The Study Of Genomics Of Strain Kocuria Sp.KD4

The genus Kocuria belongs to the Actinobacteria phyla Micrococcaceae family.The strains of this genus have high activities,and have strong salt-alkali resistance,high and low temperature resistance,radiation resistance,which has aroused widespread concern in academia.Kochia sp.KD4 was isolated from Lake Vida in the northernmost part of the McMurdo Dry Valleys in Antarctica.It had strong antioxidant capacity and had a strong ability to remove superoxide anion free radicals and hydroxyl free radicals.At the same time,it was found that it could grow in 10% NaCl and pH11 medium.This shows that it had a strong salt-alkali resistance.However,the mechanism of the antioxidant and salt-alkali resistance of strain KD4 is unclear.It is of great significance for us to mining the genome of strain KD4 to understand the adaptation mechanism of the strain of genus Kochia to extreme environments and to exploit new antioxidant substances.The strain KD4 was the research object of this dissertation.The method of culture,identification,genomic DNA extraction,whole genome library construction and sequencing,whole genome annotation and function analysis,phylogenetic analysis,genome comparative analysis were used to analyze the genome of strain KD4 and explore its metabolic processes and environmental adaptation mechanisms.The following results were achieved:(1)The strain KD4 belonged to species Kocuria indica,and its genome consists of a circular chromosome with a size of 2.8 Mb.The Kocuria sp.KD4 genome is composed of a circular chromosome with a length of 2,806,716 bp,and its G + C percentage is 68.83%.The genome chromosome encodes a total of 2520 ORFs,with an average length of about 996 bp,and the sequence of the coding gene accounts for 88.71% of the entire chromosome.In addition,there are 22 tandem repeat regions in the genome.The length of the tandem repeat region is 34791 bp.There are 59 total RNAs,including 9 rRNA,47 tRNA and 3 ncRNAs.The strain KD4 was formed an independent clade with Kocuria indica NIO-1021 on the phylogenetic tree which was construct with protein sequences of 44 housekeeping genes.(2)The metabolic pathway of Kocuria sp.KD4 was revealed.The genome of strain KD4 was annotated with COG and KEGG,and the metabolic pathway of strain KD4 was obtained.The genome of strain KD4 contains all the enzyme genes for glycolysis,dicarboxylic acid cycle,and pentose phosphate pathways;has complete metabolic pathways for D-xylulose,mannoic acid,D-fructose,and raffinose;possess the relevant enzymes for the metabolism of large molecular polysaccharides including starch and sucrose;contains a complete amino acid,purine and pyrimidine synthesis of key enzyme genes required by the metabolic pathway;has all genes to encode the necessary enzyme for combine ammonia through glutamate metabolism and nitrate reduction pathway into a whole nitrogen cycle;finds the complete synthetic pathway of riboflavin,niacin,lipoic acid,pantothenic acid and COA;in addition,possesses the key genes of degradation pathways for exogenous substances,including benzoic acid degradation,propionate degradation,azathioprine,fluorouracil and methyl dihydroxybenzoate.(3)The strain Kocuria sp.KD4 has genes response to the high salinity,high radiation,cold and oligotrophic environments.There are a large number of genes encoding the stress in the genome of the strain KD4,such as 12 genes related to osmoregulation,28 genes encoding two-component signaling proteins,39 genes of ABC transport system,and 8 genes related to active oxygen elimination.At the same time,via gene horizontal transfer,KD4 obtained many genes related to catalase body,molecular chaperone,environmental stress,prokaryotic defense system,and DNA replication and repair.The presence of these genes enables the strian KD4 to tolerate the high salinity,high radiation,cold and oligotrophic environment of the Vida lake in Antarctic.