Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243.

Strains of Eggerthella lenta are capable of oxidation-reduction reactions capable of oxidizing and epimerizing bile acid hydroxyl groups. Several genes encoding these enzymes, known as hydroxysteroid dehydrogenases (HSDH) have yet to be identified. It is also uncertain whether the products of E.

Functional Redundancy in Perchlorate and Nitrate Electron Transport Chains and Rewiring Respiratory Pathways to Alter Terminal Electron Acceptor Preference.

Most dissimilatory perchlorate reducing bacteria (DPRB) are also capable of respiratory nitrate reduction, and preferentially utilize nitrate over perchlorate as a terminal electron acceptor. The similar domain architectures and phylogenetic relatedness of the nitrate and perchlorate respiratory complexes suggests a common evolutionary history and a potential for functionally redundant electron carriers. In this study, we identify key genetic redundancies in the electron transfer pathways from the quinone pool(s) to the terminal nitrate and perchlorate reductases in PS (hereafter referred to as PS).

Functional genomics of lipid metabolism in the oleaginous yeast .

The basidiomycete yeast (also known as ) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded T-DNA insertions.

Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation.

Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater.

YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance.

Mitogen-activated protein kinases (MAPKs) cascades play essential roles in plants by transducing developmental cues and environmental signals into cellular responses. Among the latter are microbe-associated molecular patterns perceived by pattern recognition receptors (PRRs), which trigger immunity. We found that YODA (YDA) - a MAPK kinase kinase regulating several Arabidopsis developmental processes, like stomatal patterning - also modulates immune responses.

Grazing alters net ecosystem C fluxes and the global warming potential of a subtropical pasture.

The impact of grazing on C fluxes from pastures in subtropical and tropical regions and on the environment is uncertain, although these systems account for a substantial portion of global C storage. We investigated how cattle grazing influences net ecosystem CO and CH exchange in subtropical pastures using the eddy covariance technique. Measurements were made over several wet-dry seasonal cycles in a grazed pasture, and in an adjacent pasture during the first three years of grazer exclusion.

Correction to: Identification and characterization of a galacturonic acid transporter from and its application for fermentation processes.

[This corrects the article DOI: 10.1186/1754-6834-7-20.].

Biotechnological Applications of Microbial (Per)chlorate Reduction.

While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration.

The major cellulases CBH-1 and CBH-2 of Neurospora crassa rely on distinct ER cargo adaptors for efficient ER-exit.

Filamentous fungi are native secretors of lignocellulolytic enzymes and are used as protein-producing factories in the industrial biotechnology sector. Despite the importance of these organisms in industry, relatively little is known about the filamentous fungal secretory pathway or how it might be manipulated for improved protein production. Here, we use Neurospora crassa as a model filamentous fungus to interrogate the requirements for trafficking of cellulase enzymes from the endoplasmic reticulum to the Golgi.

a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts.

Background: Economical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts.

Results: In this study, the carotenogenic yeast was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications.

Diversity in stomatal function is integral to modelling plant carbon and water fluxes.

Stomatal pores on leaf surfaces respond to environmental and physiological signals to regulate leaf gas exchange. Mathematical models can predict stomatal conductance (g ), with one parameter (m or g ) reflecting the sensitivity of g to the photosynthetic rate (A), atmospheric carbon dioxide concentration and atmospheric humidity, and a second parameter (g ) representing the minimum g . Such models are solved iteratively with a photosynthesis model to form the core of many models of crop or ecosystem carbon and water fluxes.

Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H and CO compared to organotrophic growth with fructose.

Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H), carbon dioxide (CO), and carbon monoxide (CO), or with H and CO.

Network of nutrient-sensing pathways and a conserved kinase cascade integrate osmolarity and carbon sensing in .

Identifying nutrients available in the environment and utilizing them in the most efficient manner is a challenge common to all organisms. The model filamentous fungus is capable of utilizing a variety of carbohydrates, from simple sugars to the complex carbohydrates found in plant cell walls. The zinc binuclear cluster transcription factor CLR-1 is necessary for utilization of cellulose, a major, recalcitrant component of the plant cell wall; however, expression of in the absence of an inducer is not sufficient to induce cellulase gene expression.

Network reconstruction and systems analysis of plant cell wall deconstruction by .

