Identification of an l-Arabitol Transporter from Aspergillus niger

l-arabitol is an intermediate of the pentose catabolic pathway in fungi but can also be used as a carbon source by many fungi, suggesting the presence of transporters for this polyol. In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. Growth and expression profiles as well as sugar consumption analysis indicated that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Moreover, l-arabitol production from wheat bran was increased in a metabolically engineered A. niger mutant by the deletion of latA, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi

On the origin of vanillyl alcohol oxidases

Vanillyl alcohol oxidase (VAO) is a fungal flavoenzyme that converts a wide range of para-substituted phenols. The products of these conversions, e.g. vanillin, coniferyl alcohol and chiral aryl alcohols, are of interest for several industries. VAO is the only known fungal member of the 4-phenol oxidising (4PO) subgroup of the VAO/PCMH flavoprotein family. While the enzyme has been biochemically characterised in great detail, little is known about its physiological role and distribution in fungi. We have identified and analysed novel, fungal candidate VAOs and found them to be mostly present in Pezizomycotina and Agaricomycotina. The VAOs group into three clades, of which two clades do not have any characterised member. Interestingly, bacterial relatives of VAO do not form a single outgroup, but rather split up into two separate clades. We have analysed the distribution of candidate VAOs in fungi, as well as their genomic environment. VAOs are present in low frequency in species of varying degrees of relatedness and in regions of low synteny. These findings suggest that fungal VAOs may have originated from bacterial ancestors, obtained by fungi through horizontal gene transfer. Because the overall conservation of fungal VAOs varies between 60 and 30% sequence identity, we argue for a more reliable functional prediction using critical amino acid residues. We have defined a sequence motif P-x-x-x-x-S-x-G-[RK]-N-x-G-Y-G-[GS] that specifically recognizes 4PO enzymes of the VAO/PCMH family, as well as additional motifs that can help to further narrow down putative functions. We also provide an overview of fingerprint residues that are specific to VAOs

Mapping the polysaccharide degradation potential of Aspergillus niger

<p>Abstract</p> <p>Background</p> <p>The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation.</p> <p>Results</p> <p>Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from <it>Aspergillus niger</it>, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan.</p> <p>Conclusions</p> <p>The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in <it>A. niger</it>.</p

Occurrence and function of enzymes for lignocellulose degradation in commercial Agaricus bisporus cultivation

The white button mushroom Agaricus bisporus is economically the most important commercially produced edible fungus. It is grown on carbon- and nitrogen-rich substrates, such as composted cereal straw and animal manure. The commercial mushroom production process is usually performed in buildings or tunnels under highly controlled environmental conditions. In nature, the basidiomycete A. bisporus has a significant impact on the carbon cycle in terrestrial ecosystems as a saprotrophic decayer of leaf litter. In this mini-review, the fate of the compost plant cell wall structures, xylan, cellulose and lignin, is discussed. A comparison is made from the structural changes observed to the occurrence and function of enzymes for lignocellulose degradation present, with a special focus on the extracellular enzymes produced by A. bisporus. In addition, recent advancements in whole genome level molecular studies in various growth stages of A. bisporus in compost are reviewed.Peer reviewe

Control and possible applications of a novel carrot-spoilage basidiomycete, Fibulorhizoctonia psychrophila

A novel cold-tolerant fungus, Fibulorhizoctonia psychrophila, was isolated from a refrigerated carrot storage facility and identified as an anamorph of Athelia, often classified in Rhizoctonia s.l. Growth of this fungus was observed between 0 and 20°C with an optimum at 9–12°C, while incubation of mycelium grown at 15–32°C resulted in absence of growth even after the fungus was transferred back to 15°C. Growth was inhibited in the presence of the antifungals sorbic acid or natamycin, in particular when the fungus was incubated at 18°C. F. psychrophila produces polysaccharide degrading enzymes that, when compared to enzymes from the ascomycete fungus Aspergillus niger, retain a larger proportion of their activity at lower temperatures. This indicates that F. psychrophila could be used as a source for novel industrial enzymes that are active at 4–15°C

Самосборка низкоразмерных систем Al, Ni, Ti и Si в условиях околоравновесной конденсации

