A developmental view of microRNA function

MicroRNAs (miRNAs) are genomically encoded small non-coding RNAs that regulate flow of genetic information by controlling translation or stability of mRNAs. Recent recognition that many miRNAs are expressed in a tissue-specific manner during development of organisms, from worms to humans, has revealed a novel mechanism by which the proteome is regulated during the dynamic events of cell-lineage decisions and morphogenesis. Advances in the understanding of miRNA biogenesis, target recognition and participation in regulatory networks demonstrate a role for miRNAs in lineage decisions of progenitor cells and organogenesis. Future discoveries in this area are likely to reveal developmental-regulation and disease mechanisms related to miRNAs.     

Depletion of acyl-coenzyme A-binding protein affects sphingolipid synthesis and causes vesicle accumulation and membrane defects in Saccharomyces cerevisiae

Deletion of the yeast gene ACB1 encoding Acb1p, the yeast homologue of the acyl-CoA-binding protein (ACBP), resulted in a slower growing phenotype that adapted into a faster growing phenotype with a frequency >1:10(5). A conditional knockout strain (Y700pGAL1-ACB1) with the ACB1 gene under control of the GAL1 promoter exhibited an altered acyl-CoA profile with a threefold increase in the relative content of C18:0-CoA, without affecting total acyl-CoA level as previously reported for an adapted acb1Delta strain. Depletion of Acb1p did not affect the general phospholipid pattern, the rate of phospholipid synthesis, or the turnover of individual phospholipid classes, indicating that Acb1p is not required for general glycerolipid synthesis. In contrast, cells depleted for Acb1p showed a dramatically reduced content of C26:0 in total fatty acids and the sphingolipid synthesis was reduced by 50-70%. The reduced incorporation of [(3)H]myo-inositol into sphingolipids was due to a reduced incorporation into inositol-phosphoceramide and mannose-inositol-phosphoceramide only, a pattern that is characteristic for cells with aberrant endoplasmic reticulum to Golgi transport. The plasma membrane of the Acb1p-depleted strain contained increased levels of inositol-phosphoceramide and mannose-inositol-phosphoceramide and lysophospholipids. Acb1p-depleted cells accumulated 50- to 60-nm vesicles and autophagocytotic like bodies and showed strongly perturbed plasma membrane structures. The present results strongly suggest that Acb1p plays an important role in fatty acid elongation and membrane assembly and organization.     

Iron nutrition affects cadmium accumulation and toxicity in rice plants

The effect of iron (Fe) nutrition on cadmium (Cd) toxicity and accumulation in rice plants was studied using a hydroponic system. The inhibitory effect of Cd on plant growth and chlorophyll content (SPAD value) was dependent on Fe level and the genotype. Malondialdehyde (MDA) content in leaves and roots was not much affected by an increased Cd stress at 0.171 mg l⁻¹ Fe, but it showed a rapid increase when the plants were exposed to moderate (1.89 mg l⁻¹) and high (16.8 mg l⁻¹) Fe levels. High Fe nutrition caused a marked reduction in Cd content in both leaves and roots. Fe content in plants was lower at high Cd (5.0 μM) stress than at low Cd (<1.0 μM) stress. Cd stress increased both superoxide dismutase (SOD) and peroxidase (POD) activities at low and moderate Fe levels. However, with high Fe level, it increased the POD activity, but reduced the SOD activity. Our results substantiate the hypothesis that cell membrane-bound iron transporter (carrier) involved in high-affinity iron transport systems can also transport Cd, and both these ions may compete for this common carrier. The study further showed that there were significant correlations between MDA and Fe contents in leaves and roots of rice plants. It is suggested that the occurrence of oxidative stress in plants exposed to Cd stress is mediated by Fe nutrition. The present results also show that Cd stress affects the uptake of Cu and Zn.     

Dyrk1A haploinsufficiency affects viability and causes developmental delay and abnormal brain morphology in mice

DYRK1A is the human orthologue of the Drosophila minibrain (mnb) gene, which is involved in postembryonic neurogenesis in flies. Because of its mapping position on chromosome 21 and the neurobehavioral alterations shown by mice overexpressing this gene, involvement of DYRK1A in some of the neurological defects of Down syndrome patients has been suggested. To gain insight into its physiological role, we have generated mice deficient in Dyrk1A function by gene targeting. Dyrk1A(-/-) null mutants presented a general growth delay and died during midgestation. Mice heterozygous for the mutation (Dyrk1A(+/-)) showed decreased neonatal viability and a significant body size reduction from birth to adulthood. General neurobehavioral analysis revealed preweaning developmental delay of Dyrk1A(+/-) mice and specific alterations in adults. Brains of Dyrk1A(+/-) mice were decreased in size in a region-specific manner, although the cytoarchitecture and neuronal components in most areas were not altered. Cell counts showed increased neuronal densities in some brain regions and a specific decrease in the number of neurons in the superior colliculus, which exhibited a significant size reduction. These data provide evidence about the nonredundant, vital role of Dyrk1A and suggest a conserved mode of action that determines normal growth and brain size in both mice and flies.     

