木质纤维素酶基因资源挖掘及真菌酶系改造

简述了木质纤维素酶基因资源挖掘的策略和方法及其在丝状真菌酶系改造中的应用。从候选基因的获取(木质纤维素酶基因资源的挖掘和高效利用)、外源基因的表达、酶系的复配和重构等方面综述了丝状真菌酶系改造的最新进展,并提出了丝状真菌酶系改造中亟须解决的关键问题。     

丝状真菌纤维素酶合成诱导及转录调控

利用廉价可再生木质纤维素资源水解产生的可发酵糖生产生物能源和生物基化学品是近年来国内外研究的热点。纤维素酶酶解是木质纤维素原料生物降解的重要手段,但目前纤维素酶生产成本过高,限制了纤维素生物转化和生物炼制的工业化应用。对丝状真菌纤维素酶基因表达和调控进行研究,有利于进一步选育纤维素酶高产菌株,降低纤维素酶生产成本。随着高通量测序及丝状真菌遗传操作等技术的进步,对丝状真菌纤维素酶诱导和基因表达调控机理有了更深入的认识。本文综述了近年来丝状真菌纤维素酶诱导和纤维素酶基因表达调控的最新进展,重点论述糖转运蛋白、转录因子和染色质重塑对纤维素酶表达调控的影响,并对利用人工锌指蛋白进行丝状真菌纤维素酶诱导调控研究进行了展望。     

木质纤维素降解酶生产菌株的遗传改造及应用

通过纤维素酶将木质纤维素向生物新能源的转化对经济社会的可持续发展具有重要意义,被用于纤维素酶制剂工业化生产的微生物大多属于丝状真菌,但丝状真菌的遗传操作困难,且纤维素酶诱导机制尚未阐明,严重制约了纤维素酶高产菌株选育与应用。本文综述了近年来纤维素酶高产菌株遗传操作方法的进展,重点论述了丝状真菌合成纤维素酶过程中的信号感应、信号传导、转录调控的研究,通过理性改造以提高纤维素酶生产菌株的产酶能力,并且总结展望了丝状真菌在工业生产中的应用。     

斜卧青霉去泛素化蛋白酶CREB的缺失提高纤维素酶的生产

斜卧青霉Penicillium decumbens T.是1种重要的产纤维素酶丝状真菌,能有效地降解利用木质纤维素生产第2代生物燃料。为了提高斜卧青霉纤维素酶的产量,构建了去泛素化酶基因creB的敲除盒,并通过同源双交换重组的方法,获得了creB基因缺失突变株ΔcreB。该突变株呈现明显的纤维素酶表达分泌抗葡萄糖代谢阻遏效应,ΔcreB菌株的滤纸酶活、内切纤维素酶活、木聚糖酶活以及外切纤维素酶活分别提高1.8倍、1.71倍、2.06倍以及2.04倍,其胞外蛋白质含量提高了2.68倍。确定了creB基因缺失突变株具有抗碳源代谢物阻遏的生理现象,CREB对斜卧青霉生产纤维素酶的能力具有显著影响,为系统改造丝状真菌高产纤维素酶菌株提供了理论指导。     

丝状真菌降解转化纤维素的机制与遗传改良前景简

丝状真菌可以分泌大量纤维素酶及辅助酶来降解纤维素底物,也是目前工业上纤维素酶的主要生产者。回顾并综述了丝状真菌降解转化纤维素的酶系和机制进展,详细总结了组学研究在纤维素酶研究上的新成果,并探讨了提高丝状真菌酶系效率和产量的遗传改良策略。     

丝状真菌降解转化纤维素的机制与遗传改良前景

丝状真菌可以分泌大量纤维素酶及辅助酶来降解纤维素底物,也是目前工业上纤维素酶的主要生产者。回顾并综述了丝状真菌降解转化纤维素的酶系和机制进展,详细总结了组学研究在纤维素酶研究上的新成果,并探讨了提高丝状真菌酶系效率和产量的遗传改良策略。     

