Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines

In Drosophila, the PIWI proteins, Aubergine (Aub), AGO3, and Piwi are expressed in germlines and function in silencing transposons by associating with PIWI‐interacting RNAs (piRNAs). Recent studies show that PIWI proteins contain symmetric dimethyl‐arginines (sDMAs) and that dPRMT5/Capsuleen/DART5 is the modifying enzyme. Here, we show that Tudor (Tud), one of Tud domain‐containing proteins, associates with Aub and AGO3, specifically through their sDMA modifications and that these three proteins form heteromeric complexes. piRNA precursor‐like molecules are detected in these complexes. The expression levels of Aub and AGO3, along with their degree of sDMA modification, were not changed by tud mutations. However, the population of transposon‐derived piRNAs associated with Aub and AGO3 was altered by tud mutations, whereas the total amounts of small RNAs on Aub and AGO3 was increased. Loss of dprmt5 did not change the stability of Aub, but impaired its association with Tud and lowered piRNA association with Aub. Thus, in germline cells, piRNAs are quality‐controlled by dPRMT5 that modifies PIWI proteins, in tight association with Tud.     

Faunal turnover at the end of the Cretaceous in the North Pacific region: Implications from combined magnetostratigraphy and biostratigraphy of the Maastrichtian Senpohshi Formation in the eastern Hokkaido Island,northern Japan

A combined magnetostratigraphic and biostratigraphic study has been performed on the Maastrichtian Senpohshi Formation in eastern Hokkaido Island, northern Japan, which is an approximately 1300 m thick section mainly composed of hemipelagic mudstone. The identification of magnetic polarity was possible at 51 horizons, whereby four magnetozones were recognized. These magnetozones were correlatable to geomagnetic polarity chrons C31r to C30n, suggesting that the age of the Senpohshi Formation is spanning from middle to upper part of the Maastrichtian (ca. 69–67 Ma).The magnetostratigraphy of the Senpohshi Formation established in this study enables a direct age correlation to the Maastrichtian successions in other regions. Thus, this detailed chronology of the formation contributes to paleontological studies of the Maastrichtian in the North Pacific region. For instance, this magnetostratigraphic age assessment implies the following: (1) the stratigraphic range of the ammonite Pachydiscus flexuosus contains polarity chrons from the lower part of C31r to the lower part of C31n, (2) the first occurrence (FO) of the calcareous nannofossil Nephrolithus frequens in the North Pacific region is correlatable to polarity chron C30n or below, and (3) the FO of the bivalve “Inoceramus” awajiensis is located within polarity chrons from C31r to the upper part of C31n. This suggests that the inoceramid extinction event in the North Pacific region might have occurred during polarity chrons from C31r to the upper part of C31n (ca. 70.5–67.8 Ma), which is 2.3–5.0 Myr prior to the Cretaceous/Paleogene boundary. The trend of the Maastrichtian faunal turnover in the North Pacific is well consistent with those of other regions, brings a new evidence for understanding the global faunal turnover in the Maastrichtian, just before Cretaceous/Paleogene mass extinction.     

Autophagy Is Enhanced and Floral Development Is Impaired in AtHVA22d RNA Interference Arabidopsis

