engleski

Deviations from canonical genome organization in different measles virus strains

Measles virus (MV) is an enveloped RNA virus with single-strand, negative sense, nonsegmented genome. It belongs to genus Morbillivirus within the subfamily Paramyxovirinae, family Paramyxoviridae. The canonical genome organization of MV is characterized by total size of 15 894 nucleotides (nts) and defined length of every region, both coding and non-coding. Same as other members of this subfamily, MV replicates efficiently only when the nucleotide length of its genome is an even multiple of 6 (“rule of 6”). Another characteristic inherent to all viruses belonging to subfamily Paramyxovirinae is precise pseudo-templated nucleotide addition that occurs in two instances during transcription: (a) reiterative copying of short runs of template uridylates in polyadenilation of viral mRNAs ; and (b)programmed co-transcriptional insertion of non-templated G residues during transcription of P gene. A pseudo-templated RNA editing mechanism that would be systematically induced during replication has so far not been identified. Currently, 54 complete genomic MV cDNA sequences can be found in the open public databases, all conforming to the rule of 6. Still, in 10 strains we detected deviations from canonical genome organization due to short, mutually compensating insertions and deletions located within homopolymeric stretches or next to them. These 10 strains can be grouped in 3 clusters, based on their passage histories or epidemiological data. There are no indications that the clusters are somehow evolutionary linked, other than the fact that all strains belong to clade D. In 8 strains the total genome length is 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 10 identified strains, one of deviation point is located within the same, 28 nts long segment (positions 5051-5078 in genomic cDNA of canonical strains) that is part of the longest untranslated region in MV genome, indicating that 5051-5078 segment could be involved in preservation of viral genomic structure. This untranslated region, located between ORFs for matix protein and fusion protein, counts for 6.4 % of the total MV genome length and its functions are poorly understood. A mechanism involved in genome length corrections that occurred in 10 non-canonical strains was either (a) random indel-mutation that restored polyhexameric genome length, followed by a stringent selection for virus in which the correction was close to the point of deviation, or (b) non-random indel-mutation, introduced after the viral replication complex had “sensed” the deviation from the rule of 6. As we found that the same narrow genomic region was mutated in different MV strains, our analysis favours the hypothesis that viral polymerase detects that aberrations during replication have occurred and acts by inserting a correcting mutation at a precise site in the nascent molecule.

measles virus ; genome organisation ; indel-mutations ; genome structure

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