Microbial community composition and dynamics in a semi-industrial-scale facility operating under the MixAlco™ bioconversion platform

Aims:  To monitor microbial community dynamics in a semi‐industrial‐scale lignocellulosic biofuel reactor system and to improve our understanding of the microbial communities involved in the MixAlco? biomass conversion process. Methods and Results:  Reactor microbial communities were characterized at six time points over the course of an 80‐day, mesophilic, semi‐industrial‐scale fermentation using community qPCR and 16S rRNA tag‐pyrosequencing. We found the communities to be dynamic, bacterially dominated consortia capable of changing quickly in response to reactor conditions. Clostridia‐ and Bacteroidetes‐like organisms dominated the reactor communities, but ultimately the communities established consortia containing complementary functional capacities for the degradation of lignocellulosic materials. Eighteen operational taxonomic units were found to share strong correlations with reactor acid concentration and may represent taxa integral to fermentor performance. Conclusions:  The results of this study indicate that the emergence of complementary functional classes within the fermentor consortia may be a trait that is consistent across scales, and they suggest that there may be flexibility with respect to the specific identities of the organisms involved in the fermentor’s degradation and fermentation processes. Significance and Impact of the Study:  This study provides new information regarding the composition, dynamics and potential flexibility of the microbial communities associated with the MixAlco? process and is likely to inform the improvement of this and other applications that employ mixed microbial communities.     

Biochemical characterization of the chloroplastic β-carbonic anhydrase from Flaveria bidentis (L.) “Kuntze”

Abstract

C₃ and C₄ plant carbonic anhydrases (CAs) are zinc-enzymes that catalyze the reversible hydration of CO₂. They are sub-divided in three classes: α, β and γ, being distributed between both photosynthetic subtypes. The C₄ dicotyledon species Flaveria bidentis (L.) “Kuntze” contains a small gene family encoding three distinct β-CAs, named FbiCA1, FbiCA2 and FbiCA3. We have expressed and purified recombinant FbiCA1, which is localized in the chloroplast where it is thought to play a role in lipid biosynthesis and antioxidant activity, and biochemically characterized it by spectroscopic and inhibition experiments. FbiCA1 is a compact octameric protein that is moderately inhibited by carboxylate molecules. Surprisingly, pyruvate, but not lactate, did not inhibit FbiCA1 at concentrations up to 10?mM, suggesting that its capacity to tolerate high pyruvate concentration reflects the high concentration of pyruvate in the chloroplasts of bundle-sheath and mesophyll cells involved in C₄ photosynthesis.     

Mesorhizobium ciceri LMS-1 expressing an exogenous 1-aminocyclopropane-1-carboxylate (ACC) deaminase increases its nodulation abilities and chickpea plant resistance to soil constraints

Aims: Our goal was to understand the symbiotic behaviour of a Mesorhizobium strain expressing an exogenous 1‐aminocyclopropane‐1‐carboxylate (ACC) deaminase, which was used as an inoculant of chickpea (Cicer arietinum) plants growing in soil. Methods and Results: Mesorhizobium ciceri LMS‐1 (pRKACC) was tested for its plant growth promotion abilities on two chickpea cultivars (ELMO and CHK3226) growing in nonsterilized soil that displayed biotic and abiotic constraints to plant growth. When compared to its wild‐type form, the M. ciceri LMS‐1 (pRKACC) strain showed an increased nodulation performance of c. 125 and 180% and increased nodule weight of c. 45 and 147% in chickpea cultivars ELMO and CHK3226, respectively. Mesorhizobium ciceri LMS‐1 (pRKACC) was also able to augment the total biomass of both chickpea plant cultivars by c. 45% and to reduce chickpea root rot disease susceptibility. Conclusions: The results obtained indicate that the production of ACC deaminase under free living conditions by Mesorhizobium strains increases the nodulation, plant growth abilities and biocontrol potential of these strains. Significance and Impact of the Study: This is the first study regarding the use of a transformed rhizobial strain expressing an exogenous ACC deaminase in different plant cultivars growing in soil. Hence, obtaining Mesorhizobium strains with high ACC deaminase activity is a matter of extreme importance for the development of inoculants for field applications.     

The fragmentation mechanism of β-(N-alkyl/arylamino)-α,β-unsaturated carboxylates under electrospray ionization conditions

Summary. The positive ion mass spectrometric behavior of six β-(N-alkyl/arylamino)-α,β-unsaturated carboxylates, α-(1-alkyl/arylaminoethylidene)-γ-lactones, has been studied under electrospray ionization conditions. Their fragmentation pathways are described and supported by tandem mass spectrometry. The protonated compounds are apt to eliminate a water, and a water plus a oxacyclopent-2-yne molecule. Some of the compounds show a tendency to undergo a four-membered ring contraction rearrangement to lose a carbon dioxide. The fragmentation patterns of these compounds exhibit a strong substituent dependency.     

