Martin J Simard et al. (2002) European Worm Meeting "New players in RNA interference: Implication of rde-1 homologues."

Craig C Mello, Martin J Simard, Erbay Yigit

[European Worm Meeting, 2002]

In a variety of organisms, double stranded RNA (dsRNA) has been shown to induce gene silencing phenomenon called RNA interference (RNAi), in which small RNAs derived from the dsRNA trigger destruction of homologous cellular RNAs. In previous genetic screens, we have indentified several rde (RNA interference-deficient) mutants that define genetic loci required for RNAi in Caenorhabditis elegans [Tabara et al, Cell 99: 123-132 (1999)]. Among these, the rde- 1 gene encodes a member of a functionally novel but highly conserved eukaryotic gene family implicated in gene silencing in various organisms including C. elegans, fungi, plant and Drosophila. To date, we have identified 27 homologues of rde-1 in C. elegans genome. In order to address if these rde-1 homologues could also play a role in RNA interference, we have injected dsRNAs targeting all the 27 rde-1 homologues. The gene-silencing of four subclass of genes affects either the somatic or germline-specific RNAi. Interestingly, two homologues of rde-1, alg-1 and alg-2, previously described to be required for the processing and the activity of lin-4 and let-7 in development [Grishok et al, Cell 106: 23-34 (2001)], interact with small temporal RNAs (i.e. LIN-4 and LET-7) in vivo. We are currently investigating the cellular proteins interacting specifically with rde-1 homologues in vivo.

Martin J Simard et al. (2004) East Coast Worm Meeting "Microarrays analysis of two essential factors required for RNAi, RDE-1 and RDE-4"

Danila Ulyanov, Juerg Straubhaar, Darryl Conte Jr, Martin J Simard, Craig C Mello, Jennifer A Keys

[East Coast Worm Meeting, 2004]

Recently, RNA interference has emerged as a method of choice for specifically knocking out expression of studied genes in a myriad of biological fields. The RNA interference (RNAi) is produced by the destruction of cellular RNAs homologous to small RNAs species called small interfering RNA (siRNA). In Caenorhabditis elegans, the siRNAs are derived from a long dsRNA deliver into the animal either by injection or by feeding the nematode with bacteria expressing the dsRNA trigger. In previous genetic screens, we and others have identified several rde (RNA interference-deficient) mutants that are required for RNAi in C. elegans [Tabara et al, Cell 99: 123-132 (1999), Ketting et al, Cell 99: 133-141 (1999)]. Among the isolated genes essential for RNA interference, the mutants alleles of rde-1 and rde-4 are required to produce RNAi initiated by exogenous dsRNA and are not required for transposon silencing like observed with mut-7. In order to uncover new functions for RDE-1 and RDE-4, we have conducted a microarrays analysis on a mutant allele of each of them. In the class of genes up- or down-regulated in both rde-1 and rde-4 mutant background, we are observing cluster of genes associated to innate immunity response in C. elegans. This observation may uncover a new function for RNAi pathway genes in nematode. We are currently testing the possible role of rde-1, rde-4 and other rde genes in worm immunity.

Martin J Simard et al. (2002) East Coast Worm Meeting "Two homologues of rde-1, alg-1 and alg-2, are implicated in RNA interference and microRNA pathways."

Craig C Mello, Erbay Yigit, Martin J Simard

[East Coast Worm Meeting, 2002]

In a variety of organisms, double stranded RNA (dsRNA) has been shown to induce a gene silencing phenomenon called RNA interference (RNAi). During RNAi long trigger dsRNA molecules are processed into small 22-24 nucleotide (nt) RNAs (siRNAs) that are thought to guide the destruction of complementary cellular RNAs. In previous genetic screens, we have identified several rde (RNA interference-deficient) mutants that define genetic loci required for RNAi in Caenorhabditis elegans [Tabara et al, Cell 99: 123-132 (1999)]. Among these, the rde-1 gene encodes a member of a functionally novel but highly conserved eukaryotic gene family implicated in gene silencing in various organisms including C. elegans, fungi, plants and Drosophila. To date, we have identified 27 homologues of rde-1 in C. elegans genome. Among these, alg-1 and alg-2 were previously shown to be required for the processing and the activity of two natural small RNAs (miRNAs), lin-4 and let-7, that function in development [Grishok et al, Cell 106: 23-34 (2001)]. Here we show that ALG-1 and ALG-2 interact with miRNAs (i.e. LIN-4 and LET-7) in vivo. Surprisingly, although as reported previously alg-1 and alg-2 are not required for somatic RNAi we find that these genes are required for RNAi in the germline. These findings suggest that RDE-1 homologs function in RNAi at more than one step and reveal yet another connection between the RNAi and miRNA pathways.

