Wendy Wong et al. (2006) European Worm Meeting "The Integrative Interaction Map for Caenorhabditis elegans"

Wendy Wong, Andrew Fraser

[European Worm Meeting, 2006]

. Wendy Wong and Andrew Fraser. C. elegans is a popular model system for the systematic analysis. However, relatively little is known for its networks of genetic interactions. We hereby construct an integrative interaction map for C. elegans by integrating diverse functional genomics Datasets. We will also present some of the novel tools in querying the interaction map for answering powerful biological hypotheses.

Ewbank JJ et al. (1997) International C. elegans Meeting "Expression and activity of clk-1"

Ewbank JJ, Lemieux JY, Felkai S, Labbe J-C, Hekimi S

[International C. elegans Meeting, 1997]

Mutations in clk-1 affect biological timing and extend longevity (Wong et al., Genetics, 139: 1247, (1995); Lakowski and Hekimi, Science, 272: 1010, (1996)). clk-1 encodes a protein of 187 amino acids that is highly conserved from yeast to mammals. The yeast homologue is the metabolic regulator Cat5p/Coq7p. clk-1 complements the phenotype of cat5/coq7 mull mutants, demonstrating that clk-1 and its yeast homolgue have a common biochemical function (Ewbank et al., Science, 275: 982, (1997)). We have now found that clk-1 is expressed at high levels in all somatic cells throughout development. Furthermore, under heat shock conditions the transcription of clk-1 and/or the stability of its message requires the activity of CLK-1. We are currently using Northern analysis, reporter constructs and antisera to study clk-1 expression further. We are particularly interested in the effects of temperature on clk-1 expression and determining the subcellular localization of CLK-1. We are also analyzing the phenotypic effects of everexpressing wild type or mutant versions of CLK-1 and investigating the molecular correlates of the maternal effect displayed by clk-1 (Wong et al., (1995)).

Lakowski B et al. (1996) East Coast Worm Meeting "The Clock genes interact to determine lifespan by a novel mechanism"

Lakowski B, Hekimi S

[East Coast Worm Meeting, 1996]

Mutations in the genes clk-1, clk-2, clk-3 and gro-1 are all maternally rescued and lead to a very similar phenotype: a pleiotropic alteration of developmental and behavioral timing (Hekimi et al. 1995, Wong et al. 1995). Mutations in the best characterized of these genes, clk-1, lengthen early embryonic cell cycles, embryonic and post-embryonic development, the periods rhythmic behaviors, such as defecation, and ultimately total lifespan (Wong et al. 1995). We have determined that mutations in all four of these genes increase both mean and maximum lifespan. To examine how these genes interact genetically, we made seven double mutant strains containing combinations of Clock mutations. Although there is a range of severity, all double mutants take longer to develop than mutants in the individual constituent genes. Most double mutants also have much longer mean and maximum lifespans than the individual Clock mutants. The strongest double mutant combination, clk-3(qm38); clk-1(qm30), takes four times as long to develop and lives three times as long as N2. Life span extension in clk mutants and gro-1 is not dependent on the activity of daf-16, which is essential for the life extension seen in age-1, daf-2 and daf-23 mutants, suggesting that the Clock genes and the dauer genes act in different pathways. To examine the effect of carrying a life extending mutation from two different pathways, we made a daf-2(e1370) clk-1(e2519) double mutant. daf-2 clk-1 double mutants live longer than either daf-2 or clk-1 and can live up to five times as long as N2. This is the greatest increase in lifespan recorded for any organism by any means. By other criterion, lifespan extension in the Clock mutants also appears to be mechanistically distinct from that of the dauer mutants. For example, when dauer mutants are raised at the permissive temperature, adult lifespan is lengthened without any increase in the length of development. However, in Clock mutants, increased adult lifespan is accompanied by changes in developmental and behavioral timing. In particular, mean adult lifespan and the length of post-embryonic development are strongly correlated among all clk single and double mutants. These observations lead us to suggest that Clock mutants have a slower "rate of living" than the wild type, which may lead to longer lifespan, possibly by slowing the production of reactive byproducts of metabolism. Hekimi et al. Genetics 141, 1351 (1995). Wong et al. Genetics 139, 1247 (1995).

