Bioinformatic Analysis Of The NBS-LRR Gene Family In Arabidopsis Thaliana

Disease resistance genes (R genes) are crucial components of the hypersensitive response (HR), a plant defense mechanism that results in localized cell death. Most characterized R genes encode putative intracellular receptors, which contain either a coiled-coil (CC) or a Toll/Interleukin-1 receptor (TIR) domain at their N-terminal end, followed by a nucleotide binding site (NBS). At the C-terminal end, these proteins consist of a series of leucine rich repeats (LRRs). Some known R proteins contain a nucleotide binding site and leucine-rich repeat domains (NBS-LRR proteins). NBS-LRR proteins may recognize the presence of the pathogen directly or indirectly.The completion of model plant Arabidopsis thaliana genome project made it possible for the experiments of genomic sequencing and protein sequencing and structural analysis to produce considerable initial data about biomolecule, which is biologically important for the biomacromolecule information collection, disposal, memorization, classification, retrieval and analysis, and also significant for the resolution of plant disease resistance mechanism and excavation of disease resistance genes.In this paper, a full set of disease resistance (R) candidate genes encoding NBS-LRR in a complete genome of Arabidopsis thaliana was identified and characterized by structural diversities, physical positions, and phylogenetic relationships. The result showed: 204 genes which contained NBS were found in Arabidopsis thaliana genome; the above genes could be classified into 16 sub-types. Meanwhile, the disposition of various kinds of genes in five chromosomes was determined by the chromosomal localization in Arabidopsis thanliana genome tool which was provided by TAIR database. The results showed the disproportion disposition of NBS-LRR gene on chromosomes. There was no obvious disposition regularity found on different chromosomes of various kinds of genes. The Arabidopsis thanliana family genes on different chromosomes exist in the form of monogenic or gene clusters. 71.6 % of the NBS genes were located in gene clusters showed that there is more copy phenomenon in the evolution of disease resistance genes of Arabidopsis thanlianaBy the method of structural domain forecasting in Pfam website, NBS-LRR protein sequence was analyzed. It was found that NBS-LRR gene family had the NBS, LRR and TIR structural domain feature. Generally, LRR structural domains existed in the form of dispersion or cascade connection, but most of NBS and TIR structural domains exist in the form of single modality. At the same time, other structural domains were found in BNS-LRR gene family, including 12 structural domains such as DUF641, PAâ…¡, Pkinase, RCC1, FYVE, DZC, LIM, NACHT, WRKY, RPW8 et al.Arabidopsis thanliana NBS-LRR gene family was further amino acids multi-sequence contrasted and systematic tree analyzed and the gene family was found to have four sub-families. NBS sector of motif gene which contains TIR and which contains CC-NBS-LRR in NBS-LRR typus genes of Arabidopsis thanliana existed in different evolution offsets in cladogram and there was no TIR and CC-NBS-LRR solitary offset, which proved that the evolution mode of the two kinds of genes shared the same evolution way. By the contrast of the amino acid sequence of the correlated 13 disease resistance genes in the reported NBS-LRR family, the result showed these genes could be divided into three sub-families. The first one included 6 genes and the high supporting grade of the offset proved that there was a close kinship in the evolution process.The sequence analysis for the total length of 2500bp of upstream 500bp and downstream 2000bp on NBS-LRR gene promoter TSS showed that the free energy disposition of upstream and downstream sequence on TSS were different. In Arabidopsis thanliana NBS-LRR gene family promoters, the downstream stability stepped up, which was showed by the free energy of downstream on TSS stepping down; on the contrary, the upstream promoter stability stepping down, which was showed by the free energy stepping up. Direct correlation between GC composition and promoter region free energy was shown obviously. DNA bend ability played an important role in transcriptional control. Seen from the whole disposition of promoter bend ability, downstream had high bend ability than upstream on TSS with an overall upsteam stepping down and downstream stepping up.DNA stability is mainly decided by its interactive dinucleotide sum. Genome DNA sequence showed differences in many aspects on nucleotide composition. This study, by the analysis for the Arabidopsis thanliana NBS-LRR gene family promoter region composition, revealed the different disposition of different composition on TSS upstream and downstream. AT, AA, TT, TC and TA in nucleotide composition of Arabidopsis thanliana had different disposition on TSS upstream and downstream.As a big family in Arabidopsis thanliana genes, Arabidopsis thanliana disease resistance gene contains a large amount of information to be uncovered. Bioinformatics opened up a new and high-efficient analytic and studying way. This paper had a study and classification for the volume dose of NBS typus disease resistance in Arabidopsis thanliana genome, and also provided a significant theoretical base, by way of systemic embryology analysis and forecasting for promoter region, in order to speed up the disease resistance gene cloning in Arabidopsis thanliana, to study the mechanism of disease resistance and to speed up the breeding for disease resistance by way of using disease resistance genes. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges. This bioinformatics analysis of the NBS-LRR gene family provides a definitive resource for ongoing functional and evolutionary studies of the other family of plant genes.