Martin J et al. (2009) Nucleic Acids Res "Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics."

Yin Y, Mitreva M, Martin J, Wang Z, Wylie T, Abubucker S

[Nucleic Acids Res, 2009]

Nematode.net (http://nematode.net) is a publicly available resource dedicated to the study of parasitic nematodes. In 2000, the Genome Center at Washington University (GC) joined a consortium including the Nematode Genomics group in Edinburgh, and the Pathogen Sequencing Unit of the Sanger Institute to generate expressed sequence tags (ESTs) as an inexpensive and efficient solution for gene discovery in parasitic nematodes. As of 2008 the GC, sampling key parasites of humans, animals and plants, has generated over 500 000 ESTs and 1.2 million genome survey sequences from more than 30 non-Caenorhabditis elegans nematodes. Nematode.net was implemented to offer user-friendly access to data produced by this project. In addition to sequence data, the site hosts: assembled NemaGene clusters in GBrowse views characterizing composition and protein homology, functional Gene Ontology annotations presented via the AmiGO browser, KEGG-based graphical display of NemaGene clusters mapped to metabolic pathways, codon usage tables, NemFam protein families which represent conserved nematode-restricted coding sequences not found in public protein databases, a web-based WU-BLAST search tool that allows complex querying and other assorted resources. The primary aim of Nematode.net is the dissemination of this diverse collection of information to the broader scientific community in a way that is useful, consistent, centralized and enduring.

Martin GM (2011) FASEB J "The biology of aging: 1985-2010 and beyond."

Martin GM

[FASEB J, 2011]

In this contribution to the series of reflective essays celebrating the 25th anniversary of The FASEB Journal, our task is to assess the growth of research on the biology of aging during this period and to suggest where we might be heading during the next 25 yr. A review of the literature suggests a healthy acceleration of progress during the past decade, perhaps largely due to progress on the genetics of longevity of model organisms. Progress on the genetics of health span in these model organisms has lagged, however. Research on the genetic basis of the remarkable interspecific variations in life span has only recently begun to be seriously addressed. The spectacular advances in genomics should greatly accelerate progress. Research on environmental effects on life span and health span needs to be accelerated. Stochastic variations in gene expression in aging have only recently been addressed. These can lead to random departures from homeostasis during aging.-Martin, G. M. The biology of aging: 1985-2010 and beyond.

Bowerman BA et al. (1994) Worm Breeder's Gazette "The Maternal Gene skn-4 and the Specification of Ventral Blastomere Fates in the Early C. elegans Embryo"

Bowerman BA, Shelton CA, Thorpe CJ, Martin PR

[Worm Breeder's Gazette, 1994]

THE MATERNAL GENE SKN-4 AND THE SPECIFICATION OF VENTRAL BLASTOMERE FATES IN THE EARLY C. ELEGANS EMBRYO Bruce Bowerman, Paula R. Martin, Christopher J. Thorpe, and Christopher A. Shelton. The Institute of Molecular Biology, University of Oregon, Eugene, OR 97403.

Martin E et al. (2016) J Vis Exp "Novel Metrics to Characterize Embryonic Elongation of the Nematode Caenorhabditis elegans."

Martin E, Rocheleau-Leclair O, Jenna S

[J Vis Exp, 2016]

Dissecting the signaling pathways that control the alteration of morphogenic processes during embryonic development requires robust and sensitive metrics. Embryonic elongation of the nematode Caenorhabditis elegans is a late developmental stage consisting of the elongation of the embryo along its longitudinal axis. This developmental stage is controlled by intercellular communication between hypodermal cells and underlying body-wall muscles. These signaling mechanisms control the morphology of hypodermal cells by remodeling the cytoskeleton and the cell-cell junctions. Measurement of embryonic lethality and developmental arrest at larval stages as well as alteration of cytoskeleton and cell-cell adhesion structures in hypodermal and muscle cells are classical phenotypes that have been used for more than 25 years to dissect these signaling pathways. Recent studies required the development of novel metrics specifically targeting either early or late elongation and characterizing morphogenic defects along the antero-posterior axis of the embryo. Here, we provide detailed protocols enabling the accurate measurement of the length and the width of the elongating embryos as well as the length of synchronized larvae. These methods constitute useful tools to identify genes controlling elongation, to assess whether these genes control both early and late phases of this stage and are required evenly along the antero-posterior axis of the embryo.

