Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans

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Chitinases Are Essential for Sexual Development but Not Vegetative Growth in Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic pathogen that mainly infects immunocompromised individuals. The fungal cell wall of C. neoformans is an excellent target for antifungal therapies since it is an essential organelle that provides cell structure and integrity. Importantly, it is needed for localization or attachment of known virulence factors, including melanin, phospholipase, and the polysaccharide capsule. The polysaccharide fraction of the cryptococcal cell wall is a complex structure composed of chitin, chitosan, and glucans. Chitin is an indispensable component of many fungal cell walls that contributes significantly to cell wall strength and integrity. Fungal cell walls are very dynamic, constantly changing during cell division and morphogenesis. Hydrolytic enzymes, such as chitinases, have been implicated in the maintenance of cell wall plasticity and separation of the mother and daughter cells at the bud neck during vegetative growth in yeast. In C. neoformans we identified four predicted endochitinases, CHI2, CHI21, CHI22, and CHI4, and a predicted exochitinase, hexosaminidase, HEX1. Enzymatic analysis indicated that Chi2, Chi22, and Hex1 actively degraded chitinoligomeric substrates. Chi2 and Hex1 activity was associated mostly with the cellular fraction, and Chi22 activity was more prominent in the supernatant. The enzymatic activity of Hex1 increased when grown in media containing only N-acetylglucosamine as a carbon source, suggesting that its activity may be inducible by chitin degradation products. Using a quadruple endochitinase deletion strain, we determined that the endochitinases do not affect the growth or morphology of C. neoformans during asexual reproduction. However, mating assays indicated that Chi2, Chi21, and Chi4 are each involved in sexual reproduction. In summary, the endochitinases were found to be dispensable for routine vegetative growth but not sexual reproduction.Cryptococcus neoformans is an opportunistic fungal pathogen that causes cryptococcosis in immunocompromised individuals. The incidence of cryptococcosis continues to rise in direct proportion to the spread of the human immunodeficiency virus (for review, see Casadevall and Perfect [7]). It is estimated that up to 13% of AIDS patients in the United States will develop life-threatening cryptococcal meningitis, and in some parts of Africa this estimate increases to 40% (7). Current antifungal therapies for treatment of cryptococcosis are inadequate. Amphotericin B, which is believed to interact with membrane sterols (ergosterol) to produce an aggregate that forms a transmembrane channel is effective, but toxic (50, 62). Fluconazole inhibits cytochrome P-450-dependent 14α-sterol demethylase, which leads to the depletion of ergosterol and the accumulation of sterol precursors and results in the formation of a plasma membrane with altered structure and function. It is fungistatic and has high relapse rates (18, 41, 42, 50, 62). Flucytosine can be toxic and resistance occurs frequently (9, 41, 42, 50, 62). The newest class of antifungals to emerge is the echinocandins that targets an essential fungal enzyme required for the synthesis of a β-(1,3)-glucan in the fungal cell wall (17, 34). In addition, the echinocandins have been shown to be safe and effective for treatment of specific fungal infections, including candidiasis and aspergillosis caused by Candida albicans and Aspergillus fumigatus, respectively (23, 59). However, even though C. neoformans possesses the target enzyme β-(1,3)-glucan synthase and in vitro assays have shown the enzyme''s activity to be inhibited by the echinocandin caspofungin (34), C. neoformans still exhibits resistance to this class of drugs (26).Because fungi are eukaryotes and share many biochemical processes with their host, antifungal drug design has been problematic. The cell wall is a prominent structure that differentiates fungi from mammalian host cells. For all fungi, this organelle is essential and provides structure as well as integrity; thus, the cell wall components or their biosynthetic pathways make attractive drug targets. In addition, the cell wall of C. neoformans is associated with a variety of known virulence factors that are important for host-pathogen interactions, and it contains polymers including chitin and chitosan that are necessary for the viability of C. neoformans. The first virulence factor that a host cell encounters is the polysaccharide capsule. The capsule attachment to the outer portion of the cell wall requires α-(1-3)-glucan (15, 46). Another cell wall associated virulence factor is the melanin pigment (61) that is produced by two laccase proteins, Lac1 and Lac2 (38, 44). Lac1 is responsible for generating the majority of melanin and is localized to the cell wall (38, 63, 69). Chitin and chitosan are essential components of the cell wall that have been shown to contribute to the overall