Development Genes and Evolution

, Volume 220, Issue 1, pp 41–52

Bioinformatic analysis of P granule-related proteins: insights into germ granule evolution in nematodes

  • Luis A. Bezares-Calderón
  • Arturo Becerra
  • Laura S. Salinas
  • Ernesto Maldonado
  • Rosa E. Navarro
Original Article

DOI: 10.1007/s00427-010-0327-3

Cite this article as:
Bezares-Calderón, L.A., Becerra, A., Salinas, L.S. et al. Dev Genes Evol (2010) 220: 41. doi:10.1007/s00427-010-0327-3

Abstract

Germ cells in many animals possess a specialized cytoplasm in the form of granules that contain RNA and protein complexes essential for the function and preservation of the germline. The mechanism for the formation of these granules is still poorly understood; however, the lack of conservation in their components across different species suggests evolutionary convergence in the assembly process. Germ granules are assumed to be present in all nematodes with a preformed germline. However, few studies have clearly identified these structures in species other than Caenorhabditis elegans and even less have carried functional analysis to provide a broader panorama of the granules composition in the phylum. We adopted a bioinformatics approach to investigate the extension of conservation in nematodes of some known C. elegans germ granule components, as a proxy to understand germ granules evolution in this phylum. Unexpectedly, we found that, in nematodes, the DEAD box RNA helicase Vasa, a conserved protein among different phyla, shows a complex history of clade-specific duplications and sequence divergence. Our analyses suggest that, in nematodes, Vasa’s function might be shared among proteins like LAF-1, VBH-1, and GLH-1/-2/-3 and GLH-4. Key components of P granules assembly in C. elegans, like the PGL protein family, are only preserved in Caenorhabditis species. Our analysis suggests that germ granules assembly may not be conserved in nematodes. Studies on these species could bring insight into the basic components required for this pathway.

Keywords

Nematodes’ evolution Germ granules RNA helicases C. elegans 

Supplementary material

427_2010_327_MOESM1_ESM.pdf (18.4 mb)
Table S1WormBase protein sequence names of GenBank Gis used in phylogenetic analyses (PDF 18829 kb)
427_2010_327_MOESM2_ESM.pdf (5.5 mb)
Table S2WormBase and predicted protein homologs discarded from phylogenetic analyses (PDF 5600 kb)
427_2010_327_MOESM3_ESM.pdf (8.3 mb)
Table S3Protein predictions using AUGUSTUS or GENEMARK.HMM (PDF 8511 kb)

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Luis A. Bezares-Calderón
    • 1
  • Arturo Becerra
    • 2
  • Laura S. Salinas
    • 1
  • Ernesto Maldonado
    • 1
  • Rosa E. Navarro
    • 1
  1. 1.Departamento de Biología Celular y Desarrollo, Instituto de Fisiología CelularUniversidad Nacional Autónoma de MéxicoMéxicoMéxico
  2. 2.Facultad de CienciasUniversidad Nacional Autónoma de MéxicoMéxicoMéxico