Complete Genome Sequencing And Analysis Of Phenylobacterium Zucineum

Phenylobacterium zucineum strain HLK1~T is a facultative intracellular species recently isolated from the human leukemia cell line K562.P.zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter. Phylogenetic analysis based on 16S rDNA revealed that P.zucineum belongs to the genus Phenylobacterium.P.zucineum was the only bacterium reported to invade eukaryotic cells in the genus Phenylobacterium.To better understand the basic metabolism and high capacity of environmental adaptation of this facultative intracellular bacterium from genomic perspective,we carry out the whole genome sequencing of P.zucineum.This work would present the main findings on the genomic analysis of P.zucineum.The P.zucineum genome consists of a circular chromosome(3,996,255 bp) and a circular plasmid(382,976 bp).It encodes 3,861 putative proteins,42 tRNAs,and a 16S-23S-5S rDNA operon.P.zucineum genome encodes a large number of two-component transduction systems protein,transcriptional regulator,extracytoplasmic function sigma factors and heat-shock related proteins.Further comparative genome analysis indicated that P.zucineum has the highest fraction of two-component transduction proteins among common facultative bacteria and even has the fraction of transcriptional regulator higher than mean level of multiple bacteria which are well accepted as bacteria with the highest capacity of environmental adaptation.Notably,P.zucineum genome harbors the largest number of heat-shock related proteins among analyzed 93 bacteria which occupy the major phylogenic positions and live in the major representative environmental niches.Therefore,the high number of environmental stress proteins encoded in P.zucineum genome may partial account for its high capacity of environmental transition and adaptation.Both phylogenetic analyses based on 16S rDNA gene and comparative protein profiles analysis indicated that P.zucineum is phylogenetically closest to Caulobacter crescentus,a model species for bacterial cell cycle research.Comparative genomic analysis indicated that about 60%of P.zucineum protein-coding genes have C.crescentus orthologs.There is no apparent synteny between the C.crescentus chromosome and P. zucineum countpart.We also found most of P.zucineum specific stress genes are located in plasmid.Both horizontal gene transfer and gene duplication within plasmid play important roles in the shaping of P.zucineum plasmid stress proteins profiles.Researches have revealed CtrA,GcrA,DnaA and two-component transduction proteins play important roles in C.crescentus cell cycle regulation.Comparative analysis indicated cell cycle regulation system is well conserved between P.zucineum and C. crescentus.Detailly,P.zucineu and C.crescentus ctrA gene have identical promoters(p1 and p2) and the DNA methyltransferase(CcrM) recognization motif(GAnTC).P.zucineu has all the orthologs participating in C.crescentus ctrA gene transcription,CtrA phosphorylation and proteolytic degradation.The fraction of CtrA-regulated genes with orthologs in P.zucineum is significantly greater than the mean level of the whole genome. P.zucineum and C.crescentus CtrA-regulated genes have structure similar CtrA binding sites.Potential GcrA-regulated genes and DnaA-regulated genes involving in replication, recombination or repair are well conserved between P.zucineum and C.crescentus two-component transduction genes required for cell cycle progression,growth or morphogenesis are more conserved than that function in stress environment.This work presents the first complete bacterial genomic analysis in the genus Phenylobacterium.Genome annotation facilitates us to identify the genetic basis of P. zirconium's physiological features,such as phenylalanine utilization,intracellular living style and the high capacity of environmental adaptation.Comparative genomic analysis indicated that the cell cycle regulation systems are well conserved between P.zucineum and Caulobacter crescentus,a well known cell cycle research model prokaryote.