Lemieux JY et al. (1997) International C. elegans Meeting "TOWARDS THE MOLECULAR CHARACTERIZATION OF THE BIOLOGICAL TIMING GENE gro-1"

Lakowski B, Barnes TM, Lemieux JY, Hekimi S

[International C. elegans Meeting, 1997]

In a screen for C. elegans viable maternal-effect mutants, a number of novel phenotypic classes were defined (1). One of these classes is defined by the three clk genes, mutations in which result in a mean lengthening of development and life span, and an increase in the periods of rhythmic behaviors such as defecation, swimming and pumping (1). We have found that a fourth gene, gro-1, also shows the Clk phenotype (2,3). gro-1 was first recovered by Jonathan Hodgkin as a spontaneous segregant from a wild strain (personal communication). Of the four genes, only clk-1 has been thoroughly studied; a comprehensive phenotypic analysis was carried out by Wong et. al. (2) and the molecular cloning by Ewbank et. al. (4). The molecular characterization of each of the Clk genes will aid in understanding the Clk phenotype and ultimately the processes in which these genes are involved. We have mapped gro-1 to the interval between dpy-17 and clk-1 on LGIII. Injection of individual cosmids spanning this region identified three overlapping cosmids which were capable of rescue. Using the available genomic sequence, we tested individual predicted genes from the common rescuing region. This led to the identification of a single gene necessary and sufficient for rescue. The subsequent sequencing of the gene from the gro-1 mutant strain identified the e2400 lesion, confirming the gene assignment. Studies are now underway to determine the expression pattern of GRO-1. Details will be presented at the meeting. 1. Hekimi, S. et. al. Genetics 141: 1351-1364. 2. Wong, A. et. al. Genetics 139: 1247-1259. 3. Lakowski, B. and S. Hekimi. Science. 272: 1010-1013. 4. Ewbank, J. J. et. al. Science 275: 980-983.

Murakami S et al. (1996) West Coast Worm Meeting "LIFE-EXTENSION PATHWAY IN C.ELEGANS"

Johnson TE, Dames SA, Murakami S, Tedesco PM, Duhon SA

[West Coast Worm Meeting, 1996]

Life extension is conferred either by mutants extending adult life (Age), including age-1, daf-2, daf-23, daf-28, spe-26, and an allele of clk-1. Another mode of life extension is conferred by mutants delaying developmental stage (Clk), including clk-1, clk-2, clk-3, gro-1(Wong et al., 1995; Lakowski and Hekimi, 1996). Three groups have identified a life-extension pathway formed by some Daf mutations (Dorman et al., 1995; Larsen et al., 1995; Murakami and Johnson, 1996). We found that the pathway is not limited to Daf mutations but includes other types of the Age mutants (Murakami and Johnson, 1996). Interestingly, the pathway confers UV resistance, suggesting that UV resistance is a good indicator of Age. It is also consistent with the hypothesis that stress resistance is a rate limiting factor determining longevity. We are also testing whether the Age-pathway can confer other types of stress such as H2O2 and heat.

Wong, Garry et al. (2019) International Worm Meeting "miRToolsGallery: a microRNA bioinformatics resources database portal."