Autophagy is an intracellular process in which a portion of cytoplasm is transported into vacuoles for recycling. Physiological roles of autophagy in plants include recycling nutrients during senescence, sustaining life during starvation, and the formation of central digestive vacuoles. The regulation of autophagy and the formation of autophagosomes, spherical double membrane structures containing cytoplasm moving toward vacuoles, are poorly understood. HVA22 is a gene originally cloned from barley (Hordeum vulgare), which is highly induced by abscisic acid and environmental stress. Homologs of HVA22 include Yop1 in yeast, TB2/DP1 in human, and AtHVA22a to -e in Arabidopsis (Arabidopsis thaliana). Reverse genetics followed by a cell biology approach were employed to study the function of HVA22 homologs. The AtHVA22d RNA interference (RNAi) Arabidopsis plants produced small siliques with reduced seed yield. This phenotype cosegregated with the RNAi transgene. Causes of the reduced seed yield include short filaments, defective carpels, and dysfunctional pollen grains. Enhanced autophagy was observed in the filament cells. The number of autophagosomes in root tips of RNAi plants was also increased dramatically. The yop1 deletion mutant of Saccharomyces cerevisiae was used to verify our hypothesis that HVA22 homologs are suppressors of autophagy. Autophagy activity of this mutant during nitrogen starvation increased in 5 min and reached a plateau after 2 h, with about 80% of cells showing autophagy, while the wild-type cells exhibited low levels of autophagy following 8 h of nitrogen starvation. We conclude that HVA22 homologs function as suppressors of autophagy in both plants and yeast. Potential mechanisms of this suppression and the roles of abscisic acid-induced HVA22 expression in vegetative and reproductive tissues are discussed.     

A Nonsense Mutation in a Cinnamyl Alcohol Dehydrogenase Gene Is Responsible for the Sorghum brown midrib6 Phenotype

