Dataset Information

Conserved microsynteny of NPR1 with genes encoding a signal calmodulin-binding protein and a CK1-class protein kinase in Beta vulgaris and two other eudicots.

ABSTRACT: NPR1 is a gene of central importance in enabling plants to resist microbial attack. Therefore, knowledge of nearby genes is important for genome analysis and possibly for improving disease resistance. In this study, systematic DNA sequence analysis, gene annotation, and protein BLASTs were performed to determine genes near the NPR1 gene in Beta vulgaris L., Medicago truncatula Gaertn, and Populus trichocarpa Torr. & Gray, and to access predicted function. Microsynteny was discovered for NPR1 with genes CaMP, encoding a chloroplast-targeted signal calmodulin-binding protein, and CK1PK, a CK1-class protein kinase. Conserved microsynteny of NPR1, CaMP, and CK1PK in three diverse species of eudicots suggests maintenance during evolution by positive selection for close proximity. Perhaps close physical linkage contributes to coordinated expression of these particular genes that may control critically important processes including nuclear events and signal transduction.

SUBMITTER: Kuykendall D

PROVIDER: S-EPMC2579331 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Conserved microsynteny of NPR1 with genes encoding a signal calmodulin-binding protein and a CK1-class protein kinase in Beta vulgaris and two other eudicots.

Kuykendall David D Shao Jonathan J Murphy Tammy T

International journal of plant genomics 20081030

NPR1 is a gene of central importance in enabling plants to resist microbial attack. Therefore, knowledge of nearby genes is important for genome analysis and possibly for improving disease resistance. In this study, systematic DNA sequence analysis, gene annotation, and protein BLASTs were performed to determine genes near the NPR1 gene in Beta vulgaris L., Medicago truncatula Gaertn, and Populus trichocarpa Torr. & Gray, and to access predicted function. Microsynteny was discovered for NPR1 wit ...[more]

PMID: 18989375

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Project description:BACKGROUND:Common bean (Phaseolus vulgaris L.) is an important part of the human diet and serves as a source of natural products. Identification and understanding of genes in P. vulgaris is important for its improvement. Characterization of expressed sequence tags (ESTs) is one of the approaches in understanding the expressed genes. For the understanding of genes expression in P. vulgaris pod-tissue, research work of ESTs generation was initiated by constructing cDNA libraries using 5-day and 20-day old bean-pod-tissues. Altogether, 5972 cDNA clones were isolated to have ESTs. While processing ESTs, we found a transcript for calmodulin (CaM) gene. It is an important gene that encodes for a calcium-binding protein and known to express in all eukaryotic cells. Hence, this study was undertaken to analyse and annotate it. OBJECTIVE:The objective of this study was to analyze and annotate P. vulgaris CaM (PvCaM) gene cDNA and its deduced protein (amino acids) sequence. MATERIALS AND METHODS:Both strands of PvCaM cDNA clone were sequenced using M13 forward and reverse primer to elucidate the nucleotide sequence. The cDNA sequence and deduced protein sequence were analyzed and annotated using bioinformatics tools available online. The secondary structures and three-dimensional (3D) structure of PvCaM protein were predicted using the Phyre automatic fold recognition server. RESULTS:Results showed that PvCaM cDNA is 818 bp in length. The cDNA analysis results showed that it contains an open reading frame that encodes for 149 amino acid residues. The deduced protein sequence analysis results showed the presence of conserved domains required for CaM function. The predicted secondary structures and 3D structure are analogous to the Solanum tuberosum CaM. CONCLUSIONS:This study analyzed and annotated PvCaM cDNA and protein. However, in order to obtain a complete understanding of PvCaM protein, further study on its expression, structure and regulation is essential.

Dataset Information

Conserved microsynteny of NPR1 with genes encoding a signal calmodulin-binding protein and a CK1-class protein kinase in Beta vulgaris and two other eudicots.

Publications

Conserved microsynteny of NPR1 with genes encoding a signal calmodulin-binding protein and a CK1-class protein kinase in Beta vulgaris and two other eudicots.

Similar Datasets

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