Identification of the CRE-1 Cellulolytic Regulon in Neurospora crassa

Background: In filamentous ascomycete fungi, the utilization of alternate carbon sources is influenced by the zinc finger transcription factor CreA/CRE-1, which encodes a carbon catabolite repressor protein homologous to Mig1 from Saccharomyces cerevisiae. In Neurospora crassa, deletion of cre-1 results in increased secretion of amylase and b-galactosidase. Methodology/Principal Findings: Here we show that a strain carrying a deletion of cre-1 has increased cellulolytic activity and increased expression of cellulolytic genes during growth on crystalline cellulose (Avicel). Constitutive expression of cre-1 complements the phenotype of a N. crassa Dcre-1 strain grown on Avicel, and also results in stronger repression of cellulolytic protein secretion and enzyme activity. We determined the CRE-1 regulon by investigating the secretome and transcriptome of a Dcre-1 strain as compared to wild type when grown on Avicel versus minimal medium. Chromatin immunoprecipitation-PCR of putative target genes showed that CRE-1 binds to only some adjacent 59-SYGGRG-39 motifs, consistent with previous findings in other fungi, and suggests that unidentified additional regulatory factors affect CRE-1 binding to promoter regions. Characterization of 30 mutants containing deletions in genes whose expression level increased in a Dcre-1 strain under cellulolytic conditions identified novel genes that affect cellulase activity and protein secretion

The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

<p>Abstract</p> <p>Background</p> <p>The identification and characterization of the transcriptional regulatory networks governing the physiology and adaptation of microbial cells is a key step in understanding their behaviour. One such wide-domain regulatory circuit, essential to all cells, is carbon catabolite repression (CCR): it allows the cell to prefer some carbon sources, whose assimilation is of high nutritional value, over less profitable ones. In lower multicellular fungi, the C2H2 zinc finger CreA/CRE1 protein has been shown to act as the transcriptional repressor in this process. However, the complete list of its gene targets is not known.</p> <p>Results</p> <p>Here, we deciphered the CRE1 regulatory range in the model cellulose and hemicellulose-degrading fungus <it>Trichoderma reesei </it>(anamorph of <it>Hypocrea jecorina</it>) by profiling transcription in a wild-type and a delta-<it>cre1 </it>mutant strain on glucose at constant growth rates known to repress and de-repress CCR-affected genes. Analysis of genome-wide microarrays reveals 2.8% of transcripts whose expression was regulated in at least one of the four experimental conditions: 47.3% of which were repressed by CRE1, whereas 29.0% were actually induced by CRE1, and 17.2% only affected by the growth rate but CRE1 independent. Among CRE1 repressed transcripts, genes encoding unknown proteins and transport proteins were overrepresented. In addition, we found CRE1-repression of nitrogenous substances uptake, components of chromatin remodeling and the transcriptional mediator complex, as well as developmental processes.</p> <p>Conclusions</p> <p>Our study provides the first global insight into the molecular physiological response of a multicellular fungus to carbon catabolite regulation and identifies several not yet known targets in a growth-controlled environment.</p

Correlation of gene expression and protein production rate - a system wide study

<p>Abstract</p> <p>Background</p> <p>Growth rate is a major determinant of intracellular function. However its effects can only be properly dissected with technically demanding chemostat cultivations in which it can be controlled. Recent work on <it>Saccharomyces cerevisiae </it>chemostat cultivations provided the first analysis on genome wide effects of growth rate. In this work we study the filamentous fungus <it>Trichoderma reesei </it>(<it>Hypocrea jecorina</it>) that is an industrial protein production host known for its exceptional protein secretion capability. Interestingly, it exhibits a low growth rate protein production phenotype.</p> <p>Results</p> <p>We have used transcriptomics and proteomics to study the effect of growth rate and cell density on protein production in chemostat cultivations of <it>T. reesei</it>. Use of chemostat allowed control of growth rate and exact estimation of the extracellular specific protein production rate (SPPR). We find that major biosynthetic activities are all negatively correlated with SPPR. We also find that expression of many genes of secreted proteins and secondary metabolism, as well as various lineage specific, mostly unknown genes are positively correlated with SPPR. Finally, we enumerate possible regulators and regulatory mechanisms, arising from the data, for this response.</p> <p>Conclusions</p> <p>Based on these results it appears that in low growth rate protein production energy is very efficiently used primarly for protein production. Also, we propose that flux through early glycolysis or the TCA cycle is a more fundamental determining factor than growth rate for low growth rate protein production and we propose a novel eukaryotic response to this i.e. the lineage specific response (LSR).</p

Glacial geomorphology and cosmogenic 10Be and 26Al exposure ages in the northern Dufek Massif, Weddell Sea embayment, Antarctica