brown midrib6 (bmr6) affects phenylpropanoid metabolism, resulting in reduced lignin concentrations and altered lignin composition in sorghum (Sorghum bicolor). Recently, bmr6 plants were shown to have limited cinnamyl alcohol dehydrogenase activity (CAD; EC 1.1.1.195), the enzyme that catalyzes the conversion of hydroxycinnamoyl aldehydes (monolignals) to monolignols. A candidate gene approach was taken to identify Bmr6. Two CAD genes (Sb02g024190 and Sb04g005950) were identified in the sorghum genome based on similarity to known CAD genes and through DNA sequencing a nonsense mutation was discovered in Sb04g005950 that results in a truncated protein lacking the NADPH-binding and C-terminal catalytic domains. Immunoblotting confirmed that the Bmr6 protein was absent in protein extracts from bmr6 plants. Phylogenetic analysis indicated that Bmr6 is a member of an evolutionarily conserved group of CAD proteins, which function in lignin biosynthesis. In addition, Bmr6 is distinct from the other CAD-like proteins in sorghum, including SbCAD4 (Sb02g024190). Although both Bmr6 and SbCAD4 are expressed in sorghum internodes, an examination of enzymatic activity of recombinant Bmr6 and SbCAD4 showed that Bmr6 had 1 to 2 orders of magnitude greater activity for monolignol substrates. Modeling of Bmr6 and SbCAD4 protein structures showed differences in the amino acid composition of the active site that could explain the difference in enzyme activity. These differences include His-57, which is unique to Bmr6 and other grass CADs. In summary, Bmr6 encodes the major CAD protein involved in lignin synthesis in sorghum, and the bmr6 mutant is a null allele.Plant cell walls constitute a vast reserve of fixed carbon. Cellulose and lignin are the first and second most abundant polymers on the planet, respectively (Jung and Ni, 1998). The world community has started to look to biomass as substrates for plant-based biologically sustainable fuels, which would mitigate carbon dioxide emission and reduce petroleum dependence (Sarath et al., 2008; Schmer et al., 2008). In the current generation of biofuels, ethanol is being synthesized via the fermentation of grain starch or sugarcane juice. For the next generation of biofuels, research is being directed toward the conversion of lignocellulosic biomass into biofuels (Chang, 2007). As bioenergy technologies progress, the conversion of biomass to biofuels could involve a range of chemical, biochemical, and fermentation processes to produce biofuels; alternate biofuels, such as butanol or dimethylfuran, are also on the horizon (Ezeji et al., 2007; Roman-Leshkov et al., 2007). Most liquid biofuel production processes will likely rely on the conversion of the cell wall polysaccharides cellulose and hemicellulose into monomeric sugars.Plant cell walls consist of a complex polysaccharide moiety composed of cellulose microfibrils, composed of β-1,4-linked Glc polymers (Carpita and McCann, 2000). Connecting the cellulose microfibrils to each other is a hemicellulose network, whose structure and composition are species dependent, and which is mainly composed of glucuronoarabinoxylans in grasses (Carpita and McCann, 2000). Lignin, a nonlinear heterogeneous polymer derived from aromatic precursors, cross-links these polysaccharides, rigidifying and reinforcing the cell wall structure (Carpita and McCann, 2000). The addition of lignin polymers to the polysaccharide matrix creates a barrier that is chemically and microbially resistant.Lignin can block the liberation of sugars from the cell wall polysaccharide moieties, release compounds that can inhibit microbes used for fermenting sugars to fuels, and adhere to hydrolytic enzymes. Understanding lignin synthesis, structure, and function to increase cell wall digestibility has long been a goal for forage improvement and paper processing (Mackay et al., 1997; Jung and Ni, 1998). Recently, manipulating lignin has also become an important target for bioenergy feedstock improvement (Chen and Dixon, 2007; Li et al., 2008).Lignin is derived from the phenylpropanoid pathway and contains primarily three types of phenolic subunits: p-hydroxyphenyl, guaiacyl, and syringyl units (Dixon et al., 2001). The phenolic aldehyde precursors are reduced into their corresponding alcohols (monolignols) and subsequently transported to the cell wall (Fig. 1), where laccases and peroxidases catalyze lignin polymerization through the formation of monolignol radicals (Boerjan et al., 2003). Therefore, most research efforts to manipulate lignin have focused on biosynthesis of the monolignols. Most of the enzymes involved in monolignol synthesis have been cloned and characterized in Arabidopsis (Arabidopsis thaliana) and other dicot species, using both mutagenic and transgenic approaches to study the impact of these gene products on dicot cell walls (Anterola and Lewis, 2002). However, there are significant differences in the architecture, polysaccharide composition, and phenylpropanoid composition of grass cell walls compared with those of dicots (Carpita and McCann, 2000; Vogel and Jung, 2001). For example, grasses contain significant amounts of p-coumaric acid and ferulic acid that are cross-linked to cell wall polysaccharides through ester and ether linkages in addition to their presence in lignin (Grabber et al., 1991; Boerjan et al., 2003). Because many of the proposed dedicated bioenergy crops are grasses, there is a need to identify and understand the function of the gene products involved in lignin biosynthesis in these species (Vermerris et al., 2007; Li et al., 2008; Sarath et al., 2008).Open in a separate windowFigure 1.The CAD enzyme and its role in the monolignol biosynthetic pathway. A, CAD catalyzes the conversion of cinnamyl aldehydes to alcohols using NADPH as its cofactor. p-Coumaryl aldehyde and alcohol, R₁ and R₂ = H; caffeoyl aldehyde and alcohol, R₁ and R₂ = OH; coniferyl aldehyde and alcohol, R₁ = H and R₂ = OCH₃; sinapyl aldehyde and alcohol, R₁ and R₂ = OCH₃. B, A simplified model of the lignin biosynthetic pathway where CAD catalyzes the final step in monolignol biosynthesis.The brown midrib phenotype has been useful for identifying mutants affecting lignin synthesis in grasses because it is a visible phenotype. Spontaneous brown midrib mutants were first discovered in maize (Zea mays; Jorgenson, 1931) and were subsequently generated in sorghum (Sorghum bicolor) using diethyl sulfate mutagenesis (Porter et al., 1978). Brown midrib mutants in maize, sorghum, and pearl millet (Pennisetum glaucum) have increased forage digestibility for livestock (Cherney et al., 1990; Akin et al., 1993; Jung et al., 1998; Oliver et al., 2004). In maize and sorghum, there are at least four brown midrib loci in their respective genomes (Jorgenson, 1931; Porter et al., 1978; Gupta, 1995). The genes encoding bm3 in maize and bmr12 in sorghum are the only loci cloned to date, and both encode highly similar caffeic acid O-methyl transferases (Vignols et al., 1995; Bout and Vermerris, 2003). A second brown midrib locus associated with reduced cinnamyl alcohol dehydrogenase (CAD) activity has been identified both in maize (bm1; Halpin et al., 1998) and sorghum (bmr6; Bucholtz et al., 1980; Pillonel et al., 1991). CAD is a member of the alcohol dehydrogenase superfamily of proteins that catalyzes the conversion of the hydroxycinnamoyl aldehydes into alcohols prior to their incorporation into lignin polymers (Fig. 1). Reduced CAD activity results in increased digestibility on dry weight basis, altered cell wall architecture, reduced lignin level, and the incorporation of phenolic aldehydes into lignin in sorghum and maize (Pillonel et al., 1991; Provan et al., 1997; Halpin et al., 1998; Marita et al., 2003; Shi et al., 2006; Palmer et al., 2008). The reduced CAD activity in bm1 has been genetically mapped to a region of the maize genome that contained a CAD gene, ZmCAD2 (Halpin et al., 1998), but a mutation was not identified. However, it has recently been shown that bm1 down-regulated the expression of several lignin biosynthetic genes, suggesting its gene product may be a regulatory protein (Shi et al., 2006; Guillaumie et al., 2007).To identify the mutation responsible for the bmr6 phenotype and to characterize how bmr6 impacts the lignin biosynthetic pathway, a candidate gene approach was taken. Here, we describe the cloning and characterization of Bmr6 and a related protein, SbCAD4. The identification and characterization of Bmr6 has revealed the major monolignol CAD protein in the grasses, which is likely to aid the development of new strategies to increase conversion of sorghum and other grass feedstocks to biofuels.     

