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Biochim Biophys Acta,
2016]
BothDrosophila melanogaster and Caenorhabditis elegans (C. elegans) are useful model organisms to study in vivo roles of NF-Y during development. Drosophila NF-Y (dNF-Y) consists of three subunits dNF-YA, dNF-YB and dNF-YC. In some tissues, dNF-YC-related protein Mes4 may replace dNF-YC in dNF-Y complex. Studies with eye imaginal disc-specific dNF-Y-knockdown flies revealed that dNF-Y positively regulates the sevenless gene encoding a receptor tyrosine kinase, a component of the ERK pathway and negatively regulates the Sensless gene encoding a transcription factor to ensure proper development of R7 photoreceptor cells together with proper R7 axon targeting. dNF-Y also controls the Drosophila Bcl-2 (debcl) to regulate apoptosis. In thorax development, dNF-Y is necessary for both proper Drosophila JNK (basket) expression and JNK signaling activity that is responsible for thorax development. Drosophila
p53 gene was also identified as one of the dNF-Y target genes in this system. C. elegans contains two forms of NF-YA subunit, CeNF-YA1 and CeNF-YA2. C. elegans NF-Y (CeNF-Y) therefore consists of CeNF-YB, CeNF-YC and either CeNF-YA1 or CeNF-YA2. CeNF-Y negatively regulates expression of the Hox gene
egl-5 (ortholog of Drosophila Abdominal-B) that is involved in tail patterning. CeNF-Y also negatively regulates expression of the
tbx-2 gene that is essential for development of the pharyngeal muscles, specification of neural cell fate and adaptation in olfactory neurons. Negative regulation of the expression of
egl-5 and
tbx-2 by CeNF-Y provides new insight into the physiological meaning of negative regulation of gene expression by NF-Y during development. In addition, studies on NF-Y in platyhelminths are also summarized.
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Trends in Cell Biology,
1996]
Keeling and Logsdon propose that the y-like sequences from Caenorhabditis elegans and Saccharomyces cerevisiae are bona fide y-tubulins that have undergone rapid evolutionary divergence. Indeed, genetic and localization studies with the yeast epsilon-tubulin (encoded by the TUB4 gene) reveal striking similarities to the bona fide y-tubulins, whereas there is no apparent human analogue to the C. elegans delta-tubulin among the 60 available human y-tubulin expressed-sequence tags. (ESTs).
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Protein Cell,
2011]
Flea-borne transmission is a recent evolutionary adaptation that distinguishes the deadly Yersinia pestis from its progenitor Y. Pseudotuberculosis, a mild pathogen transmitted via the food-borne route. Y. Pestis synthesizes biofilms in the flea gut, which is important for fleaborne transmission. Yersinia biofilms are bacterial colonies surrounded by extracellular matrix primarily containing a homopolymer of N-acetyl-D-glucosamine that are synthesized by a set of specific enzymes. Yersinia biofilm production is tightly regulated at both transcriptional and post-transcriptional levels. All the known structural genes responsible for biofilm production are harbored in both Y. Pseudotuberculosis and Y. Pestis, but Y. Pestis has evolved changes in the regulation of biofilm development, thereby acquiring efficient arthropod-borne transmission.
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Cell Motility and the Cytoskeleton,
1995]
The tubilin family has been considered to have two members, the a- and B-tubulins, which interact to form the heterodimers which in turn assemble to form the eukaryotic microtubules. A third member, y-tubulin, was identified in 1989 and has since been shown to be specifically localized in Microtubule Organizing Centers and has been implicated in the nucleation of microtubules in vivo. Comparisons of individual a-, B-, and y-tubulin sequences within the three subfamilies yield homologies of 65-100% identity. By contrast, comparisons between the three subfamilies typically yield homologies of only about 30-40% identity. The Caenorhabditis and yeast genome projects have recently identified two putative y-tubulin sequences. Analysis of these sequences, however, shows that they are significantly different from those of bona fide y-tubulins...
