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Curr Opin Genet Dev,
1996]
The sequencing of the 100 Mb Caenorhabditis elegans genome-containing approximately 14,000 genes-is approximately 50% complete. One of its most interesting features is its compactness; introns and intergenic distances are unusually small and, surprisingly, approximately 25% of genes are contained in polycistronic transcription units (operons) with only approximately 100 bp between genes.
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Int J Parasitol,
2000]
Onchocerca volvulus, the filarial parasite that causes onchocerciasis or river blindness, contains three distinct genomes. These include the nuclear genome, the mitochondrial genome and the genome of an intracellular endosymbiont of the genus Wolbachia. The nuclear genome is roughly 1.5x10(8) bp in size, and is arranged on four chromosome pairs. Analysis of expressed sequence tags from different life-cycle stages has resulted in the identification of transcripts from roughly 4000 O. volvulus genes. Several of these transcripts are highly abundant, including those encoding collagen and cuticular proteins. Analysis of several gene sequences from O. volvulus suggests that the nuclear genes of O. volvulus are relatively compact and are interrupted relatively frequently by small introns. The intron-exon boundaries of these genes generally follow the GU-AG rule characteristic of the splice donor and acceptors of other vertebrate organisms. The nuclear genome also contains at least one repeated sequence family of a 150 bp repeat which is arranged in tandem arrays and appears subject to concerted evolution. The mitochondrial genome of O. volvulus is remarkably compact, only 13747 bp in size. Consistent with the small size of the genome, four gene pairs overlap, eight contain no intergenic regions and the remaining gene pairs are separated by small intergenic domains ranging from 1 to 46 bp. The protein-coding genes of the O. volvulus mitochondrial genome exhibit a striking codon bias, with 15/20 amino acids having a single codon preference greater than 70%. Intraspecific variation in both the nuclear and mitochondrial genomes appears to be quite limited, consistent with the hypothesis that O. volvulus has suffered a genetic bottleneck in the recent past.
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Yakugaku Zasshi,
2008]
Selenium (Se) is an essential trace element. Se is found as selenocysteine (Sec) in Se-proteins. Sec is the 21(st) amino acid, because Sec has its tRNA, the codon UGA and those components in its translational machinery. Sec UGA codon shares with major stop codon UGA. We purified Sec synthesizing enzymes, such as seryl-tRNA synthetase (SerRS), Sec synthetase (SecS) and selenophosphate synthetase (SePS). I described the procedures to prepare Sec tRNA, SerRS, SecS, SePS and [(75)Se]H(2)Se in detail. We clarified that SecS composed of two proteins, SecSalpha and SecSbeta. Sec synthesizing and incorporating systems present in Monela, Animalia and Protoctista but not in Plantae and Fungi. We showed that protozoa had Sec tRNA on which Sec was synthesized from Ser-tRNA by bovine and protozoa SecS. Some worms, such as Caenorhabditis elegans and Fasiola gigantica, also had Sec tRNA on which Sec was synthesized by bovine liver SecS or C. elegans enzymes. We showed recognition sites of mammalian Sec tRNA by SecS. The identitiy units of Sec tRNA are 9 bp aminoacyl- and 6 bp D-stems. This recognition is not the base-specific manner but the length-specific manner. From comparison of the phylogeny trees of Sec synthesizing system and translation system, we concluded that the evolution of Sec synthesizing system is older than that of the translation system.
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Genome Res,
2005]
The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and analyses, including a curated set of 19,735 protein-coding genes-with >90% directly supported by experimental evidence-and >1300 noncoding RNA genes. High-throughput efforts are under way to complete the gene sets, along with studies to characterize gene expression, function, and regulation on a genome-wide scale. The success of the worm project has had a profound effect on genome sequencing and on genomics more broadly. We now have a solid platform on which to build toward the lofty goal of a true molecular understanding of worm biology with all its implications including those for human health.
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Amino Acids,
2008]
The TOR (Target of Rapamycin) protein kinase pathway plays a central role in sensing and responding to nutrients, stress, and intracellular energy state. TOR complex 1 (TORC1) is comprised of TOR, Raptor, and Lst8 and its activity is sensitive to inhibition by the macrolide antibiotic rapamycin. TORC1 regulates protein synthesis, ribosome biogenesis, autophagy, and ultimately cell growth through the phosphorylation of S6 K, 4E-BP, and other substrates. As TORC1 activity is positively or negatively modulated in response to upstream regulators, cellular growth rate is, respectively, enhanced or suppressed. A separate multiprotein TOR complex, TORC2, is insensitive to direct inhibition by rapamycin and does not regulate growth patterns directly; TORC2 can, however, impact certain aspects of TORC1 signaling and cell survival. TOR signaling is an ancient pathway, conserved among the yeasts, Dictyostelium, C. elegans, Drosophila, mammals, and Arabidopsis. This review will focus on the regulation of TORC1 in mammalian cells in the context of amino acid sensing/regulation and intracellular ATP homeostasis, but will also include comparisons among other organisms.
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Int J Parasitol,
1998]
Caenorhabditis elegans has become a popular model system for genetic and molecular research, since it is easy to maintain and has a very fast life-cycle. Its genome is small and a virtually complete physical map in the form of cosmids and YAC clones exists. Thus it was chosen as a model system by the Genome Project for sequencing, and it is expected that by 1998 the complete sequence (100 million bp) will be available. The accumulated wealth of information about C. elegans should be a boon for nematode parasitologists, as many aspects of gene regulation and function can be studied in this simple model system. A large array of techniques is available to study many aspects of C. elegans biology. In combination with genome projects for parasitic nematodes, conserved genes can be identified rapidly. We expect many new areas of fertile research that will lead to new insights in helminth parasitology, which are based not only on the information gained from C. elegans per se, but also from its use as a heterologous system to study parasitic genes.
