Section VICurrent Issues

Publication Details

A. The Genome

The C. elegans genomic sequence has revolutionized C. elegans biology. Together with genetic, developmental, and anatomical data, it also provides a powerful resource for research in other systems. Completion of the sequence will result in a tentative list of all the genes and a description of other sequence features that, in combination with information from other genomes, will surely advance our understanding of fundamental life processes in ways not yet foreseen. When all the gene products can be identified by their sequence, the challenge remains to relate this knowledge to the biology of the organism. At present, only about 10% of the genes in C. elegans have been identified by mutation (Appendix 1; Johnsen and Baillie, this volume). Although methods for reverse genetics have been developed (Plasterk and van Leunen, this volume), efficient methods analogous to the gene replacement technologies in yeast and mammalian cells will be required to utilize the enormous amount of information that is now available. Although coding sequences attract immediate interest, analysis of noncoding chromosomal sequences should contribute to the analysis of regulatory elements and to the identification of cis-acting elements of the meiotic and mitotic machinery, including sites necessary for proper segregation of chromosomes (Albertson et al., this volume).

B. Gene Expression and Development

Trans-splicing of mRNA, first observed in C. elegans (Krause and Hirsh 1987) and later found in other nematodes, led to the discovery of operons (Blumenthal and Steward, this volume). Unexpected aspects of mRNA processing have been described, but the significance of multigenic transcription units is yet to be understood. Now that operon sequences are available, the potential relationship of gene organization and structure to developmental expression can be addressed. Mechanisms for additional controls on translation and mRNA stability are being elucidated (Anderson and Kimble, this volume). Although it is clear that maternally inherited mRNAs must be stored, then activated in specific patterns of expression observed within the early embryo, the full significance of translational regulation during development is not understood. At present, one can only guess at the complexity of this process.

The molecular analyses of genes affecting development have revealed much about the machinery of sex determination (Meyer, this volume) and intercellular signal transduction (Greenwald; Schedl; Schnabel and Priess; Antebi et al.; Riddle; all this volume) and revealed a multitude of transcription factors (McGhee and Krause, this volume). The genes encoding transcription factors couple cell linage cues and spatial patterning cues to the generation of cell type. A current challenge is to determine the relative importance of different signaling inputs and to understand how they are integrated. The task is to connect the individual examples of transcriptional control to the network of developmental events that impinge on each cell, and ultimately to the regulatory network that is the living animal. Similar signaling molecules and transcription factors have been found in Drosophila and in vertebrates. If they function in homologous processes, then it is possible that the downstream targets of these transcription factors may also be conserved. If so, analysis of the critical downstream developmental pathways will be much easier.

An important finding has been that many genes affecting the specification of cell fate function in lineages that are quite different from one another (Emmons and Sternberg; Schnabel and Priess; Greenwald; all this volume). Comparison of these different effects offers the opportunity to study how the general mechanisms of cell fate determination interact with the lineage-specific, or tissue-specific, differentiation programs. Although cells of similar fate often come from similar lineages, there are notable exceptions (Moerman and Fire, this volume).

Some differences between C. elegans and other models are notable. For example, the molecular mechanisms for sex determination and dosage compensation in C. elegans (Meyer, this volume) seem to differ markedly from those in Drosophila or mammals, although the overall genetic strategies between Caenorhabditis and Drosophila are similar. A novel regulatory mechanism involved in temporal control of developmental processes has been discovered by molecular analysis of the lin-4 gene, which encodes a regulatory antisense RNA (Ambros; Anderson and Kimble; both this volume). Although heterochronic mutants have been identified in other organisms, it is not yet known whether there are conserved pathways for control of biological timing. Finally, there are fundamental differences between C. elegans and Drosophila embryogenesis, yet some of the molecular components may be the same. Molecules that are similar in structure and function may be utilized in different ways.

Cell-cell interactions have been discovered that revise previous concepts about cell fate specification (Schnabel and Priess, this volume) in the early embryo. Asymmetrically distributed factors that account for some differences between early blastomeres have also been identified (Kemphues and Strome, this volume). The mode of action of these proteins should become clearer with identification of additional components of these systems and determination of the functional interactions between these components. The Genome Sequencing Project will speed these studies by eliminating the need for the initial cloning and sequencing steps that necessarily precede further molecular analysis.