粗糙脉孢菌木质纤维素降解利用研究进展简

粗糙脉孢菌作为木质纤维素降解真菌,不仅具有完整的木质纤维素降解酶系,而且还拥有全基因组基因敲除突变体库,是研究丝状真菌纤维素酶表达分泌和木质纤维素降解机制的优秀体系。近年来,国内外利用粗糙脉孢菌系统,在木质纤维素降解机制方面取得了显著进展,包括纤维素酶信号传导、调控以及生物质降解后糖的转运利用等。笔者就相关方面的进展进行综述,并对利用粗糙脉孢菌研究木质纤维素降解利用进行展望,总结和分析木质纤维素降解机制研究的国际前沿动态,有助于加深本领域研究人员对真菌体系纤维素降解机制的理解。     

粗糙脉孢菌木质纤维素降解利用研究进展

粗糙脉孢菌作为木质纤维素降解真菌,不仅具有完整的木质纤维素降解酶系,而且还拥有全基因组基因敲除突变体库,是研究丝状真菌纤维素酶表达分泌和木质纤维素降解机制的优秀体系。近年来,国内外利用粗糙脉孢菌系统,在木质纤维素降解机制方面取得了显著进展,包括纤维素酶信号传导、调控以及生物质降解后糖的转运利用等。笔者就相关方面的进展进行综述,并对利用粗糙脉孢菌研究木质纤维素降解利用进行展望,总结和分析木质纤维素降解机制研究的国际前沿动态,有助于加深本领域研究人员对真菌体系纤维素降解机制的理解。     

粗糙脉孢菌C2H2转录因子家族基因敲除突变体产纤维素酶筛选分析

丝状真菌的木质纤维素水解酶基因的表达很大程度上受到转录水平的调控,对纤维素酶系调控转录因子的研究对提高纤维素酶的产量具有重要意义。为了挖掘纤维素酶表达新调控基因,本研究对粗糙脉孢菌锌指转录因子C₂H₂家族的57株基因敲除突变株在以2%结晶纤维素为唯一碳源的培养条件下进行产纤维素酶水平分析筛选。通过测定发酵液的蛋白、内切β-1,4-葡聚糖酶酶活、外切纤维素酶酶活、β-葡萄糖苷酶酶活、木聚糖酶酶活及生物量,发现突变株L-38、L-85、L-40、L-64、L-99、L-07、L-86在蛋白水平及内切β-1,4-葡聚糖酶酶活水平均比野生型有25%-77%不等的显著提高,而突变株L-87、L-06在蛋白水平及内切β-1,4-葡聚糖酶酶活水平均比野生型有65%-80%不等的显著降低。这些纤维素酶新调控基因的获得为后续相关表达调控的研究提供了新素材。     

青霉生产木质纤维素降解酶系的研究进展

木质纤维素降解酶系的高效生产是实现植物生物质大规模生物炼制的重要支撑。就地生产木质纤维素降解酶,有助于降低其使用成本,提高技术经济效益。青霉是自然界常见的木质纤维素降解真菌,可以合成分泌种类多样、组分齐全的木质纤维素降解酶系,已被应用于纤维素酶制剂的工业生产。文中从就地生产降解酶,为木质纤维素生物炼制构建“糖平台”的角度,综述了青霉木质纤维素降解酶系的性质、菌株遗传改造及发酵工艺的研究进展。     

Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes

Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future.     

