Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.     

The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)

This paper describes the genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood-Ljungdahl pathway of CO and CO(2) fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into 3 mol of acetate and to grow autotrophically using H(2) and CO as electron donors and CO(2) as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO(2). Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols and aromatic compounds) and electron acceptors (CO(2), nitrate, nitrite, thiosulfate, dimethylsulfoxide and aromatic carboxyl groups). The genome consists of a single circular 2 628 784 bp chromosome encoding 2615 open reading frames (ORFs), which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. A total of 2384 (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in orthologue clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.     

Climate change,boundary increase and elongation of a pre‐existing cline: A case study in Drosophila ananassae

During the past two to three decades, Drosophila ananassae, a warm adapted tropical species, has invaded low to mid altitude localities in the western Himalayas. Due to its cold sensitivity, this species had never been recorded from higher latitudes as well as altitudes in India to the 1960s. A latitudinal cline in this desiccation‐sensitive species corresponds with southern humid tropical localities rather than northern drier subtropical localities. An extension of its cline into lowland to midland montane localities has resulted due to global climatic change as well as local thermal effects through anthropogenic impact. However, D. ananassae populations at species borders are characterized by lower genetic variability for body melanization as well as for desiccation resistance. There is a lack of thermal plastic effects for body melanization, and the observed extended cline might represent evolutionary (genetic) response due to selection pressure imposed by drier habitats. A comparison of fecundity, hatchability and viability at three growth temperatures (17, 20 and 25°C) showed significant reduction in trait values at 17°C in D. ananassae. Thus, its recent range expansion into northern montane localities might involve genetic effects on stress‐related traits and plastic effects on life history traits. We suggest that D. ananassae could serve as an indicator species for analyzing range expansion under changing climatic conditions.     

Body melanization and its adaptive role in thermoregulation and tolerance against desiccating conditions in drosophilids

Melanism seems to have evolved independently through diverse mechanisms in various taxa and different ecological factors could be responsible for selective responses. Increased body melanization at higher altitudes as well as latitudes is generally considered to be adaptive for thermoregulation. Physiological traits such as body melanization and desiccation resistance have been investigated independently in diverse insect taxa at three levels: within populations, between populations and among species. A substantial number of Drosophila studies have reported clinal variations in both these traits along latitude. A possible link between these traits had remained unexplored in wild and laboratory populations of ectothermic insect taxa, including drosophilids, to date. Simultaneous analysis of these traits in assorted darker and lighter phenotypes in each population in the present study showed parallel changes for body melanization and desiccation resistance. The mechanistic basis of evolving desiccation resistance was explained on the basis of differential rates of water loss per hour in darker versus lighter phenotypes in six populations of Drosophila melanogaster from adjacent localities differing substantially in altitude all along the Indian subcontinent. Data on cuticular impermeability suggest a possible role of melanization in desiccation tolerance. However, substantial gaps remain in extending these results to other insect taxa and further exploring the physiological and molecular changes involved in melanization for conferring desiccation resistance.     

Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity

Glucose ingestion after an overnight fast triggers an insulin‐dependent, homeostatic program that is altered in diabetes. The full spectrum of biochemical changes associated with this transition is currently unknown. We have developed a mass spectrometry‐based strategy to simultaneously measure 191 metabolites following glucose ingestion. In two groups of healthy individuals (n=22 and 25), 18 plasma metabolites changed reproducibly, including bile acids, urea cycle intermediates, and purine degradation products, none of which were previously linked to glucose homeostasis. The metabolite dynamics also revealed insulin's known actions along four key axes—proteolysis, lipolysis, ketogenesis, and glycolysis—reflecting a switch from catabolism to anabolism. In pre‐diabetics (n=25), we observed a blunted response in all four axes that correlated with insulin resistance. Multivariate analysis revealed that declines in glycerol and leucine/isoleucine (markers of lipolysis and proteolysis, respectively) jointly provide the strongest predictor of insulin sensitivity. This observation indicates that some humans are selectively resistant to insulin's suppression of proteolysis, whereas others, to insulin's suppression of lipolysis. Our findings lay the groundwork for using metabolic profiling to define an individual's ‘insulin response profile’, which could have value in predicting diabetes, its complications, and in guiding therapy.     

