基于全基因组数据解析伞菌目木质纤维素降解酶系的差异

伞菌目Agaricales隶属于担子菌门Basidiomycota、伞菌亚门Agaricomycotina,是担子菌门中最大的一个类群,能够以腐生、寄生以及共生的模式在自然环境中生存,生存范围广,对于维持生态环境的平衡具有重要的作用。本研究基于51株伞菌目真菌基因组大数据挖掘降解木质纤维素相关的碳水化合物活性酶(carbohydrate-active enzymes,CAZymes)和氧化还原酶(oxidoreductases),同时比较白腐菌、褐腐菌、腐生菌、菌根菌、植物致病菌、兼性寄生菌、动物共生菌和不明生态型真菌降解机制的差异。结果显示白腐菌和褐腐菌等木腐菌、菌根菌、兼性寄生菌、其他腐生菌、植物致病菌以及共生菌的CAZymes家族平均数目为134个、93个、101个、127个、61个和32个,而CAZymes同源的基因平均数目为398个、240个、463个、407个、418个、131个和38个,木腐菌的CAZymes家族最为丰富,但是兼性寄生菌基因数目最多;同时具有木质纤维素降解酶活性的26个家族中,基因数目分别为86个、32个、101个、86个、104个、36个和10个。在木腐菌(白腐菌和褐腐菌)、菌根菌、兼性寄生菌、腐生菌、不明生态型、植物致病菌和动物共生菌中氧化还原酶相关的基因数目为44个、35个、48个、53个、59个、6个和29个,其中不明生态型真菌的基因数目最多达到了59个,植物致病菌的数量最少。CAZymes和氧化还原酶在不同的真菌中数量和种类差别很大,与其生态类型的关系不明显,此研究丰富了木质纤维素降解机制的多样性,但是需要进一步的实验设计对其生物活性进行验证以及进行蛋白家族进化分析。     

Effects of different nitrogen sources on lignocellulose degradation and APPL production

Naphthalene utilizing bacteria were isolated from several sites above and below the discharge from a coking plant. The distribution of the bacteria was influenced by the effluent. Of these isolates, 11·4% obtained from the effluent discharge site, contained plasmids. No conjugal transfer of naphthalene utilizing ability was observed in over 1000 matings. Curing and transformation experiments demonstrated that one plasmid pNB33 (101 kb) was concerned with naphthalene catabolism.     

Inhibition of 2A-mediated ‘cleavage’ of certain artificial polyproteins bearing N-terminal signal sequences

Where 2A oligopeptide sequences occur within ORFs, the formation of the glycyl–prolyl peptide bond at the C-terminus of (each) 2A does not occur. This property can be used to concatenate sequences encoding several proteins into a single ORF: each component of such an artificial polyprotein is generated as a discrete translation product. 2A and ‘2A-like’ sequences have become widely utilised in biotechnology and biomedicine. Individual proteins may also be co- and post-translationally targeted to a variety of sub-cellular sites. In the case of polyproteins bearing N-terminal signal sequences we observed, however, that the protein downstream of 2A (no signal) was translocated into the endoplasmic reticulum (ER). We interpreted these data as a form of ‘slipstream’ translocation: downstream proteins, without signals, were translocated through a translocon pore already formed by the signal sequence at the N-terminus of the polyprotein. Here we show this effect is, in fact, due to inhibition of the 2A reaction (formation of fusion protein) by the C-terminal region (immediately upstream of 2A) of some proteins when translocated into the ER. Solutions to this problem include the use of longer 2As (with a favourable upstream context) or modifying the order of proteins comprising polyproteins.     

Efficient oleaginous yeasts for lipid production from lignocellulosic sugars and effects of lignocellulose degradation compounds on growth and lipid production

Microbial lipid production using lignocellulosic biomass is considered an alternative for biodiesel production. In this study, 418 yeast strains were screened to find efficient oleaginous yeasts which accumulated large quantities of lipid when cultivated in lignocellulosic sugars. Preliminary screening by Nile red staining revealed that 142 strains contained many or large lipid bodies. These strains were selected for quantitative analysis of lipid accumulation by shaking flask cultivation in nitrogen-limited medium II containing 70 g/L glucose or xylose or mixture of glucose and xylose in a ratio of 2:1. Rhodosporidium fluviale DMKU-SP314 produced the highest lipid concentration of 7.9 g/L when cultivated in the mixture of glucose and xylose after 9 days of cultivation, which was 55.0% of dry biomass (14.3 g/L). The main composition of fatty acids were oleic acid (40.2%), palmitic acid (25.2%), linoleic acid (17.9%) and stearic acid (11.1%). Moreover, the strain DMKU-SP314 could grow and produce lipid in a medium containing predominantly lignocellulose degradation products, namely, acetic acid, formic acid, furfural, 5-hydroxymethylfurfural (5-HMF) and vanillin, with however, some inhibitory effects. This strain showed high tolerance to acetic acid, 5-HMF and vanillin. Therefore, R. fluviale DMKU-SP314 is a promising strain for lipid production from lignocellulosic hydrolysate.     

白腐菌混合发酵产酶及对秸秆木质纤维素的降解研究

采用平板显色法从五株白腐菌中筛选出一组相容性较好且产漆酶的组合,进行了混合发酵产酶及秸秆降解实验,结果发现混合发酵相对于纯种培养具有较明显优势,不仅体系中漆酶的活性大为增强,而且拥有更全的胞外酶组成;同比情况下,混合发酵对农作物秸秆木质纤维素的降解程度也最大.     

Biotechnology in the degradation and utilization of lignocellulose

Lignocellulose is the predominant renewable resource. It uses include fuel, as the feedstock for the pulp and paper industry, and for animal nutrition. It also constitutes a large proportion of agricultural and urban waste. Biotechnology has roles in its efficient production and utilisation. The types of lignin substrates available for study of lignin biodegradation are described. The white rot fungus Phanerochaete chrysosporium is the archetypal system for the study of lignocellulose degradation, since it mineralises lignin and degrades both cellulose and hemicellulose. The salient features of the P. chrysosporium system are described. The lignin peroxidases are a family of proteins, and it is shown that expression of their genes is differential. P. chrysosporium is heterokaryotic with two gene equivalents that have abundant RFLPs. A set of basidiospore-derived strains with genetic compositions defined by such RFLPs provided the potential basis for a strain improvement programme for lignin degradation. However, analysis of this system using radiolabelled synthetic lignin (DHP) as the substrate confirmed previous evidence that both