Molecular Biology of Insect Iridescent Virus Type 6

Abstract

The genome of the insect iridescent virus type 6-Chilo iridescent virus (CIV)— contains a double-stranded linear DNA molecule of 209 kbp which is circularly permuted and terminally redundant. A defined and complete gene library of the viral genome was established which represents 100% of the CIV DNA sequences. The physical maps of the viral genome were constructed for the restriction enzymes ApaI, Asp718, BamHI, EcoRI, NcoI, PvuII, SalI, SphI, and SmaI. Although the CIV genome is linear the restriction maps of the viral genome are circular due to circular permutation of the CIV DNA molecule. The CIV genome contains repetitive DNA sequences located in the EcoRI DNA fragments H and PvuII CIV DNA fragment L (5064 bp) at the coordinates 0.535 to 0.548 and 0.920 to 0.944, respectively. A DNA element (91 bp) at the nucleotide position 1981 to 2072 of the EcoRI CIV DNA fragment H had been found to be complementary (>90%) to nine regions of the PvuII DNA fragment L. A stem-loop structure has been identified by heteroduplex mapping at the genome coordinates 0.571 to 0.582 (HindIII/EcoRI subfragment (2555 bp) of the EcoRI CIV DNA fragment H). The DNA nucleotide sequence of the PvuII DNA fragment L contains many perfect direct repeats of sizes up to 145 bp. In addition to these repetitions a cluster of four imperfect repetitive DNA elements (R1 to R4) with a complex structural arrangement was detected. R1, R2 and R3 exist in duplicate (two boxes (B)) between nucleotide positions 271 to 3466). The R4 repetitive element was found in 12 boxes (between bases 1301 and 4417). Five open reading frames (ORFs of 118 to 333 amino acid (AA) residues) were detected. The analysis of the amino acid sequences of the largest ORF revealed that the deduced amino acid sequence of the putative gene product contains two repetitions. Sequences of 43 amino acid residues of ORF 5 (160 to 202 AA) were found to be homologous within the majority of ORFs. A consensus sequence-MANL (X)₆ IGSSST(X)₆ L(X)₁ LGS(X)₁ LQISG(X)₂ L(X)₁ VN- was found in all five ORFs. The origins of DNA replication of the CIV genome were identified within the DNA sequences of the EcoRI DNA fragments C (13.5 kbp, 0.909 to 0.974 map units (m.u.)), H (9.8 kbp, 0.535 to 0.582 m.u.), M (7.3 kbp, 0.310 to 0.345 m.u.), 0 (6.6 kbp, 0.196 to 0.228 m.u.), Q (5.9 kbp, 0.603 to 0.631 m.u.), and Y (2.0 kbp, 0.381 to 0.391 m.u.).