PMID- 23185324 OWN - NLM STAT- MEDLINE DCOM- 20130514 LR - 20240313 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - The C. elegans rab family: identification, classification and toolkit construction. PG - e49387 LID - 10.1371/journal.pone.0049387 [doi] LID - e49387 AB - 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). FAU - Gallegos, Maria E AU - Gallegos ME AD - Department of Biological Sciences, California State University East Bay, Hayward, CA, USA. maria.gallegos@csueastbay.edu FAU - Balakrishnan, Sanjeev AU - Balakrishnan S FAU - Chandramouli, Priya AU - Chandramouli P FAU - Arora, Shaily AU - Arora S FAU - Azameera, Aruna AU - Azameera A FAU - Babushekar, Anitha AU - Babushekar A FAU - Bargoma, Emilee AU - Bargoma E FAU - Bokhari, Abdulmalik AU - Bokhari A FAU - Chava, Siva Kumari AU - Chava SK FAU - Das, Pranti AU - Das P FAU - Desai, Meetali AU - Desai M FAU - Decena, Darlene AU - Decena D FAU - Saramma, Sonia Dev Devadas AU - Saramma SD FAU - Dey, Bodhidipra AU - Dey B FAU - Doss, Anna-Louise AU - Doss AL FAU - Gor, Nilang AU - Gor N FAU - Gudiputi, Lakshmi AU - Gudiputi L FAU - Guo, Chunyuan AU - Guo C FAU - Hande, Sonali AU - Hande S FAU - Jensen, Megan AU - Jensen M FAU - Jones, Samantha AU - Jones S FAU - Jones, Norman AU - Jones N FAU - Jorgens, Danielle AU - Jorgens D FAU - Karamchedu, Padma AU - Karamchedu P FAU - Kamrani, Kambiz AU - Kamrani K FAU - Kolora, Lakshmi Divya AU - Kolora LD FAU - Kristensen, Line AU - Kristensen L FAU - Kwan, Kelly AU - Kwan K FAU - Lau, Henry AU - Lau H FAU - Maharaj, Pranesh AU - Maharaj P FAU - Mander, Navneet AU - Mander N FAU - Mangipudi, Kalyani AU - Mangipudi K FAU - Menakuru, Himabindu AU - Menakuru H FAU - Mody, Vaishali AU - Mody V FAU - Mohanty, Sandeepa AU - Mohanty S FAU - Mukkamala, Sridevi AU - Mukkamala S FAU - Mundra, Sheena A AU - Mundra SA FAU - Nagaraju, Sudharani AU - Nagaraju S FAU - Narayanaswamy, Rajhalutshimi AU - Narayanaswamy R FAU - Ndungu-Case, Catherine AU - Ndungu-Case C FAU - Noorbakhsh, Mersedeh AU - Noorbakhsh M FAU - Patel, Jigna AU - Patel J FAU - Patel, Puja AU - Patel P FAU - Pendem, Swetha Vandana AU - Pendem SV FAU - Ponakala, Anusha AU - Ponakala A FAU - Rath, Madhusikta AU - Rath M FAU - Robles, Michael C AU - Robles MC FAU - Rokkam, Deepti AU - Rokkam D FAU - Roth, Caroline AU - Roth C FAU - Sasidharan, Preeti AU - Sasidharan P FAU - Shah, Sapana AU - Shah S FAU - Tandon, Shweta AU - Tandon S FAU - Suprai, Jagdip AU - Suprai J FAU - Truong, Tina Quynh Nhu AU - Truong TQ FAU - Uthayaruban, Rubatharshini AU - Uthayaruban R FAU - Varma, Ajitha AU - Varma A FAU - Ved, Urvi AU - Ved U FAU - Wang, Zeran AU - Wang Z FAU - Yu, Zhe AU - Yu Z LA - eng SI - GENBANK/JQ235180 SI - GENBANK/JQ235181 SI - GENBANK/JQ235182 SI - GENBANK/JQ235183 SI - GENBANK/JQ235184 SI - GENBANK/JQ235185 SI - GENBANK/JQ235186 SI - GENBANK/JQ235187 SI - GENBANK/JQ235188 SI - GENBANK/JQ235189 SI - GENBANK/JQ235190 SI - GENBANK/JQ235191 SI - GENBANK/JQ235192 SI - GENBANK/JQ235193 SI - GENBANK/JQ235194 SI - GENBANK/JQ235195 SI - GENBANK/JQ235196 SI - GENBANK/JQ235197 SI - GENBANK/JQ235198 SI - GENBANK/JQ235199 SI - GENBANK/JQ235200 SI - GENBANK/JQ235201 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121121 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Caenorhabditis elegans Proteins) RN - EC 3.6.5.2 (rab GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Caenorhabditis elegans/*enzymology MH - Caenorhabditis elegans Proteins/chemistry/*classification/*metabolism MH - Clone Cells MH - Computational Biology/*methods MH - Conserved Sequence/genetics MH - Humans MH - Introns/genetics MH - Molecular Sequence Data MH - *Multigene Family MH - Open Reading Frames/genetics MH - Phylogeny MH - RNA Splicing/genetics MH - Reproducibility of Results MH - Sequence Alignment MH - rab GTP-Binding Proteins/chemistry/*classification/*metabolism PMC - PMC3504004 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2012/11/28 06:00 MHDA- 2013/05/15 06:00 PMCR- 2012/11/21 CRDT- 2012/11/28 06:00 PHST- 2012/01/24 00:00 [received] PHST- 2012/10/09 00:00 [accepted] PHST- 2012/11/28 06:00 [entrez] PHST- 2012/11/28 06:00 [pubmed] PHST- 2013/05/15 06:00 [medline] PHST- 2012/11/21 00:00 [pmc-release] AID - PONE-D-12-02547 [pii] AID - 10.1371/journal.pone.0049387 [doi] PST - ppublish SO - PLoS One. 2012;7(11):e49387. doi: 10.1371/journal.pone.0049387. Epub 2012 Nov 21.