香菇HMG-box转录因子lelcrp1基因的功能

【目的】研究香菇(Lentinula edodes) HMG-box转录因子LELCRP1 (Lentinula edodes lignocellulase genes regulation protein 1)在木质纤维素降解相关酶基因表达中的功能与作用。【方法】通过double-joint及同源重组方法构建lelcrp1基因RNAi载体,采用根癌农杆菌介导转化的方法转入香菇异核菌株W1菌丝中,筛选得到RNAi转化子,通过Southern杂交检测插入片段在菌株W1基因组中的拷贝数量。采用荧光定量PCR检测RNAi转化子木质纤维素降解酶基因表达水平变化,并在含有3.5μg/mL潮霉素的MYG平板上测定RNAi转化子的菌丝生长速度。【结果】获得了4个lelcrp1基因表达水平与出发菌株W1相比显著下调6–7倍的RNAi转化子。Southern杂交结果显示,lelcrp1基因RNAi片段已成功整合至香菇菌株W1基因组内,并以单拷贝形式存在。对其中2个RNAi转化子的26个木质纤维素降解酶基因表达水平进行分析,发现其中9个纤维素酶基因、1个半纤维素酶基因、2个辅助酶AA9基因和1个锰过氧化物酶基因的表达水平均表现出明显的下调。平板生长试验表明,RNAi转化子菌丝生长速度均显著慢于出发菌株W1。【结论】通过RNAi技术成功抑制了香菇异核菌株中lelcrp1基因表达水平,并导致部分纤维素及木质素酶基因表达水平相应下调,首次发现HMG-box结构域的转录因子能调控木质纤维素降解相关酶基因表达。     

角蛋白降解能力差异菌株筛选体系的建立

以微生物降解为主的羽毛生物炼制是资源化利用其的重要手段之一,但机理不明是限制其进一步应用的瓶颈。突变体库筛选性状变异菌株的正向遗传学是研究分子机理的常用方案,该方案要求高效可靠的筛选方法。然而,目前依靠测酶活方法来决定降解能力,费时费力,难以用于大规模筛选。本文通过优化羽毛培养基成分及接种菌浓度,建立了一种用于筛选不同角蛋白降解能力微生物的筛选体系。利用该体系分析由mini Tn10构建的S. maltophinia DHHJ突变体库,得到了6株羽毛角蛋白降解能力减弱的突变体,筛选结果与酶活测试100%一致。该研究结果为寻找与角蛋白降解相关基因奠定了基础。     

基于能值理论的有色金属矿产资源开采生态补偿机制

矿产资源为中国经济的高速增长提供了不竭的动力,但在其开采过程中也带来了诸多的环境问题。在当今资源、环境的约束下,如何采取适宜的量化方法来表征矿产资源开采所带来的生态环境损失,并在此基础上确定合理的生态补偿标准,成为了一项重要的研究课题。选取我国有色金属采选业为研究案例,并基于能值分析方法,核算了矿产资源开采过程中造成的直接、间接环境损失,提出了生态补偿指数,用以为生态补偿标准的制定提供参考依据。对能值分析指标的计算和分析结果表明,从可持续发展角度,生态补偿指数为89.18%,说明我国有色金属采选业的环境投入较高,需要的补偿费用较多;能值产出率为9.24,表明有色金属采选业的生产效率高;环境承载率为238,呈现高负荷状态,区域环境所承受的压力巨大;可持续发展指数为0.039,表明我国有色金属采选业处于不可持续状态,急需采取相关环境保护措施进行调整。从经济成本角度,我国有色金属采选业需要的生态环境补偿费用约为4.38×109元,现阶段征收的资源税费远低于生态恢复的治理费用,不能够覆盖生态修复治理成本。最后根据本文研究内容得出我国有色金属采选业面临的主要问题,分别从宏观角度、微观角度及长远角度3个方面给出了相应的政策建议。     

Expression profile analysis of the polygalacturonase-inhibiting protein genes in rice and their responses to phytohormones and fungal infection

Polygalacturonase-inhibiting proteins (PGIPs) are typically leucine-rich repeat (LRR) proteins that can inhibit the activity of fungal polygalacturonases (PGs). In this study, two new Ospgip genes, named Ospgip6 and Ospgip7 with consensus sequence of ten imperfect LRR motif located on rice chromosomes 8 and 9, were identified using BLAST analysis. Both of them appear to be extracellular glycoproteins. To have a global view of the dynamic gene expression pattern, seven Ospgip genes were first analyzed using the Affymetrix rice genome array data from online resource. All of these seven Ospgip genes showed variable expression patterns among tissues/organs. In order to further investigate the potential function of these Ospgip genes, the responses of Ospgip genes to the treatment of various phytohormones (abscisic acid, brassinosteroid, gibberellic acid, 3-indole acetic acid, jasmonic acid, kinetin, naphthalene acetic acid and salicylic acid) as well as fungal infection were analyzed by real-time PCR using time course array. Generally, all the Ospgip genes were slightly up-regulated in the indica rice cultivar Minghui 63 under GA(3), KT and NAA treatments (except Ospgip2, which was down-regulated under KT treatment). In the japonica rice cultivar Zhonghua 11, Ospgip genes were regulated by most treatments with the response time variability. We also analyzed putative cis-elements in the promoter regions of Ospgip genes. This dataset provided a versatile resource to understand the regulatory network of Ospgip genes during the process of phytohormones treatment and fungal infection in the model monocotyledonous plant, rice, and could aid in the transgenic breeding against rice fungal diseases. KEY MESSAGE: All the seven Ospgip genes showed variable expression patterns in Minghui 63 and their expressions were regulated by different phytohormone treatments or fungal infection in Minghui 63 and Zhonghua 11.     

