Schierenberg E et al. (1992) Seminars in Developmental Biology "The establishment of embryonic axes and determination of cell fates in embryos of the nematode Caenorhabditis elegans."

Schierenberg E, Strome S

[Seminars in Developmental Biology, 1992]

At the 4-cell stage of the C. elegans embryo, three axes can be defined: anterior-posterior (A-P), dorsal-ventral (D-V), and left-right (L-R). The A-P axis first becomes obvious in the newly fertilized 1-cell embryo. Pronouned cytoplasmic assymmetries arise along the A-P axis during the first cell cycle, after which the zygote undergoes a series of stem cell-like cleavages with an A-P orientation of the mitotic spindle; these cleavages generate several somatic founder cells and a primordial germ cell. The D-V and L-R axes are defined by the direction of spindle rotation as the 2-cell embryo divides into four cells. In contrast to the A-P axis, there do not appear to be cellular asymmetries associated with the D-V and L-R axes, and both axes can easily be reversed by micromanipulation. Thus, with respect to the roles that the embryonic axes serve in cell-fate determination in the early C. elegans embryo, it appears that internally transmitted developmental information is differentially segregated along the A-P axis, but not along the D-V or L-R axes. Instead, D-V and L-R differences in the fates of cells within lineages appear to be dictated by differential

Sommer RJ et al. (2001) Zoology (Jena) "Towards a microevolutionary approach in evolutionary developmental biology: Biogeography of the nematode genus Pristionchus (Diplogastridae)."

Schlak I, Sommer RJ, Witte H

[Zoology (Jena), 2001]

The free-living nematode Pristionchus pacificus has been described as a satellite organism for functional comparative studies in developmental biology. Like the model organism Caenorhabditis elegans, P. pacificus is easily culturable in the laboratory. P. pacificus, is a hermaphroditic species, with a 4-day life cycle, but unlike most nematodes which pass through 4 juvenile stages during their development, P. pacific:us has only three juvenile stages. The combination of cellular, genetic and molecular studies has made P. pacificus a perfect model system for studying evolutionary developmental biology. One process that has been studied in detail is the development of the vulva. Genetic and molecular studies have revealed that the function of several genes involved in vulva development differs between P. pacificus and C. elegans. Here, we review our macroevolutionary comparison between P. pacificus and C. elegans and provide data on the biogeography of the genus Pristionchus. The genus has a world-wide distribution with strains from Northern America, Europe, Madagascar and New Zealand. Sequence analyses of the rDNA internal transcribed spacer (ITS) region and mating experiments revealed that the 12 hermaphroditic strains studied, belong to three different species. Strains isolated from Northern America belong predominantly to Pristionchus pacificus, whereas the european strains are members of Pristionchus maupasi and a new species yet to be described.

Wang JT et al. (2013) Adv Exp Med Biol "Germ cell specification."

Seydoux G, Wang JT

[Adv Exp Med Biol, 2013]

The germline of Caenorhabditis elegans derives from a single founder cell, the germline blastomere P(4). P(4) is the product of four asymmetric cleavages that divide the zygote into distinct somatic and germline (P) lineages. P(4) inherits a specialized cytoplasm ("germ plasm") containing maternally encoded proteins and RNAs. The germ plasm has been hypothesized to specify germ cell fate, but the mechanisms involved remain unclear. Three processes stand out: (1) inhibition of mRNA transcription to prevent activation of somatic development, (2) translational regulation of the nanos homolog nos-2 and of other germ plasm mRNAs, and (3) establishment of a unique, partially repressive chromatin. Together, these processes ensure that the daughters of P(4), the primordial germ cells Z2 and Z3, gastrulate inside the embryo, associate with the somatic gonad, initiate the germline transcriptional program, and proliferate during larval development to generate 2,000 germ cells by adulthood.

Parker R et al. (2007) Mol Cell "P bodies and the control of mRNA translation and degradation."

Parker R, Sheth U

[Mol Cell, 2007]

Recent results indicate that many untranslating mRNAs in somatic eukaryotic cells assemble into related mRNPs that accumulate in specific cytoplasmic foci referred to as P bodies. Transcripts associated with P body components can either be degraded or return to translation. Moreover, P bodies are also biochemically and functionally related to some maternal and neuronal mRNA granules. This suggests an emerging model of cytoplasmic mRNA function in which the rates of translation and degradation of mRNAs are influenced by a dynamic equilibrium between polysomes and the mRNPs seen in P bodies. Moreover, some mRNA-specific regulatory factors, including miRNAs and RISC, appear to repress translation and promote decay by recruiting P body components to individual mRNAs.

Updike DL et al. (2009) J Androl "P granule assembly and function in Caenorhabditis elegans germ cells."

Strome S, Updike DL

[J Androl, 2009]

Germ granules are large, non-membrane-bound, ribonucleoprotein (RNP) organelles found in the germ line cytoplasm of most, if not all, animals. The term germ granule is synonymous with the perinuclear nuage in mouse and human germ cells. These large RNPs are complexed with germ line-specific cytoplasmic structures such as the mitochondrial cloud, intermitochondrial cement, and chromatoid bodies. The widespread presence of germ granules across species and the associated germ line defects when germ granules are compromised suggest that germ granules are key determinants of the identity and special properties of germ cells. The nematode Caenorhabditis elegans has been a very fruitful model system for the study of germ granules, wherein they are referred to as P granules. P granules contain a heterogeneous mixture of RNAs and proteins. To date, most of the known germ granule proteins across species, and all of the known P granule components in C elegans, are associated with RNA metabolism, which suggests that a main function of germ granules is posttranscriptional regulation. Here we review P granule structure and localization, P granule composition, the genetic pathway of P granule assembly, and the consequences in the germ line when P granule components are lost. The findings in C elegans have important implications for the germ granule function during postnatal germ cell differentiation in mammals.

Anderson P (2005) Dev Cell "A Place for RNAi."

Anderson P

[Dev Cell, 2005]

Processing bodies (P bodies) are discrete cytoplasmic foci to which mRNA is routed for degradation. In mammalian cells, they are also associated with miRNA-induced translational silencing and siRNA-induced mRNA degradation. In a recent issue of Molecular Cell, Ding and coworkers described an argonaute-interacting protein that appears to promote the assembly of P bodies in C. elegans (Ding et al., 2005).

Braeckman BP et al. (1998) Journal of Gerontology "Authors response to commentaries on Two-parameter logistic and Weibull equations provide better fits to survival-data from isogenic populations of Caenorhabditis elegans in axenic culture than does.."

Braeckman BP, Vanfleteren JR, De Vreese A

[Journal of Gerontology, 1998]

Although the classical Gompertz model ha been the standard for over a century, recent research has shown definitely that this model often fails to predict survival at old ages. Also our analyses reported in this article showed that the Weibull and 2-parameter (2-p) logistic functions provide better fits to the extremes of the survival curves of C. elegans in axenic culture. As a commentator argues, individual differences in the Gompertz dynamics of aging processes can generate a 2-p logistic survival curve for the entire population...

Voronina E (2013) Mol Reprod Dev "The diverse functions of germline P-granules in Caenorhabditis elegans."

Voronina E

[Mol Reprod Dev, 2013]

P-granules are conserved cytoplasmic organelles, similar to nuage, that are present in Caenorhabditis elegans germ cells. Based on the prevailing sterility phenotype of the component mutants, P-granules have been seen as regulators of germ cell development and function. Yet, specific germline defects resulting from P-granule failure vary, depending on which component(s) are inactivated, at which stage of development, as well as on the presence of stress factors during animal culture. This review discusses the unifying themes in many P-granule functions, with the main focus on their role as organizing centers nucleating RNA regulation in the germ cell cytoplasm.

Seydoux G (2018) J Mol Biol "The P Granules of C. elegans: A Genetic Model for the Study of RNA-Protein Condensates."

Seydoux G

[J Mol Biol, 2018]

P granules are RNA/protein condensates in the germline of C. elegans. Genetic analyses have begun to identify the proteins that regulate P granule assembly in the cytoplasm of zygotes. Among them, the RGG-domain protein PGL-3, the intrinsically-disordered protein MEG-3, and the RNA helicase LAF-1 all bind and phase separate with RNA in vitro. We discuss how RNA-induced phase separation, competition with other RNA-binding proteins, and reversible phosphorylation contribute to the asymmetric localization of P granules in the cytoplasm of newly fertilized embryos. P granules contain RNA silencing complexes that monitor the germline transcriptome and may provide an RNA memory of germline gene expression across generations.

Harayama S et al. (1992) Annu Rev Microbiol "Functional and evolutionary relationships among diverse oxygenases."

Kok M, Neidle EL, Harayama S

[Annu Rev Microbiol, 1992]

Oxygenases that incorporate one or two atoms of dioxygen into substrates are found in many metabolic pathways. In this article, representative oxygenases, principally those found in bacterial pathways for the degradation of hydrocarbons, are reviewed. Monooxygenases, discussed in this chapter, incorporate one hydroxyl group into substrates. In this reaction, two atoms of dioxygen are reduced to one hydroxyl group and one H2O molecule by the concomitant oxidation of NAD(P)H. Dioxygenases catalyze the incorporation of two atoms of dioxygen into substrates. Two types of dioxygenases, aromatic-ring dioxygenases and aromatic-ring-cleavage dioxygenases, are discussed. The aromatic-ring dioxygenases incorporate two hydroxyl groups into aromatic substrates, and cis-diols are formed. This reaction also requires NAD(P)H as an electron donor. Aromatic-ring-cleavage dioxygenases incorporate two atoms of dioxygen into aromatic substrates, and the aromatic ring is cleaved. This reaction does not require an external reductant. All the oxygenases possess a cofactor, a transition metal, flavin or pteridine, that interacts with dioxygen. The concerted reactions between dioxygen and carbon in organic compounds are spin forbidden. The cofactor is used to overcome this restriction. For the oxygenases that require the NAD(P)H cofactor, the enzyme reaction is separated into two steps, the oxidation of NAD(P)H to generate two reducing equivalents, and the hydroxylation of substrates. Flavoprotein hydroxylases that catalyze the monohydroxylation of the aromatic ring carry out these two reactions on a single polypeptide chain. In other oxygenases, the NAD(P)H oxidation and a hydroxylation reaction are catalyzed by two separate polypeptides that are linked by a short electron-transport chain. Two reducing equivalents generated by the oxidation of NAD(P)H are transferred through the electron-transport chain to the cofactor on a hydroxylase component that they reduce. Dioxygen couples with the reduced cofactor and subsequently hydroxylates substrates. The electron-transport chains associated with oxygenases contain at least two redox centers. The first redox center is usually a flavin, while the second is an iron-sulfur cluster. The electron transport is initiated by a single two-electron transfer from NAD(P)H to a flavin, followed by two single-electron transfers from the flavin to an iron-sulfur cluster. The primary sequences of many oxygenases have been determined, and according to their sequence similarities, the oxygenases can be grouped into several protein families. Among proteins of the same family, the sequences in regions involved in cofactor binding are strongly conserved. Local sequence similarities are also observed among oxygenases from different families, primarily in regions involved in cofactor binding.