strength and integrity of the cell wall (4, 5). The essentiality of the chitin component and the lack of it being present in host cells make chitin and its biosynthetic components attractive targets for drug design.Chitin is one of the most abundant polymers found in nature (1, 12). It is a linear polymer of β-(1,4)-linked N-acetylglucosamine (GlcNAc), and in fungi it is formed from cytoplasmic pools of UDP-GlcNAc. C. neoformans has eight predicted chitin synthases and three putative chitin synthase regulators for synthesis of chitin polymers. Mutational analysis indicate that two chitin synthases, Chs4 and Chs5, produce the majority of vegetative chitin, and one, Chs3, produces the majority of chitin that is converted to chitosan during vegetative growth (5). Chitosan, the deacetylated version of chitin, is produced by chitin deacetylases (EC 3.5.1.41) that remove acetyl groups from nascent chitin polymers. In C. neoformans the chitin produced by Chs3 and the chitin synthase regulator, Csr2, is deacetylated to chitosan by up to three chitin deacetylases (Cda1, Cda2, and Cda3) (4, 5). Strains of C. neoformans lacking either CHS3 or CSR2 have significantly reduced chitosan levels and are sensitive to a variety of cell wall inhibitors (5). Similarly, strains lacking all three chitin deacetylases are unable to convert chitin to chitosan and are sensitive to cell wall inhibitors (4). This indicates that chitosan is essential for the proper maintenance of cell wall integrity in C. neoformans and Chs3, Csr2, and the chitin deacetylases contribute to its formation (4, 5). Chitosan polymers of other fungi have been reported to possess various degrees of deacetylation (57). Chitin and chitosan are located throughout the lateral cell wall and bud neck regions of C. neoformans (4). During growth cellular chitin and chitosan need to be continuously remodeled, presumably through the enzymatic digestion of chitin and chitosan polymers by chitinases and or chitosanases.Chitinases (EC 3.2.1.14) are enzymes that hydrolyze the β-(1-4) linkages in polymers of chitin. Besides being in fungi, these enzymes occur in a wide variety of organisms, including viruses, bacteria, plants, and animals (1, 12). There are two major categories of chitinases: endochitinases and exochitinases. Generally, the endochitinases cleave chitin chains internally to generate low-molecular-mass multimers of GlcNAc. In contrast, the exochitinases are divided into two subcategories: chitobiosidases (EC 3.2.1.29) release diacetylchitobiose from the nonreducing end of chitin chains, and β-(1,4)-N-acetylhexosaminidases (EC 3.2.1.52) release GlcNAc from the nonreducing end of chitin oligosaccharides; both types are usually processive (12). Fungal chitosanases (EC 3.2.1.132) are less understood. They have been found in Aspergillus spp. and Gongronella sp. strain JG. Although these chitosanases have been shown to degrade chitosan, their in vitro physiological relevance has not been elucidated (8, 60).In other fungal systems chitinases are known to be involved in cell separation, hyphal growth and branching, development of reproductive structures, spore germination, and autolysis (1, 12). In the nonpathogenic model yeast Saccharomyces cerevisiae two chitinases, Cts1p and Cts2p, function independently in bud separation and spore formation, respectively (25, 27). Cts1p is the only chitinase expressed during vegetative growth, and strains lacking this enzyme display incomplete cell separation (27) that can lead to pseudohyphalike growth (25). The synthesis of the spore wall is adversely affected by the deletion of CTS2 and affects the ability of the yeast to form mature asci (19).C. neoformans reproduces predominantly by budding, but also has a defined sexual cycle that culminates in the production of basidiospores. Both the yeast and the spore forms are thought to be infectious particles (7). C. neoformans typically colonizes the lungs of a immunocompromised host, from where it can disseminate to the central nervous system (7). As such, reproduction by budding has been shown to occur within host macrophages and dendritic cells (3, 28). Because fungal chitinases in other systems such as S. cerevisiae and C. albicans have been shown to be necessary for the completion of cell division (11, 27), understanding the biosynthesis and activity of chitinases could determine whether interfering with chitinase activity would impair the ability of C. neoformans to reproduce.We hypothesized that the chitinases in C. neoformans would be involved in growth and, like the chitinases in S. cerevisiae and C. albicans, that they would degrade specific chitin during either bud separation, hyphal growth, or sporulation. In the present study we utilized a homology-based search to identify five potential chitinases in C. neoformans, the four endochitinases CHI2, CHI21, CHI22, and CHI4 and one exochitinase, HEX1. Using a panel of chitinase deletion strains we discovered that the chitinases are dispensable for “normal” vegetative growth but were necessary during development of the sexual phase of C. neoformans.     

