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.2017 Mar 21;114(12):E2401-E2410.
doi: 10.1073/pnas.1621061114. Epub 2017 Mar 6.

Multiple origins of viral capsid proteins from cellular ancestors

Affiliations

Multiple origins of viral capsid proteins from cellular ancestors

Mart Krupovic et al. Proc Natl Acad Sci U S A..

Abstract

Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions, and in some of these cases likely ancestors are identifiable among the proteins of cellular organisms. Virus genomes typically consist of distinct structural and replication modules that recombine frequently and can have different evolutionary trajectories. The present analysis suggests that, although the replication modules of at least some classes of viruses might descend from primordial selfish genetic elements, bona fide viruses evolved on multiple, independent occasions throughout the course of evolution by the recruitment of diverse host proteins that became major virion components.

Keywords: capsid proteins; nucleocapsids; origin of viruses; primordial replicons; virus evolution.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Structural diversity of viral CP and NC proteins. The pie chart shows the distribution of architectural classes among 135 virus taxa (117 families and 18 unassigned genera; Table S1). Arena, arenavirus; ATV, Acidianus two-tailed virus; Baculo-like, baculovirus-like viruses; Chy-PRO, chymotrypsin-like protease; Corona, coronavirus; CP, capsid protein; DJR, double jellyroll; Flavi, flavivirus; HBV, hepatitis B virus; NC, nucleocapsid protein; Orthomyxo, orthomyxovirus; Phlebo, phlebovirus; Reo, reovirus; Retro, retrovirus; SIRV2,Sulfolobus islandicus rod-shaped virus 2; SJR, single jellyroll; Toga, togavirus; TMV, tobacco mosaic virus; TM, transmembrane domain.
Fig. 2.
Fig. 2.
Viral and cellular SJR proteins. (A) A selection of viral SJR CP structures. The rightmost structure corresponds to the virion of STNV. (B) A selection of cellular SJR protein structures. The rightmost structure corresponds to the 60-subunit virion-like assembly of the human sTALL-1 protein. All structures are colored using the rainbow scheme from blue (N terminus) to red (C terminus). The linker region leading to the DNA-binding domain in AraC is shown in gray. (C) Relationships between cellular and viral SJR proteins. The matrix and cluster dendrograms are based on the pairwise Z score comparisons calculated using DALI. For the complete matrix, see Dataset S1. The color scale indicates the corresponding Z scores. RNA viruses are shown in green, ssDNA viruses in blue, and dsDNA viruses in red. All compared structures are indicated with the corresponding PDB identifiers. CBM, carbohydrate-binding module; NP, nucleoplasmin/nucleophosmin; PCV2, porcine circovirus 2; PRO-P, P domain of subtilisin-like proteases; SPMV, satellite panicum mosaic virus; STMV, satellite tobacco mosaic virus; TSV, tobacco streak virus.
Fig. S1.
Fig. S1.
Comparisons of cellular and viral proteins with the HK97-like fold. (A) Matrix based on the pairwise comparison of Z scores calculated using DALI. The color scale indicates the corresponding Z scores. (B) A collection of structures of encapsulins (E,Upper Row) and major capsid proteins of members of the order Caudovirales (C,Lower Rows). All structures are colored using the rainbow scheme from blue (N terminus) to red (C terminus), and the corresponding PDB identifiers are shown.
Fig. S2.
Fig. S2.
Comparison of the alphaviral capsid protein (Left) with the nonstructural protease NS3 of hepatitis C virus (HCV) (Center) and human chymotrypsin-like protease HtrA1 (Right). All structures are colored using the rainbow scheme from blue (N terminus) to red (C terminus), and the corresponding PDB identifiers are shown.
Fig. S3.
Fig. S3.
Comparison of the NC proteins from Crimean-Congo hemorrhagic fever virus (CCHFV) and Lassa mammarenavirus (LASV) and cellular exonucleases of the DEDDh superfamily. DNAP III exo is the proofreading exonuclease subunit ofE.coli DNA polymerase III. The PDB identifiers of all structures are shown. The exonuclease domains are colored using the rainbow scheme from blue (N terminus) to red (C terminus).
Fig. 3.
Fig. 3.
Cellular homologs of the retroviral proteins constituting the Gag polyprotein. (A) Proteolytic processing of the retroviral Gag polyprotein into MA, CA, and NC proteins. (B) Structural comparison of the matrix protein (Upper) of mouse mammary tumor virus (MMTV) with the N-terminal DNA-binding domain (Lower) of the tyrosine recombinase ofV.cholerae. (C) Structural comparison of a dimer of the CA C-terminal domain (CA-CTD) (Upper) of HIV-1 with the dimer of the human SCAN domain protein (Lower). (D) Structural comparison of the NC protein (Upper) of HIV-1 with the human pluripotency factor Lin28 (Lower). All structures are colored using the rainbow scheme from blue (N terminus) to red (C terminus), and the corresponding PDB identifiers are shown.
Fig. S4.
Fig. S4.
Comparison of the matrix protein Z of Lassa mammarenavirus (LASV) and the RING domain of ubiquitin (Ub) ligase E3. Both structures are colored using the rainbow scheme from blue (N terminus) to red (C terminus), and the corresponding PDB identifiers are shown.
Fig. 4.
Fig. 4.
Structural comparison of the Ebola virus MA protein with CypC. Topology diagrams (Left) and structural models (Right) are colored using the rainbow scheme from blue (N terminus) to red (C terminus), and the corresponding PDB identifiers are shown. The β-hairpin insert in CypC is colored black.
Fig. 5.
Fig. 5.
A scenario for the origin of viruses from selfish replicators upon acquisition of capsid protein genes from cellular life forms at different stages of evolution.
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