Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly

Abstract

The sea urchin embryo is a classical model system for studying the role of the cytoskeleton in such events as fertilization, mitosis, cleavage, cell migration and gastrulation. We have conducted an analysis of gene models derived from the Strongylocentrotus purpuratus genome assembly and have gathered strong evidence for the existence of multiple gene families encoding cytoskeletal proteins and their regulators in sea urchin. While many cytoskeletal genes have been cloned from sea urchin with sequences already existing in public databases, genome analysis reveals a significantly higher degree of diversity within certain gene families. Furthermore, genes are described corresponding to homologs of cytoskeletal proteins not previously documented in sea urchins. To illustrate the varying degree of sequence diversity that exists within cytoskeletal gene families, we conducted an analysis of genes encoding actins, specific actin-binding proteins, myosins, tubulins, kinesins, dyneins, specific microtubule-associated proteins, and intermediate filaments. We conducted ontological analysis of select genes to better understand the relatedness of urchin cytoskeletal genes to those of other deuterostomes. We analyzed developmental expression (EST) data to confirm the existence of select gene models and to understand their differential expression during various stages of early development.

Identification of dyneins that localize exclusively to the proximal portion of Chlamydomonas flagella

“…sequences not yet determined, the predicted sequences from the Chlamydomonas genome database were used (see Materials and Methods). The single-headed DHC type can be classified into three subgroups, IAD3, IAD4, and IAD5 types, as reported previously (Morris et al, 2006;Wickstead and Gull, 2007). Minor DHCs identified in this study are indicated by arrowheads.…”

“…7, Table 1). As shown in recent studies (Morris et al, 2006;Wickstead and Gull, 2007;Wilkes et al, 2008), single-headed DHCs as a whole makes up a single large family which can be further classified into three groups: group IAD3 comprising DHC4, DHC5 (the DHC of dynein b), DHC6 (dynein a), DHC8 (dynein e), DHC9 (dynein c) and DHC11; group IAD4 comprising DHC2 (dynein d); and group IAD5 comprising DHC3 and DHC7 (dynein g; Fig. 7).…”

“…However, the roles and distributions specific to these DHCs might not be directly correlated with those of DHC species in other eukaryotes; although the three main groups of single-headed IADs are present in all groups of eukaryotes, the diversification of multiple IADs within each group, including minor dyneins, took place late in eukaryotic evolution (Morris et al, 2006). Further functional and distribution studies will be needed in each eukaryote for a comprehensive understanding of dynein function.…”

Temperature and CO2additively regulate physiology, morphology and genomic responses of larval sea urchins,Strongylocentrotus purpuratus

“…In urchin larvae, the cytoskeleton regulates basic aspects of development, such as cell migration, mitosis and cytokinesis, organelle movements, ciliary and flagellar movements and cell shape changes [70], and the protection of cytoskeletal function is likely to be important for the completion of development. Transcriptomic and proteomic analysis of mussels (Mytilus spp.)…”

High Throughput Microinjections of Sea Urchin Zygotes

“…They produce a large number of synchronously developing transparent embryos that can be easily manipulated. Using sea urchin as a model organism, the sea urchin community has contributed to our understanding of the fertilization process [18][19][20][21] , cell biological processes [22][23][24] , and the gene regulatory networks (GRNs) [25][26][27][28] .…”