C. elegans ATAD-3 Is Essential for Mitochondrial Activity and Development

Background

Mammalian ATAD3 is a mitochondrial protein, which is thought to play an important role in nucleoid organization. However, its exact function is still unresolved.

Results

Here, we characterize the Caenorhabditis elegans (C. elegans) ATAD3 homologue (ATAD-3) and investigate its importance for mitochondrial function and development. We show that ATAD-3 is highly conserved among different species and RNA mediated interference against atad-3 causes severe defects, characterized by early larval arrest, gonadal dysfunction and embryonic lethality. Investigation of mitochondrial physiology revealed a disturbance in organellar structure while biogenesis and function, as indicated by complex I and citrate synthase activities, appeared to be unaltered according to the developmental stage. Nevertheless, we observed very low complex I and citrate synthase activities in L1 larvae populations in comparison to higher larval and adult stages. Our findings indicate that atad-3(RNAi) animals arrest at developmental stages with low mitochondrial activity. In addition, a reduced intestinal fat storage and low lysosomal content after depletion of ATAD-3 suggests a central role of this protein for metabolic activity.

Conclusions

In summary, our data clearly indicate that ATAD-3 is essential for C. elegans development in vivo. Moreover, our results suggest that the protein is important for the upregulation of mitochondrial activity during the transition to higher larval stages.     

Essential roles of snap-29 in C. elegans

SNARE domain proteins are key molecules mediating intracellular fusion events. SNAP25 family proteins are unique target-SNAREs possessing two SNARE domains. Here we report the genetic, molecular, and cell biological characterization of C. elegans SNAP-29. We found that snap-29 is an essential gene required throughout the life-cycle. Depletion of snap-29 by RNAi in adults results in sterility associated with endomitotic oocytes and pre-meiotic maturation of the oocytes. Many of the embryos that are produced are multinucleated, indicating a defect in embryonic cytokinesis. A profound defect in secretion by oocytes and early embryos in animals lacking SNAP-29 appears to be the underlying defect connecting these phenotypes. Further analysis revealed defects in basolateral and apical secretion by intestinal epithelial cells in animals lacking SNAP-29, indicating a broad requirement for this protein in the secretory pathway. A SNAP-29-GFP fusion protein was enriched on recycling endosomes, and loss of SNAP-29 disrupted recycling endosome morphology. Taken together these results suggest a requirement for SNAP-29 in the fusion of post-Golgi vesicles with the recycling endosome for cargo to reach the cell surface.     

