Coding potential and transcript analysis of fowl adenovirus 4: insight into upstream ORFs as common sequence features in adenoviral transcripts
- 1 June 2011
- journal article
- Published by Microbiology Society in Journal of General Virology
- Vol. 92 (6), 1260-1272
- https://doi.org/10.1099/vir.0.030064-0
Abstract
Recombinant fowl adenoviruses (FAdVs) have been successfully used as veterinary vaccine vectors. However, insufficient definitions of the protein-coding and non-coding regions and an incomplete understanding of virus–host interactions limit the progress of next-generation vectors. FAdVs are known to cause several diseases of poultry. Certain isolates of species FAdV-C are the aetiological agent of inclusion body hepatitis/hydropericardium syndrome (IBH/HPS). In this study, we report the complete 45667 bp genome sequence of FAdV-4 of species FAdV-C. Assessment of the protein-coding potential of FAdV-4 was carried out with the Bio-Dictionary-based Gene Finder together with an evaluation of sequence conservation among species FAdV-A and FAdV-D. On this basis, 46 potentially protein-coding ORFs were identified. Of these, 33 and 13 ORFs were assigned high and low protein-coding potential, respectively. Homologues of the ancestral adenoviral genes were, with few exceptions, assigned high protein-coding potential. ORFs that were unique to the FAdVs were differentiated into high and low protein-coding potential groups. Notable putative genes with high protein-coding capacity included the previously unreported fiber 1, hypothetical 10.3K and hypothetical 10.5K genes. Transcript analysis revealed that several of the small ORFs less than 300 nt in length that were assigned low coding potential contributed to upstream ORFs (uORFs) in important mRNAs, including the ORF22 mRNA. Subsequent analysis of the previously reported transcripts of FAdV-1, FAdV-9, human adenovirus 2 and bovine adenovirus 3 identified widespread uORFs in AdV mRNAs that have the potential to act as important translational regulatory elements.Keywords
This publication has 67 references indexed in Scilit:
- The non-essential left end region of the fowl adenovirus 9 genome is suitable for foreign gene insertion/replacementVirus Research, 2010
- Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humansProceedings of the National Academy of Sciences, 2009
- Armed replicating adenoviruses for cancer virotherapyCancer Gene Therapy, 2009
- Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trialThe Lancet, 2008
- Challenges in the development of an HIV-1 vaccineNature, 2008
- Distinguishing protein-coding and noncoding genes in the human genomeProceedings of the National Academy of Sciences of the United States of America, 2007
- Viral control of the SUMO pathway: Gam1, a model systemBiochemical Society Transactions, 2007
- LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNAGenome Research, 2003
- Sequence and transcriptional analysis of terminal regions of the fowl adenovirus type 8 genome.Journal of General Virology, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997