Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses.

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Abstract Text:

Patrick C Y Woo,Beatrice H L Wong,Yi Huang,Susanna K P Lau,Kwok-Yung Yuen,Patrick C Y Woo,Beatrice H L Wong,Yi Huang,Susanna K P Lau,Kwok-Yung Yuen,Patrick C Y Woo,Beatrice H L Wong,Yi Huang,Susanna K P Lau,Kwok-Yung Yuen,

Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G+C content in CoV-HKU1 warrants further studies.

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Publishing Authors By Initials

PC Woo,BH Wong,Y Huang,SK Lau,KY Yuen,PC Woo,BH Wong,Y Huang,SK Lau,KY Yuen,PC Woo,BH Wong,Y Huang,SK Lau,KY Yuen,

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Virology

VOLUME: 369

Page Numbers: 431-42

Journal Abbreviation: Virology

ISSN: 0042-6822

DAY: 19

MONTH: 09

YEAR: 2007

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 110674

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses.

AFFILIATION: State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Department of Microbiology, The University of Hong Kong, Hong Kong.

Country: United States

AGENCY:

GRANT:

ACRONYM:

MEDLINETA: Virology

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses Related Publications

• A 31-phosphorus neurospectroscopy study of omega-3 long-chain polyunsaturated fatty acid intervention with eicosapentaenoic acid and docosahexaenoic acid in patients with chronic refractory epilepsy.
• A model to control the epidemic of H5N1 influenza at the source.
• A randomised controlled trial of prophylactic levonorgestrel intrauterine system in tamoxifen-treated women.
• An audit on hysterectomy for benign diseases in public hospitals in Hong Kong.
• Canadian consensus conference on osteoporosis, 2006 update.
• Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children.
• CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes.
• Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome.
• Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses.
• Distribution and molecular characterization of tetracycline resistance in Laribacter hongkongensis.
• Dynamics of an ultrasonic transducer used for wire bonding.
• Evolution of antibiotic resistance mechanisms and their relevance to dialysis-related infections.
• Hepatitis B virus core-related antigens as markers for monitoring chronic hepatitis B infection.
• Hn03 metastatic parotid squamous cell carcinoma: a facial nerve preservative approach.
• Incremental linear discriminant analysis for face recognition.
• Isolation of Laribacter hongkongensis, a novel bacterium associated with gastroenteritis, from drinking water reservoirs in Hong Kong.
• Lasiodiplodia theobromae Pneumonia in a Liver Transplant Recipient.
• Lupeol suppresses cisplatin-induced nuclear factor-kappaB activation in head and neck squamous cell carcinoma and inhibits local invasion and nodal metastasis in an orthotopic nude mouse model.
• MP1 homologue-based multilocus sequence system for typing the pathogenic fungus Penicillium marneffei: a novel approach using lineage-specific genes.
• Modified four-coil phased array assembly for high-resolution MR imaging of the cerebellopontine angle.
• Natural history of hepatitis-related hepatocellular carcinoma.
• Outbreak of human metapneumovirus infection in psychiatric inpatients: implications for directly observed use of alcohol hand rub in prevention of nosocomial outbreaks.
• Plasmid profile and construction of a small shuttle vector in Laribacter hongkongensis.
• Precore and core promoter mutations at the time of HBeAg seroclearance in Chinese patients with chronic hepatitis B.
• Preface:contribution of social work to recovery and rehabilitation after the asian tsunami disaster.
• Severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection.
• Sinus elevation. Caldwell Luc approach--has it gone passed its use-by date?
• The natural history of chronic hepatitis B.
• The photodissociation dynamics of ozone at 226 and 248 nm: O(3PJ) atomic angular momentum polarization.
• Three-dimensional time-of-flight subtraction angiography of subacute cerebral hemorrhage.