Two-Component Histidine Phosphotransfer Protein Ypd1 Is Not Essential for Viability in Candida albicans

Prokaryotes and lower eukaryotes, such as yeasts, utilize two-component signal transduction pathways to adapt cells to environmental stress and to regulate the expression of genes associated with virulence. One of the central proteins in this type of signaling mechanism is the phosphohistidine intermediate protein Ypd1. Ypd1 is reported to be essential for viability in the model yeast Saccharomyces cerevisiae. We present data here showing that this is not the case for Candida albicans. Disruption of YPD1 causes cells to flocculate and filament constitutively under conditions that favor growth in yeast form. To determine the function of Ypd1 in the Hog1 mitogen-activated protein kinase (MAPK) pathway, we measured phosphorylation of Hog1 MAPK in ypd1Δ/Δ and wild-type strains of C. albicans. Constitutive phosphorylation of Hog1 was observed in the ypd1Δ/Δ strain compared to the wild-type strain. Furthermore, fluorescence microscopy revealed that green fluorescent protein (GFP)-tagged Ypd1 is localized to both the nucleus and the cytoplasm. The subcellular segregation of GFP-tagged Ypd1 hints at an important role(s) of Ypd1 in regulation of Ssk1 (cytosolic) and Skn7 (nuclear) response regulator proteins via phosphorylation in C. albicans. Overall, our findings have profound implications for a mechanistic understanding of two-component signaling pathways in C. albicans, and perhaps in other pathogenic fungi.     

Crumbs3 Is Essential for Proper Epithelial Development and Viability

First identified in Drosophila, the Crumbs (Crb) proteins are important in epithelial polarity, apical membrane formation, and tight junction (TJ) assembly. The conserved Crb intracellular region includes a FERM (band 4.1/ezrin/radixin/moesin) binding domain (FBD) whose mammalian binding partners are not well understood and a PDZ binding motif that interacts with mammalian Pals1 (protein associated with lin seven) (also known as MPP5). Pals1 binds Patj (Pals1-associated tight-junction protein), a multi-PDZ-domain protein that associates with many tight junction proteins. The Crb complex also binds the conserved Par3/Par6/atypical protein kinase C (aPKC) polarity cassette that restricts migration of basolateral proteins through phosphorylation. Here, we describe a Crb3 knockout mouse that demonstrates extensive defects in epithelial morphogenesis. The mice die shortly after birth, with cystic kidneys and proteinaceous debris throughout the lungs. The intestines display villus fusion, apical membrane blebs, and disrupted microvilli. These intestinal defects phenocopy those of Ezrin knockout mice, and we demonstrate an interaction between Crumbs3 and ezrin. Taken together, our data indicate that Crumbs3 is crucial for epithelial morphogenesis and plays a role in linking the apical membrane to the underlying ezrin-containing cytoskeleton.     

Functional Profiling of Precursor MicroRNAs Identifies MicroRNAs Essential for Glioma Proliferation

Cancer initiation and progression involve microRNAs that can function like tumor suppressors and oncogenes. The functional significance of most miRNAs is currently unknown. To determine systematically which microRNAs are essential for glioma growth, we screened a precursor microRNA library in three human glioblastoma and one astroglial cell line model systems. The most prominent and consistent cell proliferation–reducing hits were validated in secondary screening with an additional apoptosis endpoint. The functional screening data were integrated in the miRNA expression data to find underexpressed true functional tumor suppressor miRNAs. In addition, we used miRNA-target gene predictions and combined siRNA functional screening data to find the most probable miRNA-target gene pairs with a similar functional effect on proliferation. Nine novel functional miRNAs (hsa-miR-129, -136, -145, -155, -181b, -342-5p, -342-3p, -376a/b) in GBM cell lines were validated for their importance in glioma cell growth, and similar effects for six target genes (ROCK1, RHOA, MET, CSF1R, EIF2AK1, FGF7) of these miRNAs were shown functionally. The clinical significance of the functional hits was validated in miRNA expression data from the TCGA glioblastoma multiforme (GBM) tumor cohort. Five tumor suppressor miRNAs (hsa-miR-136, -145, -342, -129, -376a) showed significant underexpression in clinical GBM tumor samples from the TCGA GBM cohort further supporting the role of these miRNAs in vivo. Most importantly, higher hsa-miR-145 expression in GBM tumors yielded significantly better survival (p<0.005) in a subset of patients thus validating it as a genuine tumor suppressor miRNA. This systematic functional profiling provides important new knowledge about functionally relevant miRNAs in GBM biology and may offer new targets for treating glioma.     

