title: The C. elegans rab family: identification, classification and toolkit construction.
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).
authors.affiliation: Department of Biological Sciences, California State University East Bay, Hayward, CA, USA. maria.gallegos@csueastbay.edu
authors.forename: Maria E
authors.initials: ME
authors.lastname: Gallegos
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Balakrishnan
authors.forename: Priya
authors.initials: P
authors.lastname: Chandramouli
authors.forename: Shaily
authors.initials: S
authors.lastname: Arora
authors.forename: Aruna
authors.initials: A
authors.lastname: Azameera
authors.forename: Anitha
authors.initials: A
authors.lastname: Babushekar
authors.forename: Emilee
authors.initials: E
authors.lastname: Bargoma
authors.forename: Abdulmalik
authors.initials: A
authors.lastname: Bokhari
authors.forename: Siva Kumari
authors.initials: SK
authors.lastname: Chava
authors.forename: Pranti
authors.initials: P
authors.lastname: Das
authors.forename: Meetali
authors.initials: M
authors.lastname: Desai
authors.forename: Darlene
authors.initials: D
authors.lastname: Decena
authors.forename: Sonia Dev Devadas
authors.initials: SD
authors.lastname: Saramma
authors.forename: Bodhidipra
authors.initials: B
authors.lastname: Dey
authors.forename: Anna-Louise
authors.initials: AL
authors.lastname: Doss
authors.forename: Nilang
authors.initials: N
authors.lastname: Gor
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Gudiputi
authors.forename: Chunyuan
authors.initials: C
authors.lastname: Guo
authors.forename: Sonali
authors.initials: S
authors.lastname: Hande
authors.forename: Megan
authors.initials: M
authors.lastname: Jensen
authors.forename: Samantha
authors.initials: S
authors.lastname: Jones
authors.forename: Norman
authors.initials: N
authors.lastname: Jones
authors.forename: Danielle
authors.initials: D
authors.lastname: Jorgens
authors.forename: Padma
authors.initials: P
authors.lastname: Karamchedu
authors.forename: Kambiz
authors.initials: K
authors.lastname: Kamrani
authors.forename: Lakshmi Divya
authors.initials: LD
authors.lastname: Kolora
authors.forename: Line
authors.initials: L
authors.lastname: Kristensen
authors.forename: Kelly
authors.initials: K
authors.lastname: Kwan
authors.forename: Henry
authors.initials: H
authors.lastname: Lau
authors.forename: Pranesh
authors.initials: P
authors.lastname: Maharaj
authors.forename: Navneet
authors.initials: N
authors.lastname: Mander
authors.forename: Kalyani
authors.initials: K
authors.lastname: Mangipudi
authors.forename: Himabindu
authors.initials: H
authors.lastname: Menakuru
authors.forename: Vaishali
authors.initials: V
authors.lastname: Mody
authors.forename: Sandeepa
authors.initials: S
authors.lastname: Mohanty
authors.forename: Sridevi
authors.initials: S
authors.lastname: Mukkamala
authors.forename: Sheena A
authors.initials: SA
authors.lastname: Mundra
authors.forename: Sudharani
authors.initials: S
authors.lastname: Nagaraju
authors.forename: Rajhalutshimi
authors.initials: R
authors.lastname: Narayanaswamy
authors.forename: Catherine
authors.initials: C
authors.lastname: Ndungu-Case
authors.forename: Mersedeh
authors.initials: M
authors.lastname: Noorbakhsh
authors.forename: Jigna
authors.initials: J
authors.lastname: Patel
authors.forename: Puja
authors.initials: P
authors.lastname: Patel
authors.forename: Swetha Vandana
authors.initials: SV
authors.lastname: Pendem
authors.forename: Anusha
authors.initials: A
authors.lastname: Ponakala
authors.forename: Madhusikta
authors.initials: M
authors.lastname: Rath
authors.forename: Michael C
authors.initials: MC
authors.lastname: Robles
authors.forename: Deepti
authors.initials: D
authors.lastname: Rokkam
authors.forename: Caroline
authors.initials: C
authors.lastname: Roth
authors.forename: Preeti
authors.initials: P
authors.lastname: Sasidharan
authors.forename: Sapana
authors.initials: S
authors.lastname: Shah
authors.forename: Shweta
authors.initials: S
authors.lastname: Tandon
authors.forename: Jagdip
authors.initials: J
authors.lastname: Suprai
authors.forename: Tina Quynh Nhu
authors.initials: TQ
authors.lastname: Truong
authors.forename: Rubatharshini
authors.initials: R
authors.lastname: Uthayaruban
authors.forename: Ajitha
authors.initials: A
authors.lastname: Varma
authors.forename: Urvi
authors.initials: U
authors.lastname: Ved
authors.forename: Zeran
authors.initials: Z
authors.lastname: Wang
authors.forename: Zhe
authors.initials: Z
authors.lastname: Yu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000201:enzymology*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D002999:Clone Cells; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012326:RNA Splicing / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020691:rab GTP-Binding Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*
chemical_list: D029742:Caenorhabditis elegans Proteins; D020691:rab GTP-Binding Proteins