Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis

Extremophiles - Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to...     

The target of rapamycin kinase affects biomass accumulation and cell cycle progression by altering carbon/nitrogen balance in synchronized Chlamydomonas reinhardtii cells

Several metabolic processes tightly regulate growth and biomass accumulation. A highly conserved protein complex containing the target of rapamycin (TOR) kinase is known to integrate intra‐ and extracellular stimuli controlling nutrient allocation and hence cellular growth. Although several functions of TOR have been described in various heterotrophic eukaryotes, our understanding lags far behind in photosynthetic organisms. In the present investigation, we used the model alga Chlamydomonas reinhardtii to conduct a time‐resolved analysis of molecular and physiological features throughout the diurnal cycle after TOR inhibition. Detailed examination of the cell cycle phases revealed that growth is not only repressed by 50%, but also that significant, non‐linear delays in the progression can be observed. By using metabolomics analysis, we elucidated that the growth repression was mainly driven by differential carbon partitioning between anabolic and catabolic processes. Accordingly, the time‐resolved analysis illustrated that metabolic processes including amino acid‐, starch‐ and triacylglycerol synthesis, as well RNA degradation, were redirected within minutes of TOR inhibition. Here especially the high accumulation of nitrogen‐containing compounds indicated that an active TOR kinase controls the carbon to nitrogen balance of the cell, which is responsible for biomass accumulation, growth and cell cycle progression.     

Brain lipid composition in grey-lethal mutant mouse characterized by severe malignant osteopetrosis

The grey-lethal mouse (gl/gl) mutant most closely resembles the severe human malignant autosomal recessive OSTM1-dependent form of osteopetrosis that it has been described to be associated with neurological abnormalities. For this reason, we have analyzed the brain lipid composition (gangliosides, neutral glycosphingolipids, phospholipids and cholesterol), from gl/gl mice at different ages of development and compared with wild type mice. Both cholesterol and glycerophospholipid content and pattern in the gl/gl and control mice were very similar. In contrast, significant differences were observed in the content of several sphingolipids. Higher amount of the monosialogangliosides GM2 and GM3, and lower content of sphingomyelin, sulfatide and galactosylceramide were observed in the gl/gl brain with respect to controls. The low content of sphingomyelin, sulfatide and galactosylceramide is consistent with the immunohistochemical results showing that in the grey-lethal brain significant depletion and disorganization of the myelinated fibres is present, thus supporting the hypothesis that loss of function of the OSTM1 causes neuronal impairment and myelin deficit.     

The RON1/FRY1/SAL1 Gene Is Required for Leaf Morphogenesis and Venation Patterning in Arabidopsis

To identify genes involved in vascular patterning in Arabidopsis (Arabidopsis thaliana), we screened for abnormal venation patterns in a large collection of leaf shape mutants isolated in our laboratory. The rotunda1-1 (ron1-1) mutant, initially isolated because of its rounded leaves, exhibited an open venation pattern, which resulted from an increased number of free-ending veins. We positionally cloned the RON1 gene and found it to be identical to FRY1/SAL1, which encodes an enzyme with inositol polyphosphate 1-phosphatase and 3′ (2′),5′-bisphosphate nucleotidase activities and has not, to our knowledge, previously been related to venation patterning. The ron1-1 mutant and mutants affected in auxin homeostasis share perturbations in venation patterning, lateral root formation, root hair length, shoot branching, and apical dominance. These similarities prompted us to monitor the auxin response using a DR5-GUS auxin-responsive reporter transgene, the expression levels of which were increased in roots and reduced in leaves in the ron1-1 background. To gain insight into the function of RON1/FRY1/SAL1 during vascular development, we generated double mutants for genes involved in vein patterning and found that ron1 synergistically interacts with auxin resistant1 and hemivenata-1 but not with cotyledon vascular pattern1 (cvp1) and cvp2. These results suggest a role for inositol metabolism in the regulation of auxin responses. Microarray analysis of gene expression revealed that several hundred genes are misexpressed in ron1-1, which may explain the pleiotropic phenotype of this mutant. Metabolomic profiling of the ron1-1 mutant revealed changes in the levels of 38 metabolites, including myoinositol and indole-3-acetonitrile, a precursor of auxin.During the vegetative development of Arabidopsis (Arabidopsis thaliana), leaves are produced from the shoot apical meristem in an orchestrated program that involves patterning and cell division, expansion, and differentiation. The mature vegetative leaves of Arabidopsis are histologically simple and consist of the outer epidermis and internal mesophyll and vasculature (Tsukaya, 2005). Veins are crucial for normal leaf function, transporting water, minerals, and photosynthate and providing mechanical support to the lamina (Evert and Eichhorn, 2006). The leaves of many vascular plants, such as the angiosperms, exhibit a closed reticulate venation pattern (Roth-Nebelsick et al., 2001). In Arabidopsis, the leaf venation pattern is brochidodromous, with a single primary vein (midvein) and a series of loops formed by secondary veins that connect other secondary and higher order veins (Hickey, 1973; Candela et al., 1999).Vein differentiation must be spatially and temporally regulated throughout leaf development. Many aspects of venation patterning in plant leaves can be explained by the auxin canalization model (Sachs, 1991; Rolland-Lagan and Prusinkiewicz, 2005), which is supported by considerable experimental evidence. The role of auxin in venation pattern formation is supported by the phenotypes of mutants possessing altered auxin biosynthesis or perception (Alonso-Peral et al., 2006; Cheng et al., 2006), experimental perturbation of auxin transport (Mattsson et al., 1999; Sieburth, 1999), and the expression pattern of auxin-responsive reporter transgenes (Mattsson et al., 2003; Scarpella et al., 2006). The phenotypes of mutants impaired in auxin transport, such as scarface (sfc; Deyholos et al., 2000; Sieburth et al., 2006) and pin-formed1 (pin1; Okada et al., 1991; Gälweiler et al., 1998), and perception, such as monopteros (mp; Hardtke and Berleth,1998), are pleiotropic and include defects in vein patterning or differentiation. The sfc mutant exhibits a disconnected venation pattern (Deyholos et al., 2000), and the lateral organs of strong mp mutants display a reduced venation pattern with no peripheral veins (Przemeck et al., 1996). In contrast, the leaf venation pattern of pin1 mutants resembles that of wild-type plants treated with auxin transport inhibitors, exhibiting extra primary and secondary veins and an accumulation of vascular elements along the leaf margin (Mattsson et al., 1999).Unlike sfc, pin1, or mp, other leaf venation mutants are not primarily affected in auxin production, perception, or transport (Carland et al., 1999). Examples include cotyledon vascular pattern1 (cvp1), the cotyledons of which exhibit isolated patches of vascular tissue (Carland et al., 1999, 2002), and cvp2, which exhibits increased numbers of free-ending veins in the cotyledons and leaves (Carland et al., 1999; Carland and Nelson, 2004). CVP1 encodes the STEROL METHYLTRANSFERASE2 (SMT2) protein, an enzyme that functions in the sterol biosynthetic pathway (Carland et al., 2002). CVP2 encodes an inositol polyphosphate 5′-phosphatase (5PTase; Carland and Nelson, 2004), which mediates the hydrolysis of inositol 1,4,5-trisphosphate (IP₃), a eukaryotic second messenger with a pivotal role in calcium signaling (Berridge, 2009). IP₃ controls cytosolic calcium levels by regulating calcium release from the vacuole and endoplasmic reticulum (Krinke et al., 2007). The disconnected, open venation pattern of cvp2 cotyledons and leaves suggested a role for intracellular IP₃ levels in vascular development (Carland and Nelson, 2004). Recently, CVP2 and another 5PTase, CVP2-LIKE1 (CVL1), have been shown to regulate vein patterning through the production of a specific phosphoinositide (PI) that acts as a ligand for SFC/VASCULAR NETWORK3 (VAN3), which in turn controls the traffic of vesicles that accounts for the polar subcellular localization of PIN1 proteins (Carland and Nelson, 2009; Naramoto et al., 2009). Another inositol 5PTase, At5PTase13, has been shown to play a role in auxin-mediated vein development in cotyledons (Lin et al., 2005). Furthermore, the open vein networks present in the leaves of forked and tornado mutants (Steynen and Schultz, 2003; Cnops et al., 2006) may be due to altered auxin perception or distribution.To identify genes required for venation patterning, we screened for naturally occurring variations in the venation pattern of Arabidopsis vegetative leaves (Candela et al., 1999). In this way, we discovered the spontaneously occurring hemivenata-1 (hve-1) mutation, which causes a venation pattern that is significantly simpler than those of other wild types, such as Landsberg erecta (Ler) and Columbia-0 (Col-0). We positionally cloned the HVE gene, which encodes a CAND1 protein involved in ubiquitin-mediated auxin signaling (Alonso-Peral et al., 2006). To identify additional loci necessary for vascular patterning, we screened for venation pattern defects in a collection of leaf shape mutants isolated in our laboratory after ethyl methanesulfonate (EMS) mutagenesis (Berná et al., 1999) and found that the rotunda1-1 (ron1-1) mutant, named after the round laminae of its vegetative leaves, displays disconnected leaf veins. Here, we describe the phenotypic characterization of the ron1-1 mutant and the map-based cloning of RON1, which encodes an inositol polyphosphate 1-phosphatase that plays a role in venation patterning, as determined by morphological, reporter gene, and double mutant analyses. Our results suggest an interplay between inositol and auxin signaling in a number of developmental pathways, including those responsible for leaf venation pattern formation.     

Dynamics of lipids and metabolites during the cell cycle of Chlamydomonas reinhardtii

Metabolites and lipids are the final products of enzymatic processes, distinguishing the different cellular functions and activities of single cells or whole tissues. Understanding these cellular functions within a well‐established model system requires a systemic collection of molecular and physiological information. In the current report, the green alga Chlamydomonas reinhardtii was selected to establish a comprehensive workflow for the detailed multi‐omics analysis of a synchronously growing cell culture system. After implementation and benchmarking of the synchronous cell culture, a two‐phase extraction method was adopted for the analysis of proteins, lipids, metabolites and starch from a single sample aliquot of as little as 10–15 million Chlamydomonas cells. In a proof of concept study, primary metabolites and lipids were sampled throughout the diurnal cell cycle. The results of these time‐resolved measurements showed that single compounds were not only coordinated with each other in different pathways, but that these complex metabolic signatures have the potential to be used as biomarkers of various cellular processes. Taken together, the developed workflow, including the synchronized growth of the photoautotrophic cell culture, in combination with comprehensive extraction methods and detailed metabolic phenotyping has the potential for use in in‐depth analysis of complex cellular processes, providing essential information for the understanding of complex biological systems.