Cryptopatches Are Essential for the Development of Human GALT

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Genes necessary for directed axonal elongation or fasciculation in C. elegans.

The outgrowth of single axons through different cellular environments requires distinct sets of genes in the nematode C. elegans. Three genes are required for the pioneering circumferential outgrowth of identified motor neuron axons between the lateral hypodermal cell membrane and the basal lamina. Three other genes are required for the longitudinal outgrowth of these axons along preexisting axon bundles as well as for the fasciculation of axons within these neuron bundles. Five additional genes are required for circumferential outgrowth, longitudinal outgrowth, and fasciculation; mutations in three of these genes disrupt axon ultrastructure, suggesting that they function in axon formation rather than in axon guidance.     

Neisseria meningitidis Translation Elongation Factor P and Its Active-Site Arginine Residue Are Essential for Cell Viability

Translation elongation factor P (EF-P), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. In Escherichia coli and Salmonella enterica, the post-translational β-lysyl modification of Lys34 of EF-P is important for the EF-P activity. The β-lysyl EF-P modification pathway is conserved among only 26–28% of bacteria. Recently, it was found that the Shewanella oneidensis and Pseudomonas aeruginosa EF-P proteins, containing an Arg residue at position 32, are modified with rhamnose, which is a novel post-translational modification. In these bacteria, EF-P and its Arg modification are both dispensable for cell viability, similar to the E. coli and S. enterica EF-P proteins and their Lys34 modification. However, in the present study, we found that EF-P and Arg32 are essential for the viability of the human pathogen, Neisseria meningitidis. We therefore analyzed the modification of Arg32 in the N. meningitidis EF-P protein, and identified the same rhamnosyl modification as in the S. oneidensis and P. aeruginosa EF-P proteins. N. meningitidis also has the orthologue of the rhamnosyl modification enzyme (EarP) from S. oneidensis and P. aeruginosa. Therefore, EarP should be a promising target for antibacterial drug development specifically against N. meningitidis. The pair of genes encoding N. meningitidis EF-P and EarP suppressed the slow-growth phenotype of the EF-P-deficient mutant of E. coli, indicating that the activity of N. meningitidis rhamnosyl–EF-P for rescuing the stalled ribosomes at proline stretches is similar to that of E. coli β-lysyl–EF-P. The possible reasons for the unique requirement of rhamnosyl–EF-P for N. meningitidis cells are that more proline stretch-containing proteins are essential and/or the basal ribosomal activity to synthesize proline stretch-containing proteins in the absence of EF-P is lower in this bacterium than in others.     

Selenoproteins Are Essential for Proper Keratinocyte Function and Skin Development

Dietary selenium is known to protect skin against UV-induced damage and cancer and its topical application improves skin surface parameters in humans, while selenium deficiency compromises protective antioxidant enzymes in skin. Furthermore, skin and hair abnormalities in humans and rodents may be caused by selenium deficiency, which are overcome by dietary selenium supplementation. Most important biological functions of selenium are attributed to selenoproteins, proteins containing selenium in the form of the amino acid, selenocysteine (Sec). Sec insertion into proteins depends on Sec tRNA; thus, knocking out the Sec tRNA gene (Trsp) ablates selenoprotein expression. We generated mice with targeted removal of selenoproteins in keratin 14 (K14) expressing cells and their differentiated descendents. The knockout progeny had a runt phenotype, developed skin abnormalities and experienced premature death. Lack of selenoproteins in epidermal cells led to the development of hyperplastic epidermis and aberrant hair follicle morphogenesis, accompanied by progressive alopecia after birth. Further analyses revealed that selenoproteins are essential antioxidants in skin and unveiled their role in keratinocyte growth and viability. This study links severe selenoprotein deficiency to abnormalities in skin and hair and provides genetic evidence for the role of these proteins in keratinocyte function and cutaneous development.     

