title: Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.
abstract: Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia.
authors.affiliation: Department of Medical Genetics, Shenzhen University Health Science Center, Shenzhen, People's Republic of China.
authors.forename: Yueming
authors.initials: Y
authors.lastname: Hu
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
authors.forename: He
authors.initials: H
authors.lastname: Huang
authors.affiliation: Department of Medical Genetics, Shenzhen University Health Science Center, Shenzhen, People's Republic of China.
authors.forename: Xinjie
authors.initials: X
authors.lastname: Hui
authors.affiliation: Department of Medical Genetics, Shenzhen University Health Science Center, Shenzhen, People's Republic of China.
authors.forename: Xi
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
authors.forename: Aaron P
authors.initials: AP
authors.lastname: White
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China timjszzd@163.com wangyj@szu.edu.cn.
authors.forename: Zhendong
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Medical Genetics, Shenzhen University Health Science Center, Shenzhen, People's Republic of China timjszzd@163.com wangyj@szu.edu.cn.
authors.forename: Yejun
authors.initials: Y
authors.lastname: Wang
mesh_terms: D020816:Amino Acid Motifs; D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D016384:Consensus Sequence; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D000090263:Leucine-Rich Repeat Proteins; D008958:Models, Molecular; D016366:Open Reading Frames; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D021381:Protein Transport; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D015007:Yersinia / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D000090263:Leucine-Rich Repeat Proteins; D011506:Proteins