BackgroundThe fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.ResultsWe have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.ConclusionsMany aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1151-0) contains supplementary material, which is available to authorized users.
The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.
Photosystem II (PSII) is a large homodimeric protein-cofactor complex that acts as light-driven water:plastoquinone oxidoreductase and is located in the photosynthetic thylakoid membrane of plants, green algae and cyanobacteria. The principal function of PSII is to oxidize two water molecules at the unique Mn 4 Ca cluster to molecular (atmospheric) oxygen, 4 protons and 4 electrons. The protons serve to drive ATP synthetase and the electrons reduce plastoquinone (Q B ) to plastoquinol (Q B H 2 ) that is exported and delivers the electrons (through the cytochrome b 6 f complex) to photosystem I. Here the electrons gain a high reducing potential and serve at NADP reductase to generate NADPH that together with ATP reduces CO 2 to carbohydrates in the Calvin cycle. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-Å resolution [1] allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a, 2 pheophytin, 2 cytochrome, 2 plastoquinone, and 12 carotenoid molecules, 25 integral lipids, 1 chloride ion and the Mn 4 Ca cluster per PSII monomer. The presence of a third plastoquinone Q C and a second plastoquinone-transfer channel, which were not observed before, suggest mechanisms for plastoquinolplastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from Xenon derivative crystals indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in protontransfer reactions because it is bound through a putative water molecule to the Mn 4 Ca cluster at a distance of 6.5 Å and is close to two possible proton transfer channels.
SummaryHelicobacter pylori is a Gram-negative pathogenic microaerophile with a particular tropism for the mucosal surface of the gastric epithelium. Despite its obligatory microaerophilic character, it can metabolize D-glucose and/or D-galactose in both oxidative and fermentative pathways via a Na
A genomic strategy for the overexpression of bacterial multidrug and antibiotic resistance membrane efflux proteins in Escherichia coli is described. Expression is amplified so that the encoded proteins from a range of Gram-positive and Gram-negative bacteria comprise 5% to 35% of E. coli inner membrane protein. Depending upon their topology, proteins are produced with RGS(His)(6)-tag or a Strep-tag at the C terminus. These tags facilitate the purification of the overexpressed proteins in milligram quantities for structural studies. The strategy is illustrated for the bicyclomycin resistance efflux protein, Bcr, of E. coli.
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