Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

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Recurrent Sequence Evolution After Independent Gene Duplication

10.21203/rs.2.22450/v2 ◽

2020 ◽

Author(s):

Samuel Hermann Alexander Von Der Dunk ◽

Berend Snel

Keyword(s):

Gene Duplication ◽

Experimental Testing ◽

Parallel Evolution ◽

Gene Families ◽

Functional Differentiation ◽

Functional Change ◽

Neutral Evolution ◽

Sequence Evolution ◽

Recurrent Sequence ◽

Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

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Genetically encodable bioluminescent system from fungi

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803615115 ◽

2018 ◽

Vol 115 (50) ◽

pp. 12728-12732 ◽

Cited By ~ 40

Author(s):

Alexey A. Kotlobay ◽

Karen S. Sarkisyan ◽

Yuliana A. Mokrushina ◽

Marina Marcet-Houben ◽

Ekaterina O. Serebrovskaya ◽

...

Keyword(s):

Pichia Pastoris ◽

Gene Duplication ◽

Caffeic Acid ◽

Biosynthetic Pathway ◽

Sequence Divergence ◽

Biosynthesis Pathway ◽

Gene Duplications ◽

Biochemical Pathway ◽

Acid Biosynthesis ◽

Independent Gene

Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeastPichia pastorisalong with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.

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Recurrent Sequence Evolution After Independent Gene Duplication

10.21203/rs.2.22450/v3 ◽

2020 ◽

Author(s):

Samuel Hermann Alexander Von Der Dunk ◽

Berend Snel

Keyword(s):

Gene Duplication ◽

Experimental Testing ◽

Parallel Evolution ◽

Gene Families ◽

Functional Differentiation ◽

Functional Change ◽

Neutral Evolution ◽

Sequence Evolution ◽

Recurrent Sequence ◽

Independent Gene

Abstract Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Accordingly, genome-wide assessment has shown that recurrent sequence evolution in orthologs is chiefly explained by nearly neutral evolution. For paralogs, more frequent functional change is expected because additional copies are generally not retained if they do not acquire their own niche. Yet, it is unknown to what extent recurrent sequence differentiation is discernible after independent gene duplications in different eukaryotic taxa. Results We develop a framework that detects patterns of recurrent sequence evolution in duplicated genes. This is used to analyze the genomes of 90 diverse eukaryotes. We find a remarkable number of families with a potentially predictable functional differentiation following gene duplication. In some protein families, more than ten independent duplications show a similar sequence-level differentiation between paralogs. Based on further analysis, the sequence divergence is found to be generally asymmetric. Moreover, about 6\% of the recurrent sequence evolution between paralog pairs can be attributed to recurrent differentiation of subcellular localization. Finally, we reveal the specific recurrent patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. Conclusions The presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. We also uncover a diverse set of families with recurrent sequence evolution and reveal trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

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Evolutionary Relationship of a Fish C Type Lactate Dehydrogenase to Other Vertebrate Lactate Dehydrogenase Isozymes

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f86-130 ◽

1986 ◽

Vol 43 (5) ◽

pp. 1045-1051 ◽

Cited By ~ 26

Author(s):

Peter H. Rehse ◽

William S. Davidson

Keyword(s):

Lactate Dehydrogenase ◽

Gene Duplication ◽

Atlantic Cod ◽

Evolutionary Relationship ◽

Gene Duplications ◽

Homologous Proteins ◽

Lactate Dehydrogenase Isozymes ◽

Independent Gene ◽

Significant Difference ◽

Lactate Dehydrogenases

It is assumed that the genes for the three types of vertebrate lactate dehydrogenase isozymes (A, B, and C) arose from an ancestral lactate dehydrogenase gene by a mechanism involving gene duplications. The currently accepted model was originally proposed by Holmes in 1972 (FEBS Lett. 28: 51–55). The main points in this proposal are as follows: (1) the ancestral lactate dehydrogenase was an A type; (2) the gene for this A type lactate dehydrogenase duplicated to produce the A and B forms; and (3) the C isozymes of fish and warm-blooded vertebrates are derived from B types by successive, independent gene duplication events. More structural data have become available since this model was first put forward, and Li et al. (1983. J. Biol. Chem. 258: 7029–7032) have shown that rodent C type lactate dehydrogenases appear to be ancestral to the A and B forms. We have extended Li's reevaluation of the evolutionary relationships among vertebrate lactate dehydrogenase isozymes. Our analysis indicates that there is no significant difference in the rates of evolution along the A, B, or C lineages. This confirms that a C type rather than an A type lactate dehydrogenase was the ancestral form. A duplication of the gene for this C type gave rise to the gene which, by a further gene duplication, yielded the A and B type lactate dehydrogenase genes. In addition, amino acid compositional data reveal that the C type lactate dehydrogenase from Atlantic cod (Gadus morhua) and the C type lactate dehydrogenase isozymes of rodents are homologous proteins that are the result of divergent evolution via speciation events rather than by independent gene duplications. This novel interpretation of lactate dehydrogenase isozyme evolution is discussed with respect to the tissue specificities of C type lactate dehydrogenases in vertebrates.

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