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Proteomics,
2016]
Galactose1-4fucose (Gal1-4Fuc), a unique disaccharide unit found only on the N-glycans of Protostomia, has been intensively studied, particularly in Nematoda. Gal1-4Fuc attached to the 6-OH of the innermost GlcNAc of N-glycans has been identified as an endogenous target recognized by Caenorhabditis elegans galectin LEC-6 and might function as an endogenous ligand for other galectins as well. Interactions between galectins and N-glycans might be subject to fine-tuning through modifications of the penultimate GlcNAc and the Gal1-4Fuc unit. Similar fine-tuning is also observable in vertebrate galectins, although their major recognition unit is a Gal1-4GlcNAc. In Protostomia, it can be postulated that glycan binding proteins and their ligands have co-evolved; however, epitopes such as Gal1-4Fuc were then hijacked as targets by other organisms. Fungal (Coprinopsis cinerea) galectin 2, CGL2, binds the Gal1-4Fuc on Caenorhabditis elegans glycans to exert its nematotoxicity. Some human and mouse galectins bind to synthesized Gal1-4Fuc; as some parasitic nematodes express this motif, its recognition by mammalian galectins could hypothetically be involved in host defense, similar to fungal CGL2. In this review, we discuss the Gal1-4Fuc unit in Protostomia as a possible equivalent for the Gal1-4GlcNAc unit in vertebrates and a potential non-self glycomarker useful for pathogen recognition. This article is protected by copyright. All rights reserved.
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Trends Glycosci Glycotechnol,
1997]
The finding of Caenorhabditis elegans galectin (32 kDa) demonstrated, for the first time, the presence of the "tandem-repeat type" of galectin, which consists of two homologous domains (ca. 16 kDa). Its N- and C-terminal half domains show relatively low sequence similarity to each other (ca. 30% identity), though most (but not all) of the amino acids involved in the carbohydrate binding are conserved. The nematode 32-kDa galectin shows strong hemagglutinating activity, but its saccharide specificity is rather complex. The individual half domains have considerably distinct features in the binding to asialofetuin-agarose. Though endogenous ligand for them is not known, these observations imply that the 32-kDa nematode galectin functions as a possible "heterobifunctional cross-linker". Since this galectin is localized most abundantly in the adult cuticle, it possibly plays a role in the formation of tight and insoluble epidermal layers. A recently isolated novel nematode galectin (16 kDa) forms a non-covalent dimer, and exhibits significant hemagglutinating activity, which is inhibitable by lactose. The current progress in the C. elegans genome project has revealed the presence of a number of galectin-related genes, and at least four other tandem-repeat-type galectins (40-75% identical to the 32-kDa galectin) have been proved to be expressed. Two closely related genes encoding CRDs (carbohydrate-recognition domains) having a somewhat longer C-terminal tail have also been predicted. Because the complete genome sequence of C. elegans (1 x 108 bp) will be obtained in the near future, galectin research utilizing this model animal will hopefully provide us with new concepts about both the biological and evolutionary significance of multivalent galectin-carbohydrate
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Trends Glycosci Glycotechnol,
2001]
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Trends Microbiol,
2008]
Bubonic plague, one of history''s deadliest infections, is transmitted by fleas infected with Yersinia pestis. The bacteria can starve fleas by blocking their digestive tracts, which stimulates the insects to bite repeatedly and thereby infect new hosts. Direct examination of infected fleas, aided by in vitro studies and experiments with the nematode Caenorhabditis elegans, have established that Y. pestis forms a biofilm in the insect. The extracellular matrix of the biofilm seems to contain a homopolymer of N-acetyl-d-glucosamine, which is a constituent of many bacterial biofilms. A regulatory mechanism involved in Y. pestis biofilm formation, cyclic-di-GMP signaling, is also widespread in bacteria; yet only Y. pestis forms biofilms in fleas. Here, the historical background of bubonic plague is briefly described and recent studies investigating the mechanisms by which these unique and deadly biofilms are formed are discussed.
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Trends in Cell Biology,
1996]
The tubulin gene family consists of three types, the well-known a- and B-tubulins and the more recently discovered y-tubulin. However, genome-sequencing projects of Caenorhabditis elegans and Saccharomyces cerivisiae have revealed recently two tubulin genes eash so divergent from any known tubulin that they prompted a proposal to classify these as representatives of new families, the delta- and epsilon-tubulin, respectively, a reclassification implicit in the analysis of tubulin structure and function published recently in this journal. However, substantial evidence is accumulating from the distribution, function and phylogeny of these genes for a contrasting argument that really they are rapidly evolving orthologues of y-tubulin.
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Crit Rev Biochem Mol Biol,
2012]
The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Marino-Ramirez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Hakkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.