Martin AA et al. (2019) J Vis Exp "In Vivo Calcium Imaging in C. elegans Body Wall Muscles."

Martin AA, Alford S, Richmond JE

[J Vis Exp, 2019]

The model organism C. elegans provides an excellent system to perform in vivo calcium imaging. Its transparent body and genetic manipulability allow for the targeted expression of genetically encoded calcium sensors. This protocol outlines the use of these sensors for the in vivo imaging of calcium dynamics in targeted cells, specifically the body wall muscles of the worms. By utilizing the co-expression of presynaptic channelrhodopsin, stimulation of acetylcholine release from excitatory motor neurons can be induced using blue light pulses, resulting in muscle depolarization and reproducible changes in cytoplasmic calcium levels. Two worm immobilization techniques are discussed with varying levels of difficulty. Comparison of these techniques demonstrates that both approaches preserve the physiology of the neuromuscular junction and allow for the reproducible quantification of calcium transients. By pairing optogenetics and functional calcium imaging, changes in postsynaptic calcium handling and homeostasis can be evaluated in a variety of mutant backgrounds. Data presented validates both immobilization techniques and specifically examines the roles of the C. elegans sarco(endo)plasmic reticular calcium ATPase and the calcium-activated BK potassium channel in the body wall muscle calcium regulation.

Martin E et al. (2016) J Cell Biol "Rac1/RhoA antagonism defines cell-to-cell heterogeneity during epidermal morphogenesis in nematodes."

Jenna S, Ouellette MH, Martin E

[J Cell Biol, 2016]

The antagonism between the GTPases Rac1 and RhoA controls cell-to-cell heterogeneity in isogenic populations of cells in vitro and epithelial morphogenesis in vivo Its involvement in the regulation of cell-to-cell heterogeneity during epidermal morphogenesis has, however, never been addressed. We used a quantitative cell imaging approach to characterize epidermal morphogenesis at a single-cell level during early elongation of Caenorhabditis elegans embryos. This study reveals that a Rac1-like pathway, involving the Rac/Cdc42 guanine-exchange factor -PIX/PIX-1 and effector PAK1/PAK-1, and a RhoA-like pathway, involving ROCK/LET-502, control the remodeling of apical junctions and the formation of basolateral protrusions in distinct subsets of hypodermal cells. In these contexts, protrusions adopt lamellipodia or an amoeboid morphology. We propose that lamella formation may reduce tension building at cell-cell junctions during morphogenesis. Cell-autonomous antagonism between these pathways enables cells to switch between Rac1- and RhoA-like morphogenetic programs. This study identifies the first case of cell-to-cell heterogeneity controlled by Rac1/RhoA antagonism during epidermal morphogenesis.

Martin EM et al. (2018) J Biol Chem "Conformational flexibility within the nascent polypeptide-associated complex enables its interactions with structurally diverse client proteins."

Radford SE, Deuerling E, Gamerdinger M, Gense K, Jackson MP, Karamanos TK, Humes JR, Martin EM, Ashcroft AE

[J Biol Chem, 2018]

As newly synthesized polypeptides emerge from the ribosome, it is crucial that they fold correctly. To prevent premature aggregation, nascent chains interact with chaperones that facilitate folding or prevent misfolding until protein synthesis is complete. Nascent polypeptide-associated complex (NAC) is a ribosome-associated chaperone important for protein homeostasis. However, how NAC binds its substrates remains unclear. Using native electrospray ionization MS (ESI MS), limited proteolysis, NMR and cross-linking, we analysed the conformational properties of NAC from Caenorhabditis elegans and studied its ability to bind proteins in different conformational states. Our results revealed that NAC adopts an array of compact and expanded conformations and binds weakly to client proteins that are unfolded, folded, or intrinsically disordered, suggestive of broad substrate compatibility. Of note, we found that this weak binding retards aggregation of the intrinsically disordered protein -synuclein both in vitro and in vivo. These findings provide critical insights into the structure and function of NAC. Specifically, they reveal the ability of NAC to exploit its conformational plasticity to bind a repertoire of substrates having unrelated sequences and structures independently of actively translating ribosomes.