Changes in cuticular lipids, water loss and desiccation resistance in a tropical drosophilid: analysis of variation between and within populations

We investigated within as well as between population variability in desiccation resistance, cuticular lipid mass per fly and cuticular water loss in nine geographical populations of a tropical drosophilid, Zaprionus indianus. Interestingly, the amount of cuticular lipids and desiccation resistance in this non-melanic species are significantly higher as compared with melanic Drosophila melanogaster. On the basis of isofemale line analysis, within population trait variability in cuticular lipid mass per fly is positively correlated with desiccation resistance and negatively correlated with cuticular water loss but show lack of correlation with body size. We observed geographical variation in the amount of cuticular lipid mass per fly in Zaprionus indianus but no such divergence was found in D.melanogaster. In both the species, geographical variations in desiccation resistance are negatively correlated with cuticular water loss but the underlying mechanisms for changes in cuticular permeability are quite different. Thus, we may suggest that body melanisation and cuticular lipids may represent alternative strategies for coping with dehydration stress in melanic versus non-melanic drosophilids. For both the species, desiccation resistance and cuticular water loss are correlated with regular increase in aridity in the northern subtropical localities as compared with southern peninsular humid tropical localities. The role of climatic selection is evident from multiple regression analysis with seasonal changes in temperature and humidity (Tcv and RHcv) of the sites of origin of populations of Zaprionus indianus along latitude.     

ADIPOQ/adiponectin induces cytotoxic autophagy in breast cancer cells through STK11/LKB1-mediated activation of the AMPK-ULK1 axis

ADIPOQ/adiponectin, an adipocytokine secreted by adipocytes in the breast tumor microenvironment, negatively regulates cancer cell growth hence increased levels of ADIPOQ/adiponectin are associated with decreased breast cancer growth. However, its mechanisms of action remain largely elusive. We report that ADIPOQ/adiponectin induces a robust accumulation of autophagosomes, increases MAP1LC3B-II/LC3B-II and decreases SQSTM1/p62 in breast cancer cells. ADIPOQ/adiponectin-treated cells and xenografts exhibit increased expression of autophagy-related proteins. LysoTracker Red-staining and tandem-mCherry-GFP-LC3B assay show that fusion of autophagosomes and lysosomes is augmented upon ADIPOQ/adiponectin treatment. ADIPOQ/adiponectin significantly inhibits breast cancer growth and induces apoptosis both in vitro and in vivo, and these events are preceded by macroautophagy/autophagy, which is integral for ADIPOQ/adiponectin-mediated cell death. Accordingly, blunting autophagosome formation, blocking autophagosome-lysosome fusion or genetic-knockout of BECN1/Beclin1 and ATG7 effectively impedes ADIPOQ/adiponectin induced growth-inhibition and apoptosis-induction. Mechanistic studies show that ADIPOQ/adiponectin reduces intracellular ATP levels and increases PRKAA1 phosphorylation leading to ULK1 activation. AMPK-inhibition abrogates ADIPOQ/adiponectin-induced ULK1-activation, LC3B-turnover and SQSTM1/p62-degradation while AMPK-activation potentiates ADIPOQ/adiponectin's effects. Further, ADIPOQ/adiponectin-mediated AMPK-activation and autophagy-induction are regulated by upstream master-kinase STK11/LKB1, which is a key node in antitumor function of ADIPOQ/adiponectin as STK11/LKB1-knockout abrogates ADIPOQ/adiponectin-mediated inhibition of breast tumorigenesis and molecular analyses of tumors corroborate in vitro mechanistic findings. ADIPOQ/adiponectin increases the efficacy of chemotherapeutic agents. Notably, high expression of ADIPOQ receptor ADIPOR2, ADIPOQ/adiponectin and BECN1 significantly correlates with increased overall survival in chemotherapy-treated breast cancer patients. Collectively, these data uncover that ADIPOQ/adiponectin induces autophagic cell death in breast cancer and provide in vitro and in vivo evidence for the integral role of STK11/LKB1-AMPK-ULK1 axis in ADIPOQ/adiponectin-mediated cytotoxic autophagy.     

High Resolution X-ray Diffraction Dataset for <Emphasis Type="Italic">Bacillus licheniformis</Emphasis> Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility

Gamma glutamyl transpeptidase, (GGT) is a ubiquitous protein which plays a central role in glutathione metabolism and has myriad clinical implications. It has been shown to be a virulence factor for pathogenic bacteria, inhibition of which results in reduced colonization potential. However, existing inhibitors are effective but toxic and therefore search is on for novel inhibitors, which makes it imperative to understand the interactions of various inhibitors with the protein in substantial detail. High resolution structures of protein bound to different inhibitors can serve this purpose. Gamma glutamyl transpeptidase from Bacillus licheniformis is one of the model systems that have been used to understand the structure–function correlation of the protein. The structures of the native protein (PDB code 4OTT), of its complex with glutamate (PDB code 4OTU) and that of its precursor mimic (PDB code 4Y23) are available, although at moderate/low resolution. In the present study, we are reporting the preliminary analysis of, high resolution X-ray diffraction data collected for the co-crystals of B. licheniformis, Gamma glutamyl transpeptidase, with its inhibitor, Acivicin. Crystals belong to the orthorhombic space group P2₁2₁2₁ and diffract X-ray to 1.45 Å resolution. This is the highest resolution data reported for all GGT structures available till now. The use of SUMO fused expression system enhanced yield of the target protein in the soluble fraction, facilitating recovery of protein with high purity. The preliminary analysis of this data set shows clear density for the inhibitor, acivicin, in the protein active site.