Split genes and their expression in Kaposi's sarcoma‐associated herpesvirus

Abstract

SUMMARYA split or interrupted gene is defined as a gene consisting of introns and exons. Removal (splicing) of the intron (s) from a primary transcript (pre-mRNA) is an essential process to create a mRNA. Initial assignment of a potential protein coding region in KSHV genome was based on initiation codon context and predicted protein size larger than 100 amino acids, but the gene discontinuity was disregarded. Experimental investigation of the assigned ORFs has demonstrated that there are up to 25 split genes, more than one fourth of the total KSHV genes described in KSHV genome. This includes the genes involved in all phases (latent, immediate early, early and late) of KSHV infection. The complexity of a split gene expression depends upon the availability of a proximal promoter and polyadenylation (pA) signal. Sharing a single promoter or a single pA signal by two or three genes is not uncommon in the expression of KSHV split genes and the resulting transcripts are usually polycistronic. Among those of KSHV split genes, 15 genes express a bicistronic or tricistronic RNA and 10 genes express a monocistronic RNA. Alternative RNA splicing could happen in a particular pre-mRNA due to intron or exon inclusion or skipping or the presence of an alternative 5′ ss or 3′ ss. This may, respectively, result in at least 8 species of K8 and 14 species of K15 transcripts. This appears to be related to cell differentiation and stages of the virus infection, presumably involving in viral cis elements and trans splicing factors.

Kaposi's Sarcoma-Associated Herpesvirus ORF57 Functions as a Viral Splicing Factor and Promotes Expression of Intron-Containing Viral Lytic Genes in Spliceosome-Mediated RNA Splicing

“…It is perhaps not surprising that a viral splicing factor is needed during KSHV infection, because the KSHV genome carries more than 30 split genes whose expression requires extensive RNA splicing. This represents more than 30% of the total number of known genes in the KSHV genome (35,59,70). Among the split genes, many have a rather small intron downstream of an oversized exon, making them distinct from most mammalian pre-mRNAs, which consist of small exons and large introns.…”

Requirement of a 12-Base-Pair TATT-Containing Sequence and Viral Lytic DNA Replication in Activation of the Kaposi's Sarcoma-Associated Herpesvirus K8.1 Late Promoter

“…However, the gC promoter core has a sequence, GGGTATAAAT TCCGG, which deviates from the consensus Goldberg-Hogness sequence (GGGTATAAATA) (2) by only 1 nt, whereas the defined K8.1 12-bp promoter core, like the SV40 11-bp late ). wt and mutant (MT) doublestranded DNA oligonucleotides, equivalent to the K8.1 promoter sequences in pST41 and pST46, respectively, were labeled with 32 P and used for the protein-DNA complex formation that was resolved on a 4% native polyacrylamide gel (9 Sensitivity of trans-activated K8.1 late promoter activity to PAA and GCV in butyrate-induced JSC-1 cells. To examine whether the K8.1 promoter identified in our transient-transfection assay could represent an authentic late promoter in responding to viral DNA replication inhibitors, two versions of the K8.1 promoter, a 1-kb promoter in pST7 and a 24-bp promoter in pST41, were further analyzed in butyrate-induced JSC-1 cells in the presence or absence of PAA or ganciclovir (GCV).…”

“…The putative predicted K8.1 promoter overlaps two KSHV genes: ORF50 and K8 (32). ORF50 encodes a transactivator, RTA (replication and transcription activator), responsible for initiating all KSHV early gene expression.…”

Kaposi's Sarcoma-Associated Herpesvirus Utilizes and Manipulates RNA N 6 -Adenosine Methylation To Promote Lytic Replication

“…Due to differential splicing, the about 5,400-nucleotide (nt) KSHV ORF50 (RTA) and ORFK8 loci produce at least three different groups of transcripts, including ORF50 (RTA)/ORFK8/ORFK8.1 tricistronic mRNAs, ORFK8/ORFK8.1 bicistronic mRNAs, and monocistronic ORFK8.1 mRNAs (72). ORF50 (RTA), which is expressed from the tricistronic mRNAs, consists of two exons and one intron (Fig.…”