title: Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction.
abstract: Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.|Department of Ecosystems and Public Health, University of Calgary, Calgary, Canada.
authors.forename: Le
authors.initials: L
authors.lastname: Tang
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Songling
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Emilio
authors.initials: E
authors.lastname: Mastriani
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Fang
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Yu-Jie
authors.initials: YJ
authors.lastname: Zhou
authors.affiliation: Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China.
authors.forename: Yong-Guo
authors.initials: YG
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.
authors.forename: Randal N
authors.initials: RN
authors.lastname: Johnston
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
authors.forename: Gui-Rong
authors.initials: GR
authors.lastname: Liu
authors.affiliation: Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.|HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.|Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China.|Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
authors.forename: Shu-Lin
authors.initials: SL
authors.lastname: Liu
mesh_terms: D017124:Conserved Sequence; D021901:DNA, Intergenic; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D012475:Salmonella / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic