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[
IUBMB Life,
2007]
Most tRNAs share a common secondary structure containing a T arm, a D arm, an anticodon arm and an acceptor stem. However, there are some exceptions. Most nematode mitochondrial tRNAs and some animal mitochondrial tRNAs lack the T arm, which is necessary for binding to canonical elongation factor Tu (EF-Tu). The mitochondria of the nematode Caenorhabditis elegans have a unique EF-Tu, named EF-Tu1, whose structure has supplied clues as to how truncated tRNAs can work in translation. EF-Tu1 has a C-terminal extension of about 60 aa that is absent in canonical EF-Tu. Recent data from our laboratory strongly suggests that EF-Tu1 recognizes the D-arm instead of the T arm by a mechanism involving this C-terminal region. Further biochemical analysis of mitochondrial tRNAs and EF-Tu from the distantly related nematode Trichinella spp. and sequence information on nuclear and mitochondrial DNA in arthropods suggest that T-armless tRNAs may have arisen as a result of duplication of the EF-Tu gene. These studies provide valuable insights into the co-evolution of RNA and RNA-binding proteins. IUBMB Life, 59: 68-75, 2007.
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WormBook,
2007]
Heterorhabditis bacteriophora is an entomopathogenic nematode (EPN) mutually associated with the enteric bacterium, Photorhabdus luminescens, used globally for the biological control of insects. Much of the previous research concerning H. bacteriophora has dealt with applied aspects related to biological control. However, H. bacteriophora is an excellent model to investigate fundamental processes such as parasitism and mutualism in addition to its comparative value to Caenorhabditis elegans. In June 2005, H. bacteriophora was targeted by NHGRI for a high quality genome sequence. This chapter summarizes the biology of H. bacteriophora in common and distinct from C. elegans, as well as the status of the genome project.
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Exp Gerontol,
2011]
Reproduction shortens lifespan in practically all organisms examined so far, but the underlying mechanisms remain largely unknown to date. Here I review what evolutionary and molecular biologists have learned about such "costs of reproduction" in the fruit fly (Drosophila melanogaster) since Maynard Smith's (1958) seminal discovery that sterile mutants in D. subobscura live substantially longer than fertile wildtype flies. Together with observations from the nematode worm (Caenorhabditis elegans) and other organisms, the data from Drosophila suggest that there are at least four general principles that underlie trade-offs between reproduction and lifespan: (1) trade-offs between survival and reproduction are widespread; (2) the relationship between increased lifespan and decreased fecundity can be uncoupled under certain conditions; (3) while survival costs of reproduction might not necessarily be due to competitive resource allocation, we lack robust alternative explanations for their occurrence; and (4) physiological trade-offs between reproduction and longevity do not always translate into evolutionary genetic trade-offs. I conclude that - despite much recent progress - our current understanding of the proximate basis of survival costs of reproduction remains very limited; much future work on the genetics and physiology of such trade-offs will be required to uncover their mechanistic basis.
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[
Trends in Ecology & Evolution,
1999]
In a recent TREE news & comment, Gadagkar made some useful comments on LaMunyon and Ward's interesting study on sexual reproduction in nematodes. I think, however, that he - and LaMunyon and Ward - have confused the benefits of sex for species or demes with those for individuals or genes.
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WormBook,
2012]
About 70% of C. elegans mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders. SL1 is used to trim off the 5' ends of pre-mRNAs and replace them with the SL1 sequence. This processing event is very closely related to cis-splicing, or intron removal. The SL1 sequence is donated by a 100 nt small nuclear ribonucleoprotein particle (snRNP), the SL1 snRNP. This snRNP is structurally and functionally similar to the U snRNAs (U1, U2, U4, U5 and U6) that play key roles in intron removal and trans-splicing, except that the SL1 snRNP is consumed in the process. More than half of C. elegans pre-mRNAs are subject to SL1 trans-splicing, whereas ~30% are not trans-spliced. The remaining genes are trans-spliced by SL2, which is donated by a similar snRNP, the SL2 snRNP. SL2 recipients are all downstream genes in closely spaced gene clusters similar to bacterial operons. They are transcribed from a promoter at the 5' end of the cluster of between 2 and 8 genes. This transcription makes a polycistronic pre-mRNA that is co-transcriptionally processed by cleavage and polyadenylation at the 3' end of each gene, and this event is closely coupled to the SL2 trans-splicing event that occurs only ~100 nt further downstream. SL2 trans-splicing requires a sequence between the genes, the Ur element, that likely base pairs with the 5' splice site on the SL2 snRNP, in a manner analogous to the interaction between the 5' splice site in cis-splicing with the U1 snRNP. The key difference is that in trans-splicing, the snRNP contains the 5' splice site, whereas in cis-splicing the pre-mRNA does. Some operons, termed "hybrid operons", contain an additional promoter between two genes that can express the downstream gene or genes with a developmental profile that is different from that of the entire operon. The operons contain primarily genes required for rapid growth, including genes whose products are needed for mitochondrial function and the basic machinery of gene expression. Recent evidence suggests that RNA polymerase is poised at the promoters of growth genes, and operons allow more efficient recovery from growth-arrested states, resulting in reduction in the need for this cache of inactive RNA polymerase.
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[
WormBook,
2006]
Appropriate regulation of mRNA transcription is central to the differentiation and functions of eukaryotic cells, and to the development of complex organisms. mRNAs are synthesized by the coordinated action of a set of general transcription and mRNA modification factors. These factors and the fundamental mechanisms involved in transcription are conserved among eukaryotes, including C. elegans. Recent studies in various systems have revealed that this apparatus is not controlled through a simple on/off switch at the promoter, and that the factors and mechanisms involved in transcription are instead subject to regulation at a surprising number of different levels. In this chapter we will discuss examples in which regulation involving the general mRNA transcription apparatus or other transcription co-factors plays a central role in C. elegans development, and in which C. elegans studies have provided new insights into eukaryotic transcription mechanisms. Together, these studies have shown that regulatory mechanisms that involve the general Pol II machinery are a central participant in many aspects of C. elegans biology.
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Oncogene,
2004]
The regulation of protein stability by the ubiquitin-proteasome pathway is a critical issue central to the comprehension of the molecular basis of carcinogenesis. However, ubiquitin modification of target substrates signals many cellular processes other than proteolysis that are also important for the development of cancer. It is noteworthy that many proteins studied by clinical breast cancer researchers are involved in these ubiquitin pathways. This review summarizes recent works on such proteins including cyclins, CDK inhibitors, and the SCF in cell cycle control; the breast and ovarian cancer suppressor BRCA1-BARD1; ErbB2/HER2/Neu and its ubiquitin ligase c-Cbl or CHIP; and the estrogen receptor and its downstream target Efp. Understanding these pathways may provide some hints toward developing diagnostic tools and treatments for breast cancer patients.
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Science,
2021]
Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how "tree thinking" is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data.
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Nature Genetics,
2004]
A massive study of expressed-sequence tags from both free-living and parasitic nematodes identifies tens of thousands of genes not present in Caenorhabditis elegans. Half of these are unique to nematodes and should provide new insights into the lifestyles of parasitic nematodes.