Background: Plant biomass degradation by fungal-derived enzymes is rapidly expanding in economic importance as a clean and efficient source for biofuels. The ability to rationally engineer filamentous fungi would facilitate biotechnological applications for degradation of plant cell wall polysaccharides. However, incomplete knowledge of biomolecular networks responsible for plant cell wall deconstruction impedes experimental efforts in this direction.

Novel Strategies for the Production of Fuels, Lubricants, and Chemicals from Biomass.

Growing concern with the environmental impact of CO emissions produced by combustion of fuels derived from fossil-based carbon resources has stimulated the search for renewable sources of carbon. Much of this focus has been on the development of methods for producing transportation fuels, the major source of CO emissions today, and to a lesser extent on the production of lubricants and chemicals. First-generation biofuels such as bioethanol, produced by the fermentation of sugar cane- or corn-based sugars, and biodiesel, produced by the transesterification reaction of triglycerides with alcohols to form a mixture of long-chain fatty esters, can be blended with traditional fuels in limited amounts and also arise in food versus fuel debates.

Phosphorylation is required for the pathogen defense function of the Arabidopsis PEN3 ABC transporter.

The Arabidopsis PEN3 ABC transporter accumulates at sites of pathogen detection, where it is involved in defense against a number of pathogens. Perception of PAMPs by pattern recognition receptors initiates recruitment of PEN3 and also leads to PEN3 phosphorylation at multiple amino acid residues. Whether PAMP-induced phosphorylation of PEN3 is important for its defense function or focal recruitment has not been addressed.

Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus.

The plant cell wall polysaccharide arabinan provides an important supply of arabinose, and unraveling arabinan-degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan-degrading enzymes in the thermophilic bacterium and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-l-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endoarabinanase (CpAbn43A), a GH27 β-l-arabinopyranosidase (CpAbp27A), and two GH127 β-l-arabinofuranosidases (CpAbf127A, CpAbf127B). The genes were expressed as recombinant proteins, and the functions of the purified proteins were determined with -nitrophenyl (NP)-linked sugars and naturally occurring pectin structural elements as the substrates.

Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases.

Arabinoxylans are constituents of the human diet. Although not utilizable by the human host, they can be fermented by colonic bacteria. The arabinoxylan backbone is decorated with arabinose side chains that may be substituted with ferulic acid, thus limiting depolymerization to fermentable sugars.

The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in .

Background: Pectin is an abundant component in many fruit and vegetable wastes and could therefore be an excellent resource for biorefinery, but is currently underutilized. Fungal pectinases already play a crucial role for industrial purposes, such as for foodstuff processing. However, the regulation of pectinase gene expression is still poorly understood.

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction.

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments.

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.

In Neurospora crassa, the transcription factor COL-26 functions as a regulator of glucose signaling and metabolism. Its loss leads to resistance to carbon catabolite repression. Here, we report that COL-26 is necessary for the expression of amylolytic genes in N.

Nitrogen Fertilization Effects on Biomass Production and Yield Components of ×.

Grasses such as × and (switchgrass) can potentially be used to produce bioenergy on a large scale in the Midwestern USA. The biomass productivity of these warm-season perennial grasses, particularly × , can be substantial, even when grown with limited inputs. The literature, however, varies regarding the nitrogen requirements for × biomass production.

Implementing industrial-academic partnerships to advance bioenergy research: the Energy Biosciences Institute.

The Energy Bioscience Institute (EBI) is an example of an ambitious academic-industry collaboration. We present a summary of how the EBI was organized during the first eight years and examples of several major research thrusts within the Institute to develop renewable biodiesel, jet fuel and lubricants from carbohydrates. In particular, we describe how the multidisciplinary nature and management structure of the organization led to hybrid approaches in which bioconversions and chemical synthesis were combined to develop new products.

Programming mRNA decay to modulate synthetic circuit resource allocation.

Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence.

An Arabidopsis Lipid Flippase Is Required for Timely Recruitment of Defenses to the Host-Pathogen Interface at the Plant Cell Surface.

Deposition of cell wall-reinforcing papillae is an integral component of the plant immune response. The Arabidopsis PENETRATION 3 (PEN3) ATP binding cassette (ABC) transporter plays a role in defense against numerous pathogens and is recruited to sites of pathogen detection where it accumulates within papillae. However, the trafficking pathways and regulatory mechanisms contributing to recruitment of PEN3 and other defenses to the host-pathogen interface are poorly understood.