Wang, Changliang, Knott, K. Emily, Heikkinen, Liisa, Yang, Yang, Chen, Liang, Wong, Garry

[International Worm Meeting, 2019]

microRNAs (miRNAs) are a class of small noncoding RNA derived from primary miRNA transcripts and processed into precursors and eventually to mature miRNAs 21-22 nucleotides in length. miRNAs were originally discovered in C. elegans and are now known to be expressed in animals, plants, and viruses. miRNAs exert their actions as important regulators of cell proliferation, growth, and development via RNA silencing mechanisms. Bioinformatics resources for miRNA study have been developed, but identifying a correct tool for a specific application is tedious and laborious. In order to facilitate this process, we developed a database portal named miRToolsGallery by manual curation of approximately 1000 tools and resources. With miRToolsGallery, a user can easily locate the appropriate tool for an investigation by implementing a searchable and rankable query function. Tools are ranked by different criteria from PageRank algorithm to most recent publication date to number of publications. The portal contains tools covering a broad range of organisms including C. elegans. The tools also encompass an expansive range of applications from target identification to orthology search. Moreover, the tool is a rapid way to locate recent literature within the miRNA bioinformatics field and to identify current trends. One such trend identified with the tool was the stability and frequent use of some very old computational tools, despite the rapid and enormous advancement in knowledge of miRNA function. The resource is available at www.mirtoolsgallery.org. This research was supported in part by the Research grant of Garry Wong MYRG2016-00101-FHS.

Felkai S et al. (1998) East Coast Worm Meeting "Control of Respiration, Behavior and Aging by clk-1"

Hekimi S, Felkai S, Lemieux JY, Labbe J-C, Brown GG, Ewbank JJ

[East Coast Worm Meeting, 1998]

Mutations in the clk-1 gene of the nematode Caenorhabditis elegans affect the timing of a variety of developmental and physiological processes and increase life span (Wong et al., Genetics 139, 1247 (1995)). clk-1 encodes a protein with high similarity to yeast Coq7p as well as to predicted mammalian proteins (Ewbank et al., Science 275, 980 (1997)). Coq7p is required for respiration as it is necessary for the biosynthesis of the lipid co-factor coenzyme Q (CoQ) (also called ubiquinone). Indeed, no or very little CoQ is found in these mutants (Marbois and Clarke, J. Biol. Chem. 271, 2995 (1996)). We show that in worms CLK-1 is fully active when fused to Green Fluorescent Protein (GFP) and is found in mitochondria. We show that mitochondrial respiration is only mildly depressed in clk-1 mutants (~85% of the wild type). Furthermore, an excess of exogenous CoQ cannot restore normal respiration, suggesting that a deficiency in CoQ is not the main cause of the clk-1 phenotype. A transgene overexpressing CLK-1 activity in wild-type worms can increase respiration beyond the wild type level, accelerate behavioral rates (the defecation cycle) during aging and shorten life span, indicating that clk-1 controls these processes. These observations (that decreased respiration in clk-1 mutants results in a longer life and that increased respiration in worms overexpressing CLK-1 results in a shorter life) suggest that decreased mitochondrial respiration at older ages, which is observed in all animals, might be the result of an active process promoting longer life.

Branicky R et al. (1998) East Coast Worm Meeting "Suppressors of the Slow Defecation Phenotype of clk-1 Mutants"

Hekimi S, Branicky R

[East Coast Worm Meeting, 1998]

Mutations in the C. elegans gene clk-1 affect developmental, cellular and behavioural timing. They result in a mean lengthening of embryonic and post-embryonic development, cell cycle period, and lifespan as well as the defecation, swimming and pharyngeal pumping cycle periods (Wong et al., Genetics 139: 1247 (1995)). The structural and functional homology of CLK-1 to the yeast central metabolic regulator COQ7 (Ewbank et al., Science 275: 980 (1997)) together with other data (see abstract by Felkai et al.) suggests that CLK-1 might also regulate cellular metabolism. However, it is unclear how a mild defect in metabolism could result in the pleiotropic effects of clk-1 mutations. The present study takes a genetic approach to investigate the function of clk-1, by studying it at its interface with the defecation cycle. We conducted a screen for suppressors of the slow defecation phenotype of clk-1 worms. We found a number of new mutations which can suppress the slow defecation phenotype. These mutations can be screened for efficiently with high specificity. To determine if clk-1 interacts with other genes known to affect the periodicity of the defecation cycle, double mutants were constructed and analyzed phenotypically. We found that clk-1 interacts with both Dec-l and Dec-s genes. For example, dec-10 suppresses clk-1 but the slow defecation of dec-4 is suppressed by clk-1. Taken together, these findings suggest that the general slowdown in behaviour exhibited by clk-1 worms is not due to an energy limitation. Rather, they lend support to the theory that clk-1 is involved in the regulation of a number of distinct biological clocks.

