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[
WormBook,
2005]
This chapter reviews analytical tools currently in use for protein classification, and gives an overview of the C. elegans proteome. Computational analysis of proteins relies heavily on hidden Markov models of protein families. Proteins can also be classified by predicted secondary or tertiary structures, hydrophobic profiles, compositional biases, or size ranges. Strictly orthologous protein families remain difficult to identify, except by skilled human labor. The InterPro and NCBI KOG classifications encompass 79% of C. elegans protein-coding genes; in both classifications, a small number of protein families account for a disproportionately large number of genes. C. elegans protein-coding genes include at least ~12,000 orthologs of C. briggsae genes, and at least ~4,400 orthologs of non-nematode eukaryotic genes. Some metazoan proteins conserved in other nematodes are absent from C. elegans. Conversely, 9% of C. elegans protein-coding genes are conserved among all metazoa or eukaryotes, yet have no known functions.
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[
2007]
In the pair of the nematode Caenorhabiditis elegans serotonergic chemosensory neurons ADF, the TRPV channel protein OCR-2 interacts with another TRPV protein, OSM-9, to control the production of the neurotransmitter serotonin. The activity and specificity of OCR-2 in the serotonergic neurons is governed by structural determinants within the channel protein in concert with defined cellular components. The dynamic gating mechanisms, multiple sensory modalities, and functional conservation in diverse organisms make TRPV channels ideal candidates for the long-awaited molecular sensors that underscore the ancient role of the serotonergic system in coupling sensory cues and internal milieu to behavior and physiology.
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[
WormBook,
2005]
Ubiquitin is a highly conserved 76 amino acid polypeptide, which is covalently attached to target proteins to signal their degradation by the 26S proteasome or to modify their function or localization. Regulated protein degradation, which is associated with many dynamic cellular processes, occurs predominantly via the ubiquitin-proteasome system. Ubiquitin is conjugated to target proteins through the sequential actions of a ubiquitin-activating enzyme, ubiquitin-conjugating enzymes, and ubiquitin-protein ligases. The nematode Caenorhabditis elegans has one ubiquitin-activating enzyme, twenty putative ubiquitin-conjugating enzymes, and potentially hundreds of ubiquitin-protein ligases. Research in C. elegans has focused on the cellular functions of ubiquitin pathway components in the context of organismal development. A combination of forward genetics, reverse genetics, and genome-wide RNAi screens has provided information on the loss-of-function phenotypes for the majority of C. elegans ubiquitin pathway components. Additionally, detailed analysis of several classes of ubiquitin-protein ligases has led to the identification of their substrates and the molecular pathways that they regulate. This review presents a comprehensive overview of ubiquitin-mediated pathways in C. elegans with a description of the known components and their identified molecular, cellular, and developmental functions.
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[
1984]
The switching on or off of specific genes is a fundamental aspect of cellular differentiation during metazoan development. The molecular events involved in this switching are not yet understood, but they are now subject to analysis with the current technology available in molecular biology. Much of the work directed toward the understanding of developmental gene regulation has focused on the genes encoding the protein actin. Actin is the major thin-filament protein in both muscle and nonmuscle cells. The protein sequences of actins from a variety of tissues in several organisms have been determined, and the actin genes from a number of organisms have been isolated and are currently being studied. This work has revealed that actins are evolutionarily conserved, are encoded in most species by multigene families, and are differentially regulated, both spatially and temporally, during
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[
Methods Cell Biol,
1995]
The ultimate goal of subcellular fractionation and biochemical purification is to better understand the relationships between structure and function of proteins and protein assemblies. Examples of such relationships with respect to specific gene products include the formation of stable complexes, elucidation of catalytic activities, and subcellular localization of the organellar and supramolecular levels. The detailed aspects of such relationships are not always readily predictable from genetic or molecular studies of the gene products or from their cellular localization by immunological methods. Subcellular fractionation and biochemical purification are generally prerequisites to experimental analysis of biochemical mechanisms underlying a biological phenomenon. These approaches can mutually enhance and interact with parallel cellular, genetic, and molecular analyses. To achieve such goals, methods for isolating proteins and protein assemblies must preserve both structural integrity and biological activity. Ideally, both objectives should be met; practically, it may be critical to know which of these conditions is true. In general, specific protocols must be designed for the optimal isolation, purification, and characterization of each specific protein of interest. Additionally, one wishes to achieve as high a yield as possible; however, each step in protein purification generally produces some reduction in yield...