Hypoxia rescues early mortality conferred by superoxide dismutase deficiency

Oxidative stress is widely associated with disease and aging but the underlying mechanisms are incompletely understood. Here we show that the premature mortality of Drosophila deficient in superoxide scavengers, superoxide dismutase (SOD) 1 or SOD2, is rescued by chronic hypoxia. Strikingly, switching moribund SOD2-deficient adults from normoxia into hypoxia abruptly arrests their impending premature mortality and endows the survivors with a near-normal life span. This finding challenges the notion that irreversible oxidative damage initiated by unscavenged superoxide in the mitochondrial matrix underpins the premature mortality of SOD2-deficient adults. In contrast, switching moribund SOD1-deficient flies from normoxia into hypoxia fails to alter their mortality trajectory, suggesting that the deleterious effects of unscavenged superoxide in the cytoplasm/intermembrane space compartment are cumulative and largely irreversible. We conclude that cellular responses to superoxide-initiated oxidative stress are mediated through different compartment-specific pathways. Elucidating these pathways should provide novel insights into how aerobic cells manage oxidative stress in health, aging, and disease.     

The rapid activation of N-Ras by α-thrombin in fibroblasts is mediated by the specific G-protein Gαi2–Gβ1–Gγ5 and occurs in lipid rafts

α-thrombin is a potent mitogen for fibroblasts and initiates a rapid signal transduction pathway leading to the activation of Ras and the stimulation of cell cycle progression. While the signaling events downstream of Ras have been studied in significant detail and appear well conserved across many species and cell types, the precise molecular events beginning with thrombin receptor activation and leading to the activation of Ras are not as well understood. In this study, we examined the immediate events in the rapid response to α-thrombin, in a single cell type, and found that an unexpected degree of specificity exists in the pathway linking α-thrombin to Ras activation. Specifically, although IIC9 cells express all three Ras isoforms, only N-Ras is rapidly activated by α-thrombin. Further, although several Gα subunits associate with PAR1 and are released following stimulation, only Gα_i2 couples to the rapid activation of Ras. Similarly, although IIC9 cells express many Gβ and Gγ subunits, only a subset associates with Gα_i2, and of those, only a single Gβγ dimer, Gβ₁γ₅, participates in the rapid activation of N-Ras. We then hypothesized that co-localization into membrane microdomains called lipid rafts, or caveolae, is at least partially responsible for this degree of specificity. Accordingly, we found that all components localize to lipid rafts and that disruption of caveolae abolishes the rapid activation of N-Ras by α-thrombin. We thus report the molecular elucidation of an extremely specific and rapid signal transduction pathway linking α-thrombin stimulation to the activation of Ras.     