The green fluorescent protein (GFP) reporter (Chalfie et al. 1994) is now widely used for analysis of the timing and tissue specificity of transcription in living transgenic animals. Whereas Nomarski DIC microscopy allows one to follow cell nuclei in development, the fluorescent protein should allow visualization of changes in cell size, shape, and position. For example, the paths of migrating cells or neuronal growth cones (Antebi et al., this volume) can now be documented in much more detail in wild-type and mutant strains. Furthermore, GFP expression provides a new tool for mutant screens.

Approaches to C. elegans cell biology have been limited by the inability to purify specific cell types. The lack of a C. elegans cell culture system is a notable absence in an otherwise impressive array of experimental tools. However, cell biology has had notable successes. For example, the ability to purify sperm from males has allowed a detailed description of sperm cell biology, including a novel mechanism for cell motility (L'Hernault, this volume). The abundance and repetitive organization of muscle have allowed biochemical, ultrastructural, and immunochemical analyses that complement the genetic approaches (Moerman and Fire, this volume). The genetic approach also has produced considerable information about the structure and function of the extracellular matrix, including the collagenous cuticle (Kramer, this volume). Since the proteins that compose the extracellular matrix typically contain characteristic sequence motifs, the Genome Sequencing Project should identify most of the genes encoding matrix proteins. This will allow further characterization of the function of these components genetically.

C. Neural Networks and Behavior

An organism so well suited for genetics and electron microscopy was originally thought unlikely to be advantageous for either cell biology or physiology, particularly with regard to the nervous system. However, electrophysiological analysis of the homologous Ascaris nervous system, together with genetic and ultrastructural data from C. elegans, is producing an integrated view of neurotransmission in nematodes (Rand and Nonet, this volume). A neurophysiological approach to the neuromuscular control of pharyngeal pumping has characterized the circuitry and provided novel assays for mutant phenotypes (Avery and Thomas, this volume).

An early approach to the analysis of synaptic transmission in C. elegans involved the selection of mutants resistant to neurotransmitter agonists or antagonists (Brenner 1974). Subsequent molecular analysis revealed that some of these genes encode synaptic proteins previously identified in vertebrates, whereas others were found to encode novel proteins, and the vertebrate homologs were discovered later (Rand and Nonet, this volume). Hence, the process of synaptic transmission has been conserved, and metazoan models with tractable genetics provide unique information relevant to other animals. This is another case in which the Genome Sequencing Project will speed the identification of all the conserved components of the synaptic machinery.

A major step in the past decade has been the functional definition of neural circuits, using genetic, molecular, and cell ablation technologies. One lesson to emerge from the study of C. elegans behavior is the surprising prevalence of redundancy or overlap between neural functions. Such redundancy is best revealed by cell ablation experiments (Avery and Thomas; Bargmann and Mori; both this volume). In this sense, the C. elegans nervous system is no different from that of other animals. With only 302 neurons, it was tempting to presume that each had an essential function, but this seems not to be true based on the existing behavioral assays. However, a closer look sometimes reveals more subtle adverse effects of cell loss, so that the apparent functional redundancy is not complete (Avery and Thomas, this volume).

Because the nervous system is so well described, the roles of individual neurons in behavior can be defined despite functional overlaps. A current goal is to identify the molecules that function in sensory recognition and signaling (Bargmann and Mori; Driscoll and Kaplan; both this volume). Furthermore, the study of neural differentiation (the recognition of synaptic targets and the acquisition of chemical and behavioral specificity) has now become accessible at the organismal level by using molecular and cell ablation technologies. The problem of how sensory information is integrated can be addressed once individual behavioral circuits are characterized. Finally, the regulation of behavior over time has been demonstrated in C. elegans, but the mechanisms for this are not well understood (Jorgensen and Rankin; Bargmann and Mori; both this volume). The possible complexity of learning and memory will only become known as C. elegans learning paradigms are better established. Once it is understood how behavioral changes result from morphological or physiological changes in a neural circuit, then those specific changes can be traced back to functions of gene products in individual cells. The nematode Ascaris possesses a diversity of neuropeptides with distinct patterns of cellular localization (Cowden and Stretton 1995). It seems likely that behavior will involve a complex interplay between peptide neurotransmitters and neuromodulators (Rand and Nonet; Riddle; both this volume).

The developmental and behavioral strategies employed by C. elegans are now emerging to provide a portrait of the animal as an integrated network of molecular functions. The portrait remains incomplete, and many parts lack clear outline or detail, but the way seems open to complete the portrait with ultimate resolution.