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[
Lecture Notes in Computer Science,
2005]
The OMA project is a large-scale effort to identify groups of orthologs from complete genome data, currently 150 species. The algorithm relies solely on protein sequence information and does not require any human supervision. It has several original features, in particular a verification step that detects paralogs and prevents them from being clustered together. Consistency checks and verification are performed throughout the process. The resulting groups, whenever a comparison could be made, are highly consistent both with EC assignments, and with assignments from the manually curated database HAMAP. A highly accurate set of orthologous sequences constitutes the basis for several other investigations, including phylogenetic analysis and protein classification.
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[
WormBook,
2006]
Throughout the C. elegans sequencing project Genefinder was the primary protein-coding gene prediction program. These initial predictions were manually reviewed by curators as part of a "first-pass annotation" and are actively curated by WormBase staff using a variety of data and information. In the WormBase data release WS133 there are 22,227 protein-coding gene, including 2,575 alternatively-spliced forms. Twenty-eight percent of these have every base of every exon confirmed by transcription evidence while an additional 51% have some bases confirmed. Most of the genes are relatively small covering a genomic region of about 3 kb. The average gene contains 6.4 coding exons accounting for about 26% of the genome. Most exons are small and separated by small introns. The median size of exons is 123 bases, while the most common size for introns is 47 bases. Protein-coding genes are denser on the autosomes than on chromosome X, and denser in the central region of the autosomes than on the arms. There are only 561 annotated pseudogenes but estimates but several estimates put this much higher.
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[
1987]
Ascaris and several other parasitic nematodes undergo chromatin diminution in the somatic cell precursors of the early embryo. In 1910 Boveri hypothesized that the chromatin lost might include genes essential to the function of the germ line. We have cloned a germ line-specific cDNA which codes for the major sperm protein. Using this clone as a probe we found that these genes show no loss or rearrangement of DNA in somatic cells which have undergone chromatin diminution. Actin and a-tubulin genes from Ascaris are also unchanged following diminution. Ascaris and the free-living nematode Caenorhabditis elegans differ substantially in the numbers of actin and major sperm protein genes, in spite of conservation of gene
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[
1982]
Much of this meeting is devoted to the study of multi-gene families and the differential expression of various members during muscle development. Structural analysis of myosin and then other muscle proteins by peptide mapping and amino acid sequencing first suggested that these isoforms are the products of different genes. The use of antibodies specific to distinct structural gene products has permitted detailed investigations of myosin structure, biosynthesis and degradation, and cellular location as muscle development proceeds. The small nematode, Caenorhabditis elegans, is a laboratory animal which offers genetic dissection and manipulation as tools in deciphering of gene regulation in terms of specific protein synthesis during muscle development. The examination of specific mutants by protein chemistry and immunochemistry has already proved a powerful comination in many fields.
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[
1982]
Myosin is the central piece in the protein machinery that produces muscle contraction. In this role, the myosin molecule must serve as an energy-transducing enzyme and as the major building block of the thick filament. In differentiated muscle cells, myosin is constantly being synthesized and assembled into thick filaments. Many issues regarding the processes of myosin synthesis and assembly in muscle remain unresolved. Is the synthesis and assembly of myosin coupled? Are additional protein components required for the assembly of myosin into native thick filaments? Do different myosin isoforms play distinct structural or functional roles within thick filaments? The combined approaches of protein biochemistry, immunology, and electron microscopy have proved useful in establishing our present knowledge concerning the roles of myosin within muscle. The nematode Caenorhabditis elegans offers several experimental advantages in addition to these time-honored methods that may provide further insights concerning the process of myosin synthesis and assembly. This animal has an elegantly simple and well-defined development and anatomy of body-wall muscle cells. Genetic analysis has characterized hundreds of specific mutants in over 20 genes affecting the development, structure, and function of body-wall muscle cells. This genetic approach, in combination with biochemical, immunological, and morphological methods, promises to offer significant