Journal of Applied Biosciences (J. Appl. Biosci.) [ISSN 1997 - 5902]
Volume 10(1): 471 - 482. Published October 2008.
Predicted role of small non-coding Ribonucleic acids (ncRNAs) and Ribonucleoproteins (RNPs) in Influenza genetic shifts and drifts
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ABSTRACT
Objective: Influenza disease has been observed to be severe in animal hosts in associations with co-infection with H.Influenza species. This phenomenon is widely related to H.Influenza associated inflammation, but may as well be due to emergence of new virus strains. If the later is true, then H. Influenza may be releasing modulators of Influenza genomic variation aside of innate virus’ error prone polymerase. Group II Retroposon elements (RTE) are a mobile class of small noncoding RNAs (snRNA) with both RNA and DNA catalytic potential found distributed across organella genomes, eubacteria and archeabacteria. To aimed to investigate if H. Influenza RTE derived snRNA may be exogenous mediators of Influenza genomic splicing
Methodology and Results: we employed Insilco palindromics to search for potential cleavage sites in 8 Influenza genomic RNA segments using 14 H. Influenza derived REases; AND a search for ORF encoding RT, X and En domains in 16 H. influenza species genome databases by BLASTP with query H.s.I1. Palindromes were found distributed in order of polymerase acidic protein gene PA 14 (100%), S2 13 (93%); HA;7 (50%), NA;7 (50%), PB1;8 (57%), PB2;7 (50%), M1&2;10 (71%), S1;8 (57%), S3;9 (64%), S4;7 (50%), S5;7 (50%), S6;7 (50%), S7;6 (43%), S8;6 (43%), NP;4 (29%), and the NS1&2;3 (21%). 15 low score blast hits were found, 7 of which were MTase- subunits of putative type I R-M systems, but no ortholog of the H.s.I1 ORF except in the query source genome H.somnus.
Conclusions: While the distribution of Palindromes supports the existence of HNHc/HHVR cleavage sites in Influenza RNA, the role of Group II RTE snRNA in drifts and shifts is limited by lack of conclusive homologs of RT ORF.
Key words
Group II Retroelements; Haemophilus Influenza species; Influenza antigenic drifts and reassortments; Restriction Endonuclease (REases).
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