The C. elegans rab family: identification, classification and toolkit construction

PLoS One. 2012;7(11):e49387. doi: 10.1371/journal.pone.0049387. Epub 2012 Nov 21.

Abstract

Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Caenorhabditis elegans / enzymology*
  • Caenorhabditis elegans Proteins / chemistry
  • Caenorhabditis elegans Proteins / classification*
  • Caenorhabditis elegans Proteins / metabolism*
  • Clone Cells
  • Computational Biology / methods*
  • Conserved Sequence / genetics
  • Humans
  • Introns / genetics
  • Molecular Sequence Data
  • Multigene Family*
  • Open Reading Frames / genetics
  • Phylogeny
  • RNA Splicing / genetics
  • Reproducibility of Results
  • Sequence Alignment
  • rab GTP-Binding Proteins / chemistry
  • rab GTP-Binding Proteins / classification*
  • rab GTP-Binding Proteins / metabolism*

Substances

  • Caenorhabditis elegans Proteins
  • rab GTP-Binding Proteins

Associated data

  • GENBANK/JQ235180
  • GENBANK/JQ235181
  • GENBANK/JQ235182
  • GENBANK/JQ235183
  • GENBANK/JQ235184
  • GENBANK/JQ235185
  • GENBANK/JQ235186
  • GENBANK/JQ235187
  • GENBANK/JQ235188
  • GENBANK/JQ235189
  • GENBANK/JQ235190
  • GENBANK/JQ235191
  • GENBANK/JQ235192
  • GENBANK/JQ235193
  • GENBANK/JQ235194
  • GENBANK/JQ235195
  • GENBANK/JQ235196
  • GENBANK/JQ235197
  • GENBANK/JQ235198
  • GENBANK/JQ235199
  • GENBANK/JQ235200
  • GENBANK/JQ235201

Grants and funding

This work was funded by the Department of Biological Sciences at California State University, East Bay. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding was received for this study.