Hekimi S et al. (1995) International C. elegans Meeting "A CENTRAL PHYSIOLOGICAL CLOCK IN C. ELEGANS."

Lakowski B, Hekimi S, Wong A

[International C. elegans Meeting, 1995]

The gene clk-1 is defined by five allelic, maternal-effect mutations which affect many aspects of developmental and behavioral timing. These mutations were identified in a general screen for maternal-effect viable mutants (see abstract by Hekimi et al.). The clk-1 mutations result in a mean lengthening of embryonic and post- embryonic development, the cell cycle period and life span, as well as of the periods of the defecation, swimming and pumping cycles. These mutants also display a number of unexpected properties pertaining to timing. For example, the variability in the length of embryonic development is several times greater in the mutants than in the wild type, resulting in the occasional production of mutant embryos developing more rapidly than the most rapidly-developing wild-type embryos. In addition, the duration of embryonic development and the length of the defecation cycle of the mutants, but not of the wild-type, depends on the temperature at which their parents were raised. Finally, individual variations in the severity of distinct mutant phenotypes are correlated in a counter-intuitive way. For example, the animals with the shortest embryonic development have the longest and the most irregular defecation cycle, and those with the longest embryonic development have the shortest defecation cycle. These results suggest the existence of a central physiological clock in the worm (Wong et al. (1995) Genetics). We will present the results of our on- going phenotypic studies of clk-1 mutations and their interactions with other clock genes: clk-2, clk-3 and gro-1. See also abstracts by Lakowski and Hekimi, and Ewbank et al.

Shen, Linjing et al. (2019) International Worm Meeting "Role of Tar DNA binding protein-43 (TDP-43) in mediating alpha-synuclein (HASN) toxicity in a Parkinson's disease model."

Shen, Linjing, Wang, Changliang, Leung, Ka Lai, Wong, Garry, Chen, Liang

[International Worm Meeting, 2019]

Parkinson's disease (PD) is a progressive neurodegenerative disease mainly affecting the motor system. To date, the treatment for PD remains symptomatic, and the molecular mechanisms underlying its pathophysiology are still unclear. ?-Synuclein is the major component of protein aggregates in Lewy bodies and Lewy neurites of PD. Mutation or increased expression of ?-synuclein likely contributes to the development of PD. Treatment against the ?-synuclein aggregation might be an efficient therapeutic strategy . TAR DNA binding protein-43(TDP-43), mainly responsible for the pathology of amyotrophic lateral sclerosis, is also involved in PD. The synucleinopathy of PD is more serious when ?-synuclein proteinopathy and TDP-43 proteinopathy coexist, but the effects of interaction between ?-synuclein and TDP-43 in PD remain unclear. This study investigates the effect of TDP-43 on ?-synuclein. Our study found that the deletion of the gene tdp-1, TDP-43 ortholog in Caenorhabditis elegans (C. elegans), caused behavior defects to improve and human ?-synuclein (HASN) total protein and aggregation to decrease in the HASN overexpressing C. elegans PD model. These effects may be related to upgraded expression of genes belonging to the heat shock protein family, hsp-70, hsp-16.1, hsp-16.11, hsp-16.41, hsp-16.48, hsp-16.4, hsp-16.2, which were identified through both mRNA sequencing and RNA interference. These studies will further our knowledge on the interactions between TDP-43 and ?-synuclein and their roles in PD. The genes from the heat shock protein family might also be considered as promising therapeutic targets for PD and other ?-synuclein related diseases. This research was supported in part by the Research grant of Garry Wong MYRG2017-00123-FHS.