Design,synthesis, and evaluation of carboxyl-modified oseltamivir derivatives with improved lipophilicity as neuraminidase inhibitors

In this study, a series of carboxyl-modified oseltamivir analogs with improved lipophilicity were designed and synthesized, and their inhibitory activities against neuraminidase from influenza A virus H5N1 subtype were evaluated. The results demonstrated that compound 5m exhibited potent inhibitory activity (IC₅₀?=?1.30?±?0.23?μM), and it targeted the recently discovered 430-cavity. Compound 5m (Log D?=??0.12) is more lipophilic than oseltamivir carboxylate (Log D?=??1.69) at pH 7.4, which is potentially propitious to improved membrane permeability and oral drug absorption. Meanwhile, 5m showed high stability in human liver microsomes. The findings of this study can be valuable in identifying neuraminidase inhibitors with optimal lipophilicity and in the exploration of 430-cavity.     

交替氧化酶结构和功能研究进展

交替氧化酶(a lternative ox idase,AOX)是植物线粒体呼吸链中抗氰呼吸途径(cyan ide-res istan t resp irationpathw ay)的末端氧化酶,它广泛存在于高等植物及部分真菌和藻类中。交替氧化酶是一种双铁羧基蛋白(d i-ironcarboxy late prote in),它不仅具有其它双铁羧基蛋白共有的结构特点以及去除分子氧的功能,更重要的是它还可以通过改变自身结构等方式来主动调节抗氰呼吸途径的运行程度,进而调节细胞多方面的代谢和功能,以适应环境条件的改变,增强植物适应各种逆境的能力,调节植物生长速率,并与细胞凋亡和光合作用相关。本文主要对交替氧化酶的结构与其在植物体内功能的最新研究进展进行综述。     

Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes

The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.     

Characterization of a putative calcium-binding site in tobacco mosaic virus.

Lead has been used as a substitute for calcium binding to tobacco mosaic virus (TMV). The high atomic number of lead has allowed us to use difference maps from X-ray fiber diffraction data to characterize a calcium-binding site in the virus. The metal ligands are slightly different from those previously believed to bind calcium to TMV, although the binding site is very close to one previously described. Two acetate groups are also bound to the lead atom. There is no significant backbone conformational change in the protein as a result of metal binding; the binding is accomplished by means of relatively small movements in amino acid side chains.     

Evolution of the carboxylate Jen transporters in fungi

Synteny analysis is combined with sequence similarity and motif identification to trace the evolution of the putative monocarboxylate (lactate/pyruvate) transporters Jen1p and the dicarboxylate (succinate/fumarate/malate) transporters Jen2p in Hemiascomycetes yeasts and Euascomycetes fungi. It is concluded that a precursor form of Jen1p, named here preJen1p, arose by the duplication of an ancestral Jen2p, during the speciation of Yarrowia lipolytica, which was transferred into a new syntenic context. The Jen1p transporters differentiated from preJen1p in Kluyveromyces lactis, before the Whole Genome Duplication (WGD), and are conserved as a single copy in the Saccharomyces species. In contrast, the ancestral Jen2p was definitively lost just prior to the WGD and is absent in Saccharomyces.     

Dinuclear triply-bridged copper(II) compounds containing carboxylato bridges and di-2-pyridylamine as a ligand: synthesis, crystal structure, spectroscopic and magnetic properties

Three new triply-bridged dinuclear copper(II) compounds with carboxylato bridges, [Cu₂(μ-O₂CH)(μ-OH)(μ-Cl)(dpyam)₂](PF₆) (1), [Cu₂(μ-O₂CH)₂(μ-OH)(dpyam)₂](PF₆) (2) and [Cu₂(μ-O₂CCH₂CH₃)₂(μ-OH)(dpyam)₂](ClO₄) (3) (dpyam = di-2-pyridylamine) have been synthesized and characterized crystallographically and spectroscopically. Compound 1 consists of a dinuclear unit in which both copper(II) ions are bridged by three different ligands, i.e., formate, chloride and hydroxide anions, providing a distorted trigonal bipyramidal geometry with a CuN₂O₂Cl chromophore. Compounds 2 and 3 have two bridging formato ligands and two bridging propionato ligands, respectively, together with a hydroxo bridge. The carboxylato ligands in both compounds 2 and 3 exhibit different coordination modes. One is in a syn, syn η¹:η¹:μ₂ bridging mode and the other is in a monoatomic bridging mode. The structure of compound 2 involves a dinuclear unit, with a distorted trigonal bipyramidal geometry around each Cu(II) ion with a CuN₂O₃ chromophore. Compound 3 contains a non-centrosymmetric unit; the coordination environment around Cu(1) is a distorted square-pyramidal geometry and an intermediate geometry of sp and tbp around the Cu(II) ion. The Cu?Cu separations are 3.061, 3.113 and 3.006 Å for compounds 1, 2 and 3, respectively. The EPR spectra of all three compounds show a broad isotropic signal with a g value around 2.10.The magnetic susceptibility measurements, measured from 5 to 280 K, revealed a moderate ferromagnetic interaction between the Cu(II) ions with a singlet-triplet energy gap (J) of 79.7, 47.8 and 24.1 cm⁻¹, for compounds 1, 2 and 3, respectively. Also a very weak intermolecular antiferromagnetic interaction was observed between the dinuclear units.