engleski

Deviations from canonical genome organisation in different measles strains

The canonical genome organisation of measles virus (MV) is characterized by total size of 15 894 nucleotides (nts) and defined length of every genomic region, both coding and non-coding. Currently, 54 complete genomic MV cDNA sequences can be found in the GenBank database. Although all strains conform to the rule of 6, in 11 strains we detected small deviations from canonical genome organisation due to short insertions and deletions located within homopolymeric stretches. In 8 strains mutually compensating genome editing sites were identified, so that the total length was unchanged ; in 3 strains 7 nts were inserted at one position and 1 was deleted at the other, thereby prolonging the genome for 6 nts. In all 11 strains insertions are closer to 5' end of genomic cDNA, deletions are closer to 3' end. In 10 of 11 non-canonical strains, at least one of genome editing sites is located within a 28 nts long segment (positions 5051-5078 in genomic cDNA) that is part of 5' untranslated region (5' UTR) of the F gene. This segment is composed of 14 nts long block A with sequence G6-7C7-8, followed by 14 nts long block B whose sequence is A6-7G1-3C5-6. In block A both insertions and deletions were detected, while only deletions were found in block B. Reciprocating insertions are located in polyA/polyC stretches in 3' untranslated region of the M gene and deletions were identified in polyA stretches within F gene coding region. Owing to the fact that in ribonucleoprotein complex each nucleocapsid (N) protein associates with precisely 6 nts and that positions of certain nucleotides relative to N are not irrelevant, the identified segment in F gene 5' UTR possibly serves as a site for controlled polymerase slippage during genome replication after a deviation in N phase context has occurred.

measles virus; genome length; insertions; deletions; polymerase slippage

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