Relative importance of climate vs local factors in shaping the regional patterns of forest plant richness across northeast China

Northeast (NE) China covers three climatic zones and contains all the major forest types of NE Asia. We sampled 108 forest plots in six nature reserves across NE China to examine the influence of climate and local factors (canopy seasonality, successional stage, topography and forest structure) on geographic patterns of plant richness. We analyzed the relative effects of different factors at two spatial scales: the regional scale (across both latitude and altitude) and the local scale (along the altitudinal gradient within site). Our results showed that the relative importance of climate vs local factors differed remarkably depending on scale and functional group. While total and tree species richness were mainly limited by climate, herb and shrub richness was more related to local factors (especially at the local scale). In the climatic factors, heat sum was the major correlate of tree, shrub and total species richness, while herb richness was more associated with winter coldness. Precipitation was not a limiting factor for forest plant richness in NE China. Climate accounted for 34–76% of variation in richness at the regional scale, but explained only 0–44% at the local scale. Among the local factors, shrub species richness was sensitive to seasonal canopy openness, with higher richness in deciduous forests than in the evergreen needle-leaf forest. On the other hand, herb richness was sensitive to forest successional stage, with higher richness in middle- successional forests than in the early and late-sucessional forests. Local topography (aspect and position on slope) and forest structure (tree density) also showed remarkable influence on species richness. Our results suggest the importance of including local factors when examining large scale diversity gradient (especially for understory species), and the necessity of comparing diversity patterns among functional groups at different spatial scales.     

Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas

Zebrafish provide a highly versatile model in which to study vertebrate development. Many recent studies have elucidated early events in the organogenesis of the zebrafish pancreas; however, several aspects of early endocrine pancreas formation in the zebrafish are not homologous to the mammalian system. To better identify mechanisms of islet formation in the zebrafish, with true homology to those observed in mammals, we have temporally and spatially characterized zebrafish secondary islet formation. As is the case in the mouse, we show that Notch inhibition leads to precocious differentiation of endocrine tissues. Furthermore, we have used transgenic fish expressing fluorescent markers under the control of a Notch-responsive element to observe the precursors of these induced endocrine cells. These pancreatic Notch-responsive cells represent a novel population of putative progenitors that are associated with larval pancreatic ductal epithelium, suggesting functional homology between secondary islet formation in zebrafish and the secondary transition in mammals. We also show that Notch-responsive cells persist in the adult pancreas and possess the classical characteristics of centroacinar cells, a cell type believed to be a multipotent progenitor cell in adult mammalian pancreas.     

Genetic interaction between Bmp2 and Bmp4 reveals shared functions during multiple aspects of mouse organogenesis

Vertebrate Bmp2 and Bmp4 diverged from a common ancestral gene and encode closely related proteins. Mice homozygous for null mutations in either gene show early embryonic lethality, thereby precluding analysis of shared functions. In the current studies, we present phenotypic analysis of compound mutant mice heterozygous for a null allele of Bmp2 in combination with null or hypomorphic alleles of Bmp4. Whereas mice lacking a single copy of Bmp2 or Bmp4 are viable and have subtle developmental defects, compound mutants show embryonic and postnatal lethality due to defects in multiple organ systems including the allantois, placental vasculature, ventral body wall, skeleton, eye and heart. Within the heart, BMP2 and BMP4 function coordinately to direct normal lengthening of the outflow tract, proper positioning of the outflow vessels, and septation of the atria, ventricle and atrioventricular canal. Our results identify numerous BMP4-dependent developmental processes that are also very sensitive to BMP2 dosage, thus revealing novel functions of Bmp2.