PLoS ONE (Jan 2012)

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

  • Maria E Gallegos,
  • Sanjeev Balakrishnan,
  • Priya Chandramouli,
  • Shaily Arora,
  • Aruna Azameera,
  • Anitha Babushekar,
  • Emilee Bargoma,
  • Abdulmalik Bokhari,
  • Siva Kumari Chava,
  • Pranti Das,
  • Meetali Desai,
  • Darlene Decena,
  • Sonia Dev Devadas Saramma,
  • Bodhidipra Dey,
  • Anna-Louise Doss,
  • Nilang Gor,
  • Lakshmi Gudiputi,
  • Chunyuan Guo,
  • Sonali Hande,
  • Megan Jensen,
  • Samantha Jones,
  • Norman Jones,
  • Danielle Jorgens,
  • Padma Karamchedu,
  • Kambiz Kamrani,
  • Lakshmi Divya Kolora,
  • Line Kristensen,
  • Kelly Kwan,
  • Henry Lau,
  • Pranesh Maharaj,
  • Navneet Mander,
  • Kalyani Mangipudi,
  • Himabindu Menakuru,
  • Vaishali Mody,
  • Sandeepa Mohanty,
  • Sridevi Mukkamala,
  • Sheena A Mundra,
  • Sudharani Nagaraju,
  • Rajhalutshimi Narayanaswamy,
  • Catherine Ndungu-Case,
  • Mersedeh Noorbakhsh,
  • Jigna Patel,
  • Puja Patel,
  • Swetha Vandana Pendem,
  • Anusha Ponakala,
  • Madhusikta Rath,
  • Michael C Robles,
  • Deepti Rokkam,
  • Caroline Roth,
  • Preeti Sasidharan,
  • Sapana Shah,
  • Shweta Tandon,
  • Jagdip Suprai,
  • Tina Quynh Nhu Truong,
  • Rubatharshini Uthayaruban,
  • Ajitha Varma,
  • Urvi Ved,
  • Zeran Wang,
  • Zhe Yu

DOI
https://doi.org/10.1371/journal.pone.0049387
Journal volume & issue
Vol. 7, no. 11
p. e49387

Abstract

Read online

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).