Дисертація присвячена вивченню закономірностей структуро- утворення тривимірних мікро- та наносистем Al, Ni, Ti та Si за умов близькорівноважної стаціонарної конденсації. Вивчена залежність механізмів структуроутворення конденсату від основних параметрів технологічного процесу: часу конденсації, тиску робочого газу та потужності розряду. Проаналізовані фізичні процеси, що відбуваються під час роботи накопичувальних систем плазма-конденсат. Для цих систем розроблено математичну модель самоорганізації критично малих стаціонарних пересичень, яка вивчена за допомогою фазової площини. Досліджено вплив на кінетику формування мікро- та наносистем Al, Ni, Ti та Si взаємозв’язаних ефекту Гіббса-Томсона та польової селективності. Розроблені та апробовані за допомогою побудови фазових траєкторій математичні моделі, які описують процес самозбірки низькорозмірних систем. Встановлено, що за близько-рівноважних умов можна реалізувати різні структурно-морфологічні форми конденсатів. При цитуванні документа, використовуйте посилання http://essuir.sumdu.edu.ua/handle/123456789/24862Диссертация посвящена изучению закономерностей структуро- образования микро- и наносистем Al, Ni, Ti и Si в условиях критически малых пересыщений. Изучены процессы формирования конденсатов под влиянием структурной и полевой селективностей, степень проявления которых зависит от таких основных технологических параметров, как время конденсации, давление рабочего газа и мощность разряда. Проанализированы конструкции существующих распылитель- ных систем, разработана и создана накопительная система плазма- конденсат (НСПК) на базе планарного магнетрона и совмещенного с ним полого катода. Проанализированы происходящие в НСПК физические процессы и разработана математическая модель, описы- вающая изменение во времени таких нелинейно взаимозависимых технологических параметров, как пересыщение и температура ростовой поверхности. Методом фазовой плоскости установлена возможность самоорганизации критически малых стационарных пресыщений. С помощью математического моделирования показано, что при повышении давления рабочего газа происходит усреднение энергии распыленных атомов, что является необходимым условием повышения стационарности технологического процесса. Изучен механизм формирования фракталов Ni при осаждении предельно слабых паровых потоков на нагретые до относительно высоких температур (620 К) подложки. Показано, что снижение пересыщения паров Ni до критического значения может предельно локализировать области закрепления атомов и является основой для формирования на ростовой поверхности вискеров. Впервые показано, что диссипативная самоорганизация предельно малых стационарных пересыщений в накопительных системах плазма-конденсат приводит к консервативной самоорганизации низкоразмерных систем в виде тех или иных структурно-морфологических состояний поверхности конденсата. Изучены механизмы самосборки пористых пленок Al, трехмерных систем Ti в виде слабо связанных друг с другом ограненных или округлых кристаллов. Показано, что основой такой самосборки конденсатов является предельная минимизация свободной энергии конденсата. При этом селективная самосборка развитой поверхности металлов при проявлении полевой селективности является следствием выравнивания химических потенциалов в различных точках ростовой поверхности до уровня, при котором локальные скорости наращивания конденсатов не зависят от координат поверхности и не изменяются во времени. Изучены механизмы структурообразования конденсатов Si и разработана математическая модель, описывающая самоорганизацию островков одинаковых размеров и формы. При цитировании документа, используйте ссылку http://essuir.sumdu.edu.ua/handle/123456789/24862The aim of dissertation is the study of regularities of Al, Ni, Ti and Si micro- and nanosystems formation under the conditions of critically small supersaturations. It have been studied the processes of condensates forming at influence of structural and field selectivity, they are depend on main technological parameters of condensation process such as time of condensation, pressure of working gas and power discharge. Physical processes in the accumulative ion-plasma system have been analyzed. For this systems was created mathematical model of selforganization extremely low steady-state supersaturation and studied by method of phase plane. The influence of interdependent effects of Gibbs-Thomson and field selectivities on forming kinetic of micro- and nanosystems of Al, Ni, Ti and Si was investigated. It was created and tested due to plotting of phase trajectories mathematical models, which reply for the self-assembly process of low dimensional systems. It was established that different structuralmorphological forms of condensates could be obtain at near equilibrium conditions. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/2486

Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger

<p>Abstract</p> <p>Background</p> <p><it>Aspergillus niger </it>is an ascomycetous fungus that is known to reproduce through asexual spores, only. Interestingly, recent genome analysis of <it>A. niger </it>has revealed the presence of a full complement of functional genes related to sexual reproduction <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. An example of such genes are the dioxygenase genes which in <it>Aspergillus nidulans</it>, have been shown to be connected to oxylipin production and regulation of both sexual and asexual sporulation <abbrgrp><abbr bid="B2">2</abbr><abbr bid="B3">3</abbr><abbr bid="B4">4</abbr></abbrgrp>. Nevertheless, the presence of sex related genes alone does not confirm sexual sporulation in <it>A. niger</it>.</p> <p>Results</p> <p>The current study shows experimentally that <it>A. niger </it>produces the oxylipins 8,11-dihydroxy octadecadienoic acid (8,11-diHOD), 5,8-dihydroxy octadecadienoic acid (5,8-diHOD), lactonized 5,8-diHOD, 8-hydroxy octadecadienoic acid (8-HOD), 10-hydroxy octadecadienoic acid (10-HOD), small amounts of 8-hydroxy octadecamonoenoic acid (8-HOM), 9-hydroxy octadecadienoic acid (9-HOD) and 13-hydroxy octadecadienoic acid (13-HOD). Importantly, this study shows that the <it>A. niger </it>genome contains three putative dioxygenase genes, <it>ppoA</it>, <it>ppoC </it>and <it>ppoD</it>. Expression analysis confirmed that all three genes are indeed expressed under the conditions tested.</p> <p>Conclusion</p> <p><it>A. niger </it>produces the same oxylipins and has similar dioxygenase genes as <it>A. nidulans</it>. Their presence could point towards the existence of sexual reproduction in <it>A. niger </it>or a broader role for the gene products in physiology, than just sexual development.</p

The analysis of longitudinal quality of life measures with informative drop-out: a pattern mixture approach

The analysis of longitudinal health-related quality of life measures (HRQOL) can be seriously hampered due to informative drop-out. Random effects models assume Missing At Random and do not take into account informative drop-out. We therefore aim to correct the bias due to informative drop-out. Analyses of data from a trial comparing standard-dose and high-dose chemotherapy for patients with breast cancer with respect to long-term impact on HRQOL will serve as illustration. The subscale Physical Function (PF) of the SF36 will be used. A pattern mixture approach is proposed to account for informative drop-out. Patterns are defined based on events related to HRQOL, such as death and relapse. The results of this pattern mixture approach are compared to the results of the commonly used random effects model. The findings of the pattern mixture approach are well interpretable, and different courses over time in different patterns are distinguished. In terms of estimated differences between standard dose and high dose, the results of both approaches are slightly different, but have no consequences for the clinical evaluation of both doses. Under the assumption that drop-out is at random within the patterns, the pattern mixture approach adjusts the estimates to a certain degree. This approach accounts in a relatively simple way for informative drop-out

CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass

The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of D-xylose and L-arabinose from wheat bran, and D-galacturonic acid from sugar beet pulp.Peer reviewe