The ac53, ac78, ac101, and ac103 genes are newly discovered core genes in the family Baculoviridae

Abstract

The family Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp, which have broad biotechnological applications. A key feature to understand and manipulate them is the recognition of orthology. However, the differences in gene contents and evolutionary distances among the known members of this family make it difficult to assign sequence orthology. In this study, the genome sequences of 58 baculoviruses were analyzed, with the aim to detect previously undescribed core genes because of their remote homology. A routine based on Multi PSI-Blast/tBlastN and Multi HaMStR allowed us to detect 31 of 33 accepted core genes and 4 orthologous sequences in the Baculoviridae which were not described previously. Our results show that the ac53, ac78, ac101 (p40), and ac103 (p48) genes have orthologs in all genomes and should be considered core genes. Accordingly, there are 37 orthologous genes in the family Baculoviridae.

Fig 1

Gene order. Shown are schematic physical maps for the ac53 (A), ac78 (B), and ac101 (C) individual gene clusters. AcMNPV, Lymantria dispar MNPV (LdMNPV), CpGV, NeabNPV, and CuniNPV are the prototypes representing alphabaculoviruses of group I, alphabaculoviruses of group II, betabaculoviruses, gammabaculoviruses, and deltabaculoviruses, respectively. The relative positions and orientations of these three gene clusters are conserved in all baculovirus genomes sequenced to date. The dark arrows represent the newly discovered core genes, the dark gray arrows indicate the previously accepted core genes, and the light gray arrows represent other ORFs described among the core genes illustrated.

Fig 2

Sequence conservation. Box plots show the sequence conservation of newly discovered core genes. The percentages of similarity (A) and identity (B) for all protein pairs were calculated. To compare the CuniNPV-orthologous protein, all possible intergenus comparisons were considered (δ versus α + β + γ, δ versus α, δ versus β, δ versus γ, α versus β, α versus γ, and β versus γ, where α, β, γ, and δ indicate alphabaculoviruses, betabaculoviruses, gammabaculoviruses, and deltabaculoviruses, respectively). The boundary of the boxes closest to zero indicates the 25th percentile, the line within the box marks the median, the dashed line within the box marks the mean, and the boundary of the box furthest from zero indicates the 75th percentile. Error bars above and below the box indicate the 90th and 10th percentiles, respectively. The black circles indicate outlying points.

Fig 3

Z scores. Box plots show the Z-score distribution for the four newly discovered (Ac53, Ac78, Ac101 [P40], and Ac103 [P48]), the two undetected (Ac93 [P18] and Ac100 [P6.9]), and the other three previously recognized (Ac65 [DNApol], Ac66 [Desmoplakin], and Ac95 [helicase]) core proteins. Z scores for all proteins were calculated, and only those for gammabaculoviruses and deltabaculoviruses are shown. The dashed line is only a reference to show that for Ac53, Ac78, Ac93, Ac65, and Ac66, several outliers have values below zero.

Fig 4

Protein motifs. The schematic map of Ac53 (A), Ac78 (B), Ac101 (C), and Ac103 (D) shows conserved motifs found by the MEME tool for the 58 orthologs of each newly discovered core protein. Only the prototypes representing alphabaculoviruses of group I (AcMNPV), alphabaculoviruses of group II (LdMNPV), betabaculoviruses (CpGV), gammabaculoviruses (NeabNPV), and deltabaculoviruses (CuniNPV) are shown. The relative positions of motif 1, motif 2, and motif 3 are indicated by black, dark gray, and light gray rectangles, respectively. The length and conservation for each motif are represented by sequence logos. In Ac53, a metal binding motif is indicated. An amino acid scale indicating the location of each motif is depicted above the groups of orthologs.

Fig 5

Protein relationship analyses. (A to E) Protein relationships among all baculoviruses derived from BLASTP analysis. The E value between pairs of species is indicated above each arrow. Gray-shaded areas correspond to the different subdivisions of the Baculoviridae: α-GI, alphabaculoviruses of group I; α-GII, alphabaculoviruses of group II; β, betabaculoviruses; γ, gammabaculoviruses; δ, deltabaculoviruses. (A) Ac53. (B) Ac78. (C) Ac93. (D) Ac101. (E) Ac103. (F) Minimum (1) and maximum (2) identity values between each deltabaculovirus core protein and the corresponding sequences of other baculovirus genera. The orthologous names are mentioned with the family prototype nomenclature. The 4 newly discovered core proteins, the 2 core proteins described previously by Yuan et al. (57), and the 31 standard core proteins are indicated with black characters, boxed black characters, and dark gray characters, respectively. The insets show the core proteins (AcMNPV nomenclature) (first column) in deltabaculoviruses (second column) and the corresponding species where orthologous sequences with minimum (1) or maximum (2) identity were found (third column). In all instances, six-character codes were used (see Table S1 in the supplemental material).