Comparative protein analysis of the chitin metabolic pathway in extant organisms: A complex network approach

Chitin is a structural endogenous carbohydrate, which is a major component of fungal cell walls and arthropod exoskeletons. A renewable resource and the second most abundant polysaccharide in nature after cellulose, chitin is currently used for waste water clearing, cosmetics, medical, and veterinary applications. This work comprises data mining of protein sequences related to the chitin metabolic pathway of completely sequenced genomes of extant organisms pertaining to the three life domains, followed by meta-analysis using traditional sequence similarity comparison and complex network approaches. Complex networks involving proteins of the chitin metabolic pathway in extant organisms were constructed based on protein sequence similarity. Several usual network indices were estimated in order to obtain information on the topology of these networks, including those related to higher order neighborhood properties. Due to the assumed evolutionary character of the system, we also discuss issues related to modularity properties, with the concept of edge betweenness playing a particularly important role in our analysis. Complex network approach correctly identifies clusters of organisms that belong to phylogenetic groups without any a priori knowledge about the biological features of the investigated protein sequences. We envisage the prospect of using such a complex network approach as a high-throughput phylogenetic method.     

Transformation of Fusarium virguliforme, the Causal Agent of Sudden Death Syndrome of Soybean

Fusarium virguliforme is a soil-borne pathogen that causes sudden death syndrome (SDS) in soybean. SDS is an important disease that causes significant losses in soybean growing areas worldwide. Little is known about the interaction between F. virguliforme and soybean. We have developed a protoplast-based fungal transformation system for F. virguliforme . One of the applications of the transformation system was the production of a green fluorescent protein (GFP)-expressing fungal transformant. The GFP-expressing fungus can be used to study fungal infection processes including fungal penetration, colonization, and spread, especially at the early stages of disease development. Furthermore, in an attempt to increase the genetic resources available to identify and characterize fungal virulence genes involved in the F. virguliforme -soybean system, we generated random insertional mutations in F. virguliforme using restriction enzyme mediated integration.     

An optimized microplate assay system for quantitative evaluation of plant cell wall-degrading enzyme activity of fungal culture extracts

Developing enzyme cocktails for cellulosic biomass hydrolysis complementary to current cellulase systems is a critical step needed for economically viable biofuels production. Recent genomic analysis indicates that some plant pathogenic fungi are likely a largely untapped resource in which to prospect for novel hydrolytic enzymes for biomass conversion. In order to develop high throughput screening assays for enzyme bioprospecting, a standardized microplate assay was developed for rapid analysis of polysaccharide hydrolysis by fungal extracts, incorporating biomass substrates. Fungi were grown for 10 days on cellulose- or switchgrass-containing media to produce enzyme extracts for analysis. Reducing sugar released from filter paper, Avicel, corn stalk, switchgrass, carboxymethylcellulose, and arabinoxylan was quantified using a miniaturized colorimetric assay based on 3,5-dinitrosalicylic acid. Significant interactions were identified among fungal species, growth media composition, assay substrate, and temperature. Within a small sampling of plant pathogenic fungi, some extracts had crude activities comparable to or greater than T. reesei, particularly when assayed at lower temperatures and on biomass substrates. This microplate assay system should prove useful for high-throughput bioprospecting for new sources of novel enzymes for biofuel production.