Programmed cell death

Programmed cell death (PCD), or apoptosis, is an integral component of C. elegans development. During development, 131 cells are fated to die by apoptosis. PCD is easily observed with Nomarski optics in the C. elegans embryo; the nucleus of the apoptotic cell becomes refractile, resembling a flat button, making C. elegans an easy model for following apoptotic cell death. PCD in C. elegans can be divided into three main phases (with participating genes): specification of which cells should live or die (ces-1, ces-2, in general); activation of the cell killing machinery (egl-1, ced-9, ced-4 and ced-3); and an execution phase where the dying cell is dismantled and removed through phagocytosis (ced-1,-2,-5,-6,-7,-10 and-12), which occurs in concert with apoptotic DNA degradation (cps-6, nuc-1). Molecular and biochemical studies in C. elegans revealed programmed cell death mechanisms conserved in humans. The regulatory pathway that controls cell death is composed of conserved cell death activators and inhibitors: EGL-1 and BH3-domain-only proteins, CED-9 and Bcl-2, CED-4 and Apaf-1, and CED-3 and caspases, in nematodes and mammals, respectively. Further the degradation of chromosomal DNA involves a mitochondrial proapoptotic endonuclease: endonuclease G (EndoG), and AIF in mammals and their orthologs CPS-6 and WAH-1 in worms.

miRNA pathway

microRNA (miRNA) elements are short (20-25 nucleotides (nt)), noncoding, single-stranded RNAs that bind to complementary sequences on target messenger RNA (mRNAs), which can result in translational repression or target mRNA degradation. microRNAs are critical components of developmental timing, responses to stress, and aging. Regulating the biogenesis and metabolism of miRNAs thus has an enormous impact on the health of the organism. In the genome, miRNAs reside in intergenic regions as well as within introns and exons of protein-coding genes. miRNAs are transcribed as long primary miRNAs (pri-miRNA). These pri-miRNA transcripts form hairpin-like structures with a double stranded stem and a terminal loop. pri-miRNAs are cleaved into smaller ~65-nt long precursor miRNA (pre-miRNA) by terminal-loop binding proteins and a microprocessor complex. This complex is composed of DRSH-1/DROSHA and PASH-1/DGCR8. In humans and yeast, the pre-miRNA product is exported to the cytoplasm by Exportin-5/XPO5 and RanGTP, respectively. The closest homologs of these proteins in C. elegans include xpo-1 and Y105E8A.1/yrs-2. Once in the cytoplasm, the pre-miRNA is cleaved at the top of the terminal loop by DCR-1/DICER, producing a duplex of two mature ~22nt miRNAs.An alternative, DRSH-1/DROSHA-independent, miRNA biogensis pathway has been identified in C. elegans and Drosophila. In this pathway pre-miRNAs are created through mRNA spliced introns. These introns form Mirtron lariats, which are debranched and refolded into pre-miRNA species. Mirtron generated pre-miRNAs are exported and processed in the same way as pre-miRNAs generated through the canonical miRNA biogenesis pathway. As mentioned previously, miRNA activity functions in many biological processes and hence needs to be temporally and spatially regulated. Much of that regulation occurs at the level of miRNA biogenesis and processing through Drosha binding/associated proteins, Dicer binding proteins, or proteins that bind to pri- and/or pre-miRNAs terminal loops. These regulators control expression or activity of miRNAs on specific miRNAs or families of miRNAs. For example, DCR-1 interaction proteins, ALG-1 and ALG-2, are required for lin-4 and let-7 miRNA formation and maturation. miRNA processing can also be influenced by ADAR editing, cellular localization, proteins known to regulate transcription (such as p53, SMADs) and proteins known to regulate mRNA stability (such as KSRP).