Abstract
Highly homologous sequences 154–157 bp in length grouped under the name of “conserved non-protein-coding element” (CNE) were revealed in all of the sequenced genomes of baculoviruses belonging to the genus Alphabaculovirus. A CNE alignment led to the detection of a set of highly conserved nucleotide clusters that occupy strictly conserved positions in the CNE sequence. The significant length of the CNE and conservation of both its length and cluster architecture were identified as a combination of characteristics that make this CNE different from known viral non-coding functional sequences. The essential role of the CNE in the Alphabaculovirus life cycle was demonstrated through the use of a CNE-knockout Autographa californica multiple nucleopolyhedrovirus (AcMNPV) bacmid. It was shown that the essential function of the CNE was not mediated by the presumed expression activities of the protein- and non-protein-coding genes that overlap the AcMNPV CNE. On the basis of the presented data, the AcMNPV CNE was categorized as a complex-structured, polyfunctional genomic element involved in an essential DNA transaction that is associated with an undefined function of the baculovirus genome.
Highlights
Certain processes governing basic DNA transactions such as replication, transcription, and site-specific recombination appear to be strictly related to precisely located non-coding genomic regions that interact with the proteins involved in these processes
The latter include (i) homologous repeat regions, organized sequences interspersed at multiple locations throughout the genomes of representatives of all baculovirus genera [10], which function as enhancers [12] [13] and oris [14] [15], and (ii) the so-called non-hr oris revealed in both Alphabaculovirus [16] [17] [18] [19] and Betabaculovirus [20] genomes
These sequences were detected in all Alphabaculovirus genomes sequenced to date, whereas a BLAST search failed to detect such a conserved element (CE) in the rest of the baculovirus genomes available in the databases, namely in 14 Betabaculovirus, 3 Gammabaculovirus, and 1 Deltabaculovirus genomes
Summary
Certain processes governing basic DNA transactions such as replication, transcription, and site-specific recombination appear to be strictly related to precisely located non-coding genomic regions (non-coding functional elements, nfes) that interact with the proteins involved in these processes. The conservation of the general mechanisms of baculoviral pathogenesis can be deduced from comparative genomic studies; 37 core genes shared by all sequenced baculovirus genomes [10] [11] and common DNA nfes have been identified The latter include (i) homologous repeat regions (hrs), organized sequences interspersed at multiple locations throughout the genomes of representatives of all baculovirus genera [10], which function as enhancers [12] [13] and oris [14] [15], and (ii) the so-called non-hr oris revealed in both Alphabaculovirus [16] [17] [18] [19] and Betabaculovirus [20] genomes
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