Identification of a Conserved Non-Protein-Coding Genomic Element that Plays an Essential Role in Alphabaculovirus Pathogenesis

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.

The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis -Acting Element That Is Essential for Nucleocapsid Assembly

“…3B, upper). In contrast, because the CNE is a cis-acting element, BVs with a CNE knockout genotype could not be produced (41). As expected, only trace amounts of the target fragment corresponding to the CNE knockout genotype were amplified from the infected cells (Fig.…”

“…In contrast, 38K is a capsid protein that acts in trans during nucleocapsid assembly (31). Deletion of the CNE, 38K, or ac83 in AcMNPV results in the failure of progeny virion production (28,32,41, and this study) (Fig. 3A, t1 to t3).…”

“…The existence of the NAE in these three genera needs further investigation. Interestingly, the CNE sequence also shares a similar distribution with the NAE in baculoviruses (41).…”

“…The CNE was originally identified at the ends of the linear form of the Malacosoma neustria nucleopolyhedrovirus (ManeNPV) genome (45). The CNE has been demonstrated to act in cis for the BV production of AcMNPV and is suggested to be involved in the replication, recombination, or cleavage of the viral genome (41). In contrast, 38K is a capsid protein that acts in trans during nucleocapsid assembly (31).…”

“…A microRNA (miRNA), AcMNPV-miR-1, has been identified in the coding sequence of odv-e25 and is likely to regulate the morphogenesis of BVs and ODVs (39), but there is no evidence for its relationship with nucleocapsid assembly, and no miRNA has been identified in ac83 in a high-throughput sequencing study (40). Additionally, a conserved non-protein-coding element (CNE) in the ac152 coding region of AcMNPV has been recently identified to be an essential cis-acting element for the production of progeny virus (41), and a GGN-rich region in pp78/83 was found to be able to interact with the nucleocapsid assembly-essential protein VP1054 (24). However, it still has not been determined whether these DNA sequences function in viral DNA replication, packaging, or other processing steps.…”