Computational design of genes encoding completely overlapping protein domains: Influence of genetic code and taxonomic rank

Abstract

Overlapping genes (OLGs) with long protein-coding overlapping sequences are often excluded by genome annotation programs, with the exception of virus genomes. A recent study used a novel algorithm to construct OLGs from arbitrary protein domain pairs and concluded that virus genes are best suited for creating OLGs, a result which fitted with common assumptions. However, improving sequence evaluation using Hidden Markov Models shows that the previous result is an artifact originating from dataset-database biases. When parameters for OLG design and evaluation are optimized we find that 94.5% of the constructed OLG pairs score at least as highly as naturally occurring sequences, while 9.6% of the artificial OLGs cannot be distinguished from typical sequences in their protein family. Constructed OLG sequences are also indistinguishable from natural sequences in terms of amino acid identity and secondary structure, while the minimum nucleotide change required for overprinting an overlapping sequence can be as low as 1.8% of the sequence. Separate analysis of datasets containing only sequences from either archaea, bacteria, eukaryotes or viruses showed that, surprisingly, virus genes are much less suitable for designing OLGs than bacterial or eukaryotic genes. An important factor influencing OLG design is the structure of the standard genetic code. Success rates in different reading frames strongly correlate with their code-determined respective amino acid constraints. There is a tendency indicating that the structure of the standard genetic code could be optimized in its ability to create OLGs while conserving mutational robustness. The findings reported here add to the growing evidence that OLGs should no longer be excluded in prokaryotic genome annotations. Determining the factors facilitating the computational design of artificial overlapping genes may improve our understanding of the origin of these remarkable genetic constructs and may also open up exciting possibilities for synthetic biology.

Overlapping genes in natural and engineered genomes

“…With increasing recognition that gene overlaps are functionally important and play vital roles within natural organisms, the construction of new overlapping genes has begun to be exploited in bioengineering. Theoretical work has previously shown that the genetic code is flexible enough to accommodate artificial overlap of protein domains 147 , 148 , and even artificial proteins 149 , often with the stated aim to protect the overlapping CDS from genetic drift 150 in similar ways to that found in viruses 71 , 75 , 151 .…”

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

“…Amino acid coding with respect to complementary protein constructs, mutation, and frameshifts have been studied by many authors, including Arques and Michel [41,42], Bartonek et al [43], McGuire and Holmes [21], Štambuk [44,45], Wichmann et al [46,47], and Youvan et al [48][49][50].…”