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Complete genome of Phenylobacterium zucineum – a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562

Yingfeng Luo123, Xiaoli Xu1, Zonghui Ding1, Zhen Liu1, Bing Zhang23, Zhiyu Yan1, Jie Sun1, Songnian Hu23* and Xun Hu1*

Author Affiliations

1 Cancer Institute (Key Laboratory for Cancer Intervention and Prevention, National Ministry of Education, PR China; Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, PR China), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, PR China

2 James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, PR China

3 Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China

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BMC Genomics 2008, 9:386  doi:10.1186/1471-2164-9-386

Published: 13 August 2008



Phenylobacterium zucineum is a recently identified facultative intracellular species isolated from the human leukemia cell line K562. Unlike the known intracellular pathogens, P. zucineum maintains a stable association with its host cell without affecting the growth and morphology of the latter.


Here, we report the whole genome sequence of the type strain HLK1T. The 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 rRNA operon. Comparative genomic analysis revealed that it is phylogenetically closest to Caulobacter crescentus, a model species for cell cycle research. Notably, P. zucineum has a gene that is strikingly similar, both structurally and functionally, to the cell cycle master regulator CtrA of C. crescentus, and most of the genes directly regulated by CtrA in the latter have orthologs in the former.


This work presents the first complete bacterial genome in the genus Phenylobacterium. Comparative genomic analysis indicated that the CtrA regulon is well conserved between C. crescentus and P. zucineum.