Gtsf1l and Gtsf2 Are Specifically Expressed in Gonocytes and Spermatids but Are Not Essential for Spermatogenesis

The unknown protein family 0224 (UPF0224) includes three members that are expressed in germ-line cells in mice: Gtsf1, Gtsf1l, and {"type":"entrez-nucleotide","attrs":{"text":"BC048502","term_id":"28913420"}}BC048502 (Gtsf2). These genes produce proteins with two repeats of the CHHC Zn-finger domain, a predicted RNA-binding motif, in the N terminus. We previously reported that Gtsf1 is essential for spermatogenesis and retrotransposon suppression. In this study, we investigated the expression patterns and functions of Gtsf1l and Gtsf2. Interestingly, Gtsf1l and Gtsf2 were found to be sequentially but not simultaneously expressed in gonocytes and spermatids. Pull-down experiments showed that both GTSF1L and GTSF2 can interact with PIWI-protein complexes. Nevertheless, knocking out Gtsf1, Gtsf2, or both did not cause defects in spermatogenesis or retrotransposon suppression in mice.     

Small DNA Pieces in C. elegans Are Intermediates of DNA Fragmentation during Apoptosis

While studying small noncoding RNA in C. elegans, we discovered that protocols used for isolation of RNA are contaminated with small DNA pieces. After electrophoresis on a denaturing gel, the DNA fragments appear as a ladder of bands, ∼10 nucleotides apart, mimicking the pattern of nuclease digestion of DNA wrapped around a nucleosome. Here we show that the small DNA pieces are products of the DNA fragmentation that occurs during apoptosis, and correspondingly, are absent in mutant strains incapable of apoptosis. In contrast, the small DNA pieces are present in strains defective for the engulfment process of apoptosis, suggesting they are produced in the dying cell prior to engulfment. While the small DNA pieces are also present in a number of strains with mutations in predicted nucleases, they are undetectable in strains containing mutations in nuc-1, which encodes a DNase II endonuclease. We find that the small DNA pieces can be labeled with terminal deoxynucleotidyltransferase only after phosphatase treatment, as expected if they are products of DNase II cleavage, which generates a 3′ phosphate. Our studies reveal a previously unknown intermediate in the process of apoptotic DNA fragmentation and thus bring us closer to defining this important pathway.     

Methyl Salicylate Production and Jasmonate Signaling Are Not Essential for Systemic Acquired Resistance in Arabidopsis

Systemic acquired resistance (SAR) develops in response to local microbial leaf inoculation and renders the whole plant more resistant to subsequent pathogen infection. Accumulation of salicylic acid (SA) in noninfected plant parts is required for SAR, and methyl salicylate (MeSA) and jasmonate (JA) are proposed to have critical roles during SAR long-distance signaling from inoculated to distant leaves. Here, we address the significance of MeSA and JA during SAR development in Arabidopsis thaliana. MeSA production increases in leaves inoculated with the SAR-inducing bacterial pathogen Pseudomonas syringae; however, most MeSA is emitted into the atmosphere, and only small amounts are retained. We show that in several Arabidopsis defense mutants, the abilities to produce MeSA and to establish SAR do not coincide. T-DNA insertion lines defective in expression of a pathogen-responsive SA methyltransferase gene are completely devoid of induced MeSA production but increase systemic SA levels and develop SAR upon local P. syringae inoculation. Therefore, MeSA is dispensable for SAR in Arabidopsis, and SA accumulation in distant leaves appears to occur by de novo synthesis via isochorismate synthase. We show that MeSA production induced by P. syringae depends on the JA pathway but that JA biosynthesis or downstream signaling is not required for SAR. In compatible interactions, MeSA production depends on the P. syringae virulence factor coronatine, suggesting that the phytopathogen uses coronatine-mediated volatilization of MeSA from leaves to attenuate the SA-based defense pathway.