Loss of CHD1 causes DNA repair defects and enhances prostate cancer therapeutic responsiveness

The CHD1 gene, encoding the chromo‐domain helicase DNA‐binding protein‐1, is one of the most frequently deleted genes in prostate cancer. Here, we examined the role of CHD1 in DNA double‐strand break (DSB) repair in prostate cancer cells. We show that CHD1 is required for the recruitment of CtIP to chromatin and subsequent end resection during DNA DSB repair. Our data support a role for CHD1 in opening the chromatin around the DSB to facilitate the recruitment of homologous recombination (HR) proteins. Consequently, depletion of CHD1 specifically affects HR‐mediated DNA repair but not non‐homologous end joining. Together, we provide evidence for a previously unknown role of CHD1 in DNA DSB repair via HR and show that CHD1 depletion sensitizes cells to PARP inhibitors, which has potential therapeutic relevance. Our findings suggest that CHD1 deletion, like BRCA1/2 mutation in ovarian cancer, may serve as a marker for prostate cancer patient stratification and the utilization of targeted therapies such as PARP inhibitors, which specifically target tumors with HR defects.     

Loss of BubR1 acetylation causes defects in spindle assembly checkpoint signaling and promotes tumor formation

BubR1 acetylation is essential in mitosis. Mice heterozygous for the acetylation-deficient BubR1 allele (K243R/+) spontaneously developed tumors with massive chromosome missegregations. K243R/+ mouse embryonic fibroblasts (MEFs) exhibited a weakened spindle assembly checkpoint (SAC) with shortened mitotic timing. The generation of the SAC signal was intact, as Mad2 localization to the unattached kinetochore (KT) was unaltered; however, because of the premature degradation of K243R-BubR1, the mitotic checkpoint complex disassociated prematurely in the nocodazole-treated condition, suggesting that maintenance of the SAC is compromised. BubR1 acetylation was also required to counteract excessive Aurora B activity at the KT for stable chromosome–spindle attachments. The association of acetylation-deficient BubR1 with PP2A-B56α phosphatase was reduced, and the phosphorylated Ndc80 at the KT was elevated in K243R/+ MEFs. In relation, there was a marked increase of micronuclei and p53 mutation was frequently detected in primary tumors of K243R/+ mice. Collectively, the combined effects of failure in chromosome–spindle attachment and weakened SAC cause genetic instability and cancer in K243R/+ mice.     

Loss of glypican-3 function causes growth factor-dependent defects in cardiac and coronary vascular development

Glypican-3 (Gpc3) is a heparan sulfate proteoglycan (HSPG) expressed widely during vertebrate development. Loss-of-function mutations cause Simpson-Golabi-Behmel syndrome (SGBS), a rare and complex congenital overgrowth syndrome with a number of associated developmental abnormalities including congenital heart disease. We found that Gpc3-deficient mice display a high incidence of congenital cardiac malformations like ventricular septal defects, common atrioventricular canal and double outlet right ventricle. In addition we observed coronary artery fistulas, which have not been previously reported in SGBS. Coronary artery fistulas are noteworthy because little is known about the molecular basis of this abnormality. Formation of the coronary vascular plexus in Gpc3-deficient embryos was delayed compared to wild-type, and consistent with GPC3 functioning as a co-receptor for fibroblast growth factor-9 (FGF9), we found a reduction in Sonic Hedgehog (Shh) mRNA expression and signaling in embryonic mutant hearts. Interestingly, we found an asymmetric reduction in SHH signaling in cardiac myocytes, as compared with perivascular cells, resulting in excessive coronary artery formation in the Gpc3-deficient animals. We hypothesize that the excessive development of coronary arteries over veins enables the formation of coronary artery fistulas. This work has broad significance to understanding the genetic basis of coronary development and potentially to molecular mechanisms relevant to revascularization following ischemic injury to the heart.     

Salmonella Typhimurium infection causes defects and fastening of Caenorhabditis elegans developmental stages

Salmonella infection is known to cause a 50% reduction in the lifespan of Caenorhabditis elegans. But the mechanism behind this reduction is not reported. The current study deals with the Salmonella infection mediated egg retention in the worm leading to various developmental and morphological defects and disruption of temporal regulation of developmental timing in C. elegans. Worm’s delayed egg-laying response to Salmonella infection causes several defects in eggs, including over-folding of developing embryo, increased egg size, and losing the osmotic stress resistance. Also, the infected eggs show delayed and reduced hatching. With significantly downregulated lin-28a, col-72 and col-87, we observed a disrupted L2, but L3, L4, and adult developmental stages reach faster during infection. The precocious development of L3, L4, and the adult stage is further indicated by upregulation of stage-specific genes viz. rnh-1.3, col-158 and col-176 (L3), col-17, col-38 and col-49 (L4), and col-19, col-7 (adult). The significant upregulation of the flp-1 gene indicates reduced egglaying, and the flp-1(ok2811) null mutant further supported the Salmonella infectionmediated phenotype. Similar phenotypes are primarily evident in multiple generations up to F5 and F6. Salmonella infection causes a range of developmental anomalies and shortening of worm life span through various regulatory pathways.     

