding motifs

2010 ◽  
Vol 107 (38) ◽  
pp. 16506-16511 ◽  
Author(s):  
M. de Vega ◽  
J. M. Lazaro ◽  
M. Mencia ◽  
L. Blanco ◽  
M. Salas
Keyword(s):  
Dna Binding ◽  
Dna Polymerase ◽  
Binding Motifs ◽  
Dna Binding Motifs

scholarly journals Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yoshikazu Shimoda ◽  
Hideki Hirakawa ◽  
Shusei Sato ◽  
Kazuhiko Saeki ◽  
Makoto Hayashi
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Lotus Japonicus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nitrogen Fixing ◽  
Model Legume ◽  
Mesorhizobium Loti ◽  
Symbiotic Properties

Mesorhizobium loti is the nitrogen-fixing microsymbiont for legumes of the genus Lotus . Here, we report the whole-genome sequence of a Mesorhizobium loti strain, TONO, which is used as a symbiont for the model legume Lotus japonicus . The whole-genome sequence of the strain TONO will be a solid platform for comparative genomics analyses and for the identification of genes responsible for the symbiotic properties of Mesorhizobium species.

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