Lineage-specific expansions provide genomic complexity among sea urchin GTPases
Open accessAbstract
In every organism, GTP-binding proteins control many aspects of cell signaling. Here, we examine in silico several GTPase families from the Strongylocentrotus purpuratus genome: the monomeric Ras superfamily, the heterotrimeric G proteins, the dynamin superfamily, the SRP/SR family, and the "protein biosynthesis" translational GTPases. Identified were 174 GTPases, of which over 90% are expressed in the embryo as shown by tiling array and expressed sequence tag data. Phylogenomic comparisons restricted to Drosophila, Ciona, and humans (protostomes, urochordates, and vertebrates, respectively) revealed both common and unique elements in the expected composition of these families. Galpha and dynamin families contain vertebrate expansions, consistent with whole genome duplications, whereas SRP/SR and translational GTPases are highly conserved. Unexpectedly, Ras superfamily analyses revealed several large (5+) lineage-specific expansions in the sea urchin. For Rho, Rab, Arf, and Ras subfamilies, comparing total human gene numbers to the number of sea urchin genes with vertebrate orthologs suggests reduced genomic complexity in the sea urchin. However, gene duplications in the sea urchin increase overall numbers such that total sea urchin gene numbers approximate vertebrate gene numbers for each monomeric GTPase family. These findings suggest that lineage-specific expansions may be an important component of genomic evolution in signal transduction.
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The human and sea urchin genomes have comparable numbers of monomeric GTPases.
“The sea urchin genome did not undergo a whole-genome duplication, yet phylogenies for four Ras GTPase families (Ras, Rho, Rab, and Arf) revealed that local gene duplications occurred (Fig. 4), which ultimately resulted in a comparable number of monomeric GTPases in the human and sea urchin genomes (28).”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [28]
Phylogenies for four Ras GTPase families show that local gene duplications occurred.
“The sea urchin genome did not undergo a whole-genome duplication, yet phylogenies for four Ras GTPase families (Ras, Rho, Rab, and Arf) revealed that local gene duplications occurred (Fig. 4), which ultimately resulted in a comparable number of monomeric GTPases in the human and sea urchin genomes (28).”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [28]
The sea urchin genome did not undergo a whole-genome duplication.
“The sea urchin genome did not undergo a whole-genome duplication, yet phylogenies for four Ras GTPase families (Ras, Rho, Rab, and Arf) revealed that local gene duplications occurred (Fig. 4), which ultimately resulted in a comparable number of monomeric GTPases in the human and sea urchin genomes (28).”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [28]
Gene-specific duplications increased sea urchin GTPase numbers, resulting in complexity comparable to vertebrates.
“The pink boxes highlight gene-specific duplications that increased sea urchin GTPase numbers, resulting in a complexity comparable to vertebrates.”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [28]
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The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i>
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science · doi:10.1126/science.1133609 · Cited by 1,132 · see citing works
Self-citation
- Authors
- Beane, W. S., Voronina, E., Wessel, G. M., & McClay, D. R.
- Affiliations
- Duke University (US)
- Brown University (US)
- Corresponding author
- Beane, Wendy S.
- Venue
- Developmental Biology
- Publisher
- Elsevier BV
- Published
- 2006-12
- Volume
- 300
- Issue
- 1
- Pages
- 165-179
- ISSN
- 0012-1606 (ISSN-L)
- OpenAlex
- W2046031992
- Cited by
- 10
- References
- 3
- Citations by year
- 2019: 1 · 2014: 1
- FWCI
- 0.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Developmental Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Evolutionary Synthesis Center
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM061464, GM61464)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD14483, R01HD014483)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Kinase Regulation and GTPase Signaling
- Keywords
- GTPase, Strongylocentrotus purpuratus, sea urchins, Ras superfamily, heterotrimeric G proteins, dynamin superfamily, translational GTPases, lineage-specific gene expansion, gene duplication, whole-genome duplication, phylogenomics, genome evolution, signal transduction, embryonic gene expression
- MeSH terms
- Animals, Multigene Family, Humans, Isoenzymes, Phylogeny, Sea Urchins, Protein Biosynthesis, Genome, GTP Phosphohydrolases
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