Phylogenetic and codon usage analysis for replicase and capsid genes of porcine circovirus 3

Porcine circovirus type 3 (PCV3) is a highly contagious virus belonging to the family Circoviridae that causes the severe dermatitis and nephropathy syndrome. To date, PCV3 has a worldwide distribution and bring huge economic losses to swine industry. Replicase (Rep) and capsid (Cap) are two major coded proteins of PCV3. Considering the large number of new PCV3 isolates were reported in the past few years and the research for the codon usage pattern of Rep and Cap genes was still a gap, phylogenetic and codon usage analysis of these two genes was performed. Phylogenetic analyses showed that Rep genes in PCV3a were dispersed with no clear clusters while corresponding sequences in PCV3b clustered into two groups and Cap genes clustered into distinct clades according to different genotypes. Relative synonymous codon usage (RSCU) analysis revealed that the codon usage bias existed and effective number of codon (ENC) analysis showed that the bias was slight low. ENC-GC3s plot indicated that mutational pressure and other factors both played a role in PCV3 codon usage and neutrality plot analysis showed that natural selection was the main force influencing the codon usage pattern. The results presented here provided the important basic data on codon usage pattern of Rep and Cap genes, and a better understanding of the evolution and potential origin of PCV3.

Construction of DNA-NanoLuc luciferase conjugates for DNA aptamer-based sandwich assay using Rep protein

OBJECTIVE

We developed a DNA-NanoLuc luciferase (NnaoLuc) conjugates for DNA aptamer-based sandwich assay using the catalytic domain of the replication initiator protein derived from porcine circovirus type 2 (pRep).

RESULTS

For construction of DNA aptamer and NanoLuc conjugate using the catalytic domain of Rep from PCV2. pRep fused to NanoLuc was genetically constructed and expressed in E. coli. After purification, the activities of fused pRep and NanoLuc were evaluated, and DNA-NanoLuc conjugates were constructed via the fused pRep. Finally, constructed DNA-NanoLuc conjugates were applied for use in a DNA aptamer-based sandwich assay. Here, pRep was used not only for conjugation of the NanoLuc to the detection aptamer, but also for immobilization of the capture aptamer on the plate surface.

CONCLUSION

We have demonstrated that DNA-NanoLuc conjugates via the catalytic domain of PCV2 Rep could be applied for DNA aptamer-based sandwich assay system.

Characterization of the nuclear localization signals of duck circovirus replication proteins

Duck circovirus (DuCV) possess a circular, single-stranded DNA genome that requires the replication protein (Rep) for its replication. Based on the viral genotype, there are two categories of Rep proteins: Rep1 and Rep2. To characterize the nuclear localization signals (NLSs) conferring the nuclear localization of the Rep proteins, defined coding regions of the rep gene of two genotypes of DuCV were cloned and co-expressed with the red fluorescent protein DsRed2. The results showed that deleting the putative N-terminal NLS located at amino acid residues 10-37 of Rep1 and Rep2 abrogated nuclear translocation, while deleting the putative C-terminal NLS located at residues 244-274 of Rep1 did not significantly alter its subcellular localization, confirming that only the NLS located at residues 10-37 in the N-termini of the Rep proteins had nuclear targeting activity.

[Biological character of porcine circovirus type 2 with site mutation at interferon stimulation reaction element (ISRE) like region in Rep gene promoter]

OBJECTIVE

To explore the biological function of the interferon stimulation reaction element (ISRE) like motif CTGAAAACGAAAGA within porcine circovirus type 2 (PCV2) Rep promoter.

METHODS

Two recombinant PCV2 strains, namely PCV2 1740(G-C) and PCV2 1741(A-T), were constructed by transfecting PK15 cells with site-mutated infectious clone of PCV2 strain Denta. Replication character, genetic stability and reactive character to porcine interferon alpha (poIFN-alpha) were compared among parental PCV2 and the two mutant viruses.

RESULTS

The ISRE like motif in Rep promoter was not necessary for the replication of PCV2 because two site-mutated viral genome clones both produced infectious virus. In contrast to parental PCV2, the viral antigen positive PK15 cells of the two site-mutated PCV2 were decreased. PCV2 1740(G-C) was genetically stable in the PK15 cell while PCV2 1741(A-T) was found to have another two nucleotide mutated from 1744AC1745 to 1744TT1745 between 3rd and 7th passage in the PK15 cell. After treated with 100 U/mL porcine interferon alpha, the viral antigen positive PK15 cells and virus genomes of parental PCV2 and two site-mutated viruses were both increased. But the enhancement rate of the two site-mutated PCV2 was significantly lower than parental PCV2.

CONCLUSION

Site-mutation of ISRE like motif in Rep promoter decreased the replication and poIFN-alpha induced enhancement of PCV2 in PK15 cells. According to these above results, it maybe speculated that ISRE like motif in PCV2 Rep gene promoter contain a functional element and it may contribute to the interferon inducible enhancement of virus replication in PK15 cells.

PCV2 replicase transcripts in infected porcine kidney (PK15) cells

The Circoviridae family includes small viruses containing circular single strand DNA. There are two circoviruses described in pigs. Porcine Circovirus 2 (PCV2) has been linked to a disease termed Postweaning Multisystemic Wasting Syndrome (PMWS) whereas a close relative of this virus, termed PCV type 1 (PCV1) has been considered a non-pathogenic contaminant of the PK15 cell line. Rolling circle replication of small DNA viruses like circoviruses is mediated by a replicase (Rep) gene that is transcribed into different mRNAs by an alternative splicing mechanism. In PCV1, two transcripts Rep and Rep' implicated in DNA replication, have been identified from infected cells. These transcripts are the product of a single gene with Rep' having a different carboxyl end than Rep. Sequence comparison shows that there is a high degree of homology for the Rep gene in both viruses. In this article, we have identified three different transcripts by RT-PCR in PCV2 infected PK15 cells. Two of them have homology with their PCV1 counterparts and the third transcript, termed Rep", corresponds to another spliced version of the Rep gene. This transcript, unique to PCV2, encodes for a protein of 80 aminoacids in frame with the Rep sequence.