Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes

Virus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit the evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encod...

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Published in:The Journal of biological chemistry Vol. 300; no. 5; p. 107218
Main Authors: Legarda, Esmeralda G., Elena, Santiago F., Mushegian, Arcady R.
Format: Journal Article
Language:English
Published: United States Elsevier Inc 01.05.2024
American Society for Biochemistry and Molecular Biology
Subjects:
Amino Acid Sequence
convergent evolution of protein structure
Evolution, Molecular
genome evolution
Models, Psychological
movement proteins
Open Reading Frames
overlapping reading frames
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
Sequence Homology, Amino Acid
tombusvirus
Tombusvirus - genetics
Tombusvirus - metabolism
Viral Proteins - chemistry
Viral Proteins - genetics
Viral Proteins - metabolism
virus genomes
overlapping reading frames
virus genomes
ORF
MP
convergent evolution of protein structure
pLDDT
movement proteins
genome evolution
aBSREL
tombusvirus
CP
ISSN:0021-9258, 1083-351X, 1083-351X
Online Access:Get full text
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Summary:Virus genomes may encode overlapping or nested open reading frames that increase their coding capacity. It is not known whether the constraints on spatial structures of the two encoded proteins limit the evolvability of nested genes. We examine the evolution of a pair of proteins, p22 and p19, encoded by nested genes in plant viruses from the genus Tombusvirus. The known structure of p19, a suppressor of RNA silencing, belongs to the RAGNYA fold from the alpha+beta class. The structure of p22, the cell-to-cell movement protein from the 30K family widespread in plant viruses, is predicted with the AlphaFold approach, suggesting a single jelly-roll fold core from the all-beta class, structurally similar to capsid proteins from plant and animal viruses. The nucleotide and codon preferences impose modest constraints on the types of secondary structures encoded in the alternative reading frames, nonetheless allowing for compact, well-ordered folds from different structural classes in two similarly-sized nested proteins. Tombusvirus p22 emerged through radiation of the widespread 30K family, which evolved by duplication of a virus capsid protein early in the evolution of plant viruses, whereas lineage-specific p19 may have emerged by a stepwise increase in the length of the overprinted gene and incremental acquisition of functionally active secondary structure elements by the protein product. This evolution of p19 toward the RAGNYA fold represents one of the first documented examples of protein structure convergence in naturally occurring proteins.
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ISSN:0021-9258
1083-351X
1083-351X
DOI:10.1016/j.jbc.2024.107218