Loss of membrane targeting of Vangl proteins causes neural tube defects

In the mouse, the loop-tail mutation (Lp) causes a very severe neural tube defect, which is caused by mutations in the Vangl2 gene. In mammals, Vangl1 and Vangl2 code for integral membrane proteins that assemble into asymmetrically distributed membrane complexes that establish planar cell polarity in epithelial cells and that regulate convergent extension movements during embryogenesis. To date, VANGL are the only genes in which mutations cause neural tube defects in humans. Three independently arising Lp alleles have been described for Vangl2: D255E, S464N, and R259L. Here we report a common mechanism for both the naturally occurring Lp (S464N) and a novel ENU-induced mutation Lp(m2Jus)(R259L). We show that the S464N and R259L variants stably expressed in polarized MDCK kidney cells fail to reach the plasma membrane, their site for biological function. The mutant variants are retained intracellularly in the endoplasmic reticulum, colocalizing with ER chaperone calreticulin. Furthermore, the mutants also show a dramatically reduced half-life of ～3 h, compared to ～22 h for the wild-type protein, and are rapidly degraded in a proteasome-dependent and MG132-sensitive fashion. Coexpressing individually the three known allelic Lp variants with the wild-type protein does not influence the localization of the WT at the plasma membrane, suggesting that the codominant nature of the Lp trait in vivo is due to haploid insufficiency caused by a partial loss of function in a gene dosage-dependent pathway, as opposed to a dominant negative phenotype. Our study provides a biochemical framework for the study of recently identified mutations in hVANGL1 and hVANGL2 in sporadic or familial cases of neural tube defects.     

The Aspergillus nidulans bncA1 mutation causes defects in the cell division cycle, nuclear movement and developmental morphogenesis

Wild-type Aspergillus nidulans conidia are uninucleate. The mutation bncA1 (binucleated conidia) was first described as a single mutation located on chromosome IV that caused formation of approximately 25% binucleate and 1% trinucleate conidia. In this study, we show that bncA1 conidia exit G1 arrest earlier than the wild type. Germlings have hyphal elements with abnormal morphology, elevated numbers of randomly distributed nuclei and an irregular septation pattern. Older hyphal elements undergo mitotic catastrophe, suggesting the nuclear division cycle of internal (nonterminal) elements is not arrested. The bncA1 mutation also causes aberrant morphogenesis of the asexual reproductive structure, the conidiophore. Metulae and phialides are elongated and have incorrect numbers of nuclei. Phialides also have internal septation that appears to delineate hyphal-like elements. Heterokaryon analysis using strains with contrasting auxotrophic markers showed that the bncA1 mutation resulted in a higher frequency of diploid and multinucleated prototrophic conidia than control heterokaryons. These results suggest that in bncA1 strains multiple nuclei can move from the conidiophore vesicle to the metulae and/or from the phialide to the conidium. The bncA1 mutant also showed hypersensitivity to the anti-microtubule drugs thiabendazole and nocodazole, which is consistent with the defects in cell cycle regulation and nuclear movement. We propose that bncA has an important role in correctly regulating both the cell division cycle and nuclear movement.     

DFMO feeding lowers polyamine levels and causes developmental defects in the silkworm Bombyx mori

The domesticated silkworm Bombyx mori is an economically important insect that produces large quantities of silk during its 5th instar larval stage. Polyamines are important regulators of growth and have been shown to affect silk production, however their role in larval development is not completely understood. L-ornithine decarboxylase (ODC), a key regulatory enzyme in the polyamine biosynthetic pathway catalyzes the conversion of ornithine to putrescine, which is further broken down to spermidine and spermine. In this study, we set out to understand the role of ODC on the growth and development of silkworm larvae. We fed 5th instar larvae with α-difluoromethylornithine (DFMO), an ODC inhibitor and studied its impact on larval silk glands. Feeding DFMO did not alter the expression of L-ODC but led to a significant reduction in putrescine and spermidine levels. Furthermore, reduced cellular levels of polyamine led to increased oxidative stress and decreased cell viability. Subsequently, this resulted in several developmental defects at the pupal and moth stages. These findings highlight the importance of ODC in the growth and development of B. mori larvae.