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J Dent Res,
2008]
RNA interference (RNAi), an accurate and potent gene-silencing method, was first experimentally documented in 1998 in Caenorhabditis elegans by Fire et al., who subsequently were awarded the 2006 Nobel Prize in Physiology/Medicine. Subsequent RNAi studies have demonstrated the clinical potential of synthetic small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) in dental diseases, eye diseases, cancer, metabolic diseases, neurodegenerative disorders, and other illnesses. siRNAs are generally from 21 to 25 base-pairs (bp) in length and have sequence-homology-driven gene-knockdown capability. RNAi offers researchers an effortless tool for investigating biological systems by selectively silencing genes. Key technical aspects-such as optimization of selectivity, stability, in vivo delivery, efficacy, and safety-need to be investigated before RNAi can become a successful therapeutic strategy. Nevertheless, this area shows a huge potential for the pharmaceutical industry around the globe. Interestingly, recent studies have shown that the small RNA molecules, either indigenously produced as microRNAs (miRNAs) or exogenously administered synthetic dsRNAs, could effectively activate a particular gene in a sequence-specific manner instead of silencing it. This novel, but still uncharacterized, phenomenon has been termed ''RNA activation'' (RNAa). In this review, we analyze these research findings and discussed the in vivo applications of siRNAs, miRNAs, and shRNAs.
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WormBook,
2015]
Nearly 15% of the ~20,000 C. elegans genes are contained in operons, multigene clusters controlled by a single promoter. The vast majority of these are of a type where the genes in the cluster are ~100 bp apart and the pre-mRNA is processed by 3' end formation accompanied by trans-splicing. A spliced leader, SL2, is specialized for operon processing. Here we summarize current knowledge on several variations on this theme including: (1) hybrid operons, which have additional promoters between genes; (2) operons with exceptionally long (> 1 kb) intercistronic regions; (3) operons with a second 3' end formation site close to the trans-splice site; (4) alternative operons, in which the exons are sometimes spliced as a single gene and sometimes as two genes; (5) SL1-type operons, which use SL1 instead of SL2 to trans-splice and in which there is no intercistronic space; (6) operons that make dicistronic mRNAs; and (7) non-operon gene clusters, in which either two genes use a single exon as the 3' end of one and the 5' end of the next, or the 3' UTR of one gene serves as the outron of the next. Each of these variations is relatively infrequent, but together they show a remarkable variety of tight-linkage gene arrangements in the C. elegans genome.
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[
1982]
The nematode Caenorhabditis elegans contains a small genome of 8 X 10*7 bp of DNA. The adult animal has 953 somatic cells whose complete embryonic and postembryonic cell lineages are known. Many are muscle cells or cells containing thin filaments. C. elegans is a self-fertilizing hermaphrodite that is convenient for genetic analyses, and a detailed genetic map has been constructed. Approximately 20 muscle genes have been identified on the basis of mutant phenotypes that include uncoordinated behavior and defective muscles. Among these 20 muscle genes, only 2 have been connected with functional gene products;
unc-54 codes for a major myosin, and
unc-15 codes for paramyosin. No actin gene has been identified in C. elegans. It is possible that one of the known muscle genes codes for actin, but actin loci may be difficult to detect genetically. For example, mutations in actin genes might be lethal or cryptic if multiple, identical genes are present. Nevertheless, the actin genes of C. elegans are important objects of study because actin is an abundant protein in C. elegans, because its synthesis is regulated developmentally in specific cell lineages, and because the genetic manipulation of actin genes seems feasible once these genes are recognized and mapped. We therefore began a search for the actin genes of C. elegans using nongenetic
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Trends Glycosci Glycotechnol,
1997]
The finding of Caenorhabditis elegans galectin (32 kDa) demonstrated, for the first time, the presence of the "tandem-repeat type" of galectin, which consists of two homologous domains (ca. 16 kDa). Its N- and C-terminal half domains show relatively low sequence similarity to each other (ca. 30% identity), though most (but not all) of the amino acids involved in the carbohydrate binding are conserved. The nematode 32-kDa galectin shows strong hemagglutinating activity, but its saccharide specificity is rather complex. The individual half domains have considerably distinct features in the binding to asialofetuin-agarose. Though endogenous ligand for them is not known, these observations imply that the 32-kDa nematode galectin functions as a possible "heterobifunctional cross-linker". Since this galectin is localized most abundantly in the adult cuticle, it possibly plays a role in the formation of tight and insoluble epidermal layers. A recently isolated novel nematode galectin (16 kDa) forms a non-covalent dimer, and exhibits significant hemagglutinating activity, which is inhibitable by lactose. The current progress in the C. elegans genome project has revealed the presence of a number of galectin-related genes, and at least four other tandem-repeat-type galectins (40-75% identical to the 32-kDa galectin) have been proved to be expressed. Two closely related genes encoding CRDs (carbohydrate-recognition domains) having a somewhat longer C-terminal tail have also been predicted. Because the complete genome sequence of C. elegans (1 x 108 bp) will be obtained in the near future, galectin research utilizing this model animal will hopefully provide us with new concepts about both the biological and evolutionary significance of multivalent galectin-carbohydrate