We studied the glacial geomorphology and geochronology of two ice-free valleys in the Dufek Massif (Antarctic Specially Protected Area 119) providing new constraints on past ice sheet thickness in the Weddell Sea embayment. 10Be and 26Al cosmogenic surface exposure dating provided chronological control. Seven glacial stages are proposed. These include an alpine glaciation, with subsequent (mid- Miocene?) over-riding by a warm-based ice sheet. Subsequent advances are marked by a series of minor drift deposits at 760m altitude at .1 Ma, followed by at least two later ice sheet advances that are characterized by extensive drift sheet deposition. An advance of plateau ice field outlet glaciers from the south postdated these drift sheets. The most recent advance involved the cold-based expansion of the ice sheet from the north at the Last Glacial Maximum, or earlier, which deposited a series of bouldery moraines during its retreat. This suggests at most a relatively modest expansion of the ice sheet and outlet glaciers dominated by a lateral ice expansion of just 2–3 km and maintaining a thickness similar to that of the northern ice sheet front. These observations are consistent with other reports of modest ice sheet thickening around the Weddell Sea embayment during the Last Glacial Maximum

ExtremeEarth: The Polar Use Case

The Polar Use Case in ExtremeEarth aims to address these issues through the development of a range of valuable tools. Deep learning algorithms will be developed to extract valuable sea ice and iceberg information from the ever increasing volumes of data collected by the Copernicus Sentinel satellite constellations. These new algorithms will be implemented on the Polar Thematic Exploitation Platform (Polar TEP) providing processing resources to produce the new information products. New data sets will be released for training and validating the new algorithms. Linked data tools will extend the capabilities for data access and discovery with semantic catalogue services that scale to the volumes of big data produced in the project. Frontend services, such as the PolarTEP and the Norwegian Meteorological Institute ice charts, will provide simple user access to browse and query the data generated

Exploring former subglacial Hodgson Lake, Antarctica Paper I: site description, geomorphology and limnology

At retreating margins of the Antarctic Ice Sheet, there are a number of locations where former subglacial lakes are emerging from under the ice but remain perennially ice-covered. This paper presents a site description of one of these lakes, Hodgson Lake, situated on southern Alexander Island, west of the Antarctic Peninsula (72° 00.549′ S, 68° 27.708′ W). First, we describe the physical setting of the lake using topographic and geomorphological maps. Second, we determine local ice sheet deglaciation history and the emergence of the lake using cosmogenic isotope dating of glacial erratics cross-referenced to optically stimulated luminescence dating of raised lake shoreline deltas formed during ice recession. Third we describe the physical and chemical limnology including the biological and biogeochemical evidence for life. Results show that the ice mass over Hodgson Lake was at least 295 m thick at 13.5 ka and has progressively thinned through the Holocene with the lake ice cover reaching an altitude of c. 6.5 m above the present lake ice sometime after 4.6 ka. Thick perennial ice cover persists over the lake today and the waters have remained isolated from the atmosphere with a chemical composition consistent with subglacial melting of catchment ice. The lake is ultra-oligotrophic with nutrient concentrations within the ranges of those found in the accreted lake ice of subglacial Lake Vostok. Total organic carbon and dissolved organic carbon are present, but at lower concentrations than typically recorded in continental rain. No organisms and no pigments associated with photosynthetic or bacterial activity were detected in the water column using light microscopy and high performance liquid chromatography. Increases in SO4 and cation concentrations at depth and declines in O2 provide some evidence for sulphide oxidation and very minor bacterial demand upon O2 that result in small, perhaps undetectable changes in the carbon biogeochemistry. However, in general the chemical markers of life are inconclusive and abiotic processes such as the diffusion of pore waters into the lake from its benthic sediments are far more likely to be responsible for the increased concentrations of ions at depth. The next phases of this research will be to carry out a palaeolimnological study of the lake sediments to see what they can reveal about the history of the lake in its subglacial state, and a detailed molecular analysis of the lake water and benthos to determine what forms of life are present. Combined, these studies will test some of the methodologies that will be used to explore deep continental subglacial lakes

Expression of thermophilic xylanases in fungal hosts

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Paroxysmal Autonomic Instability with Dystonia after Pneumococcal Meningoencephalitis

Streptococcus pneumoniae is a common cause of bacterial meningitis, frequently resulting in severe neurological impairment. A seven-month-old child presenting with Streptococcus pneumoniae meningoencephalitis developed right basal ganglia and hypothalamic infarctions. Daily episodes of agitation, hypertension, tachycardia, diaphoresis, hyperthermia, and decerebrate posturing were observed. The diagnosis of paroxysmal autonomic instability with dystonia was established. The patient responded to clonidine, baclofen, and benzodiazepines. Although this entity has been reported in association with traumatic brain injury, and as a sequel to some nervous system infections, this is the first case, to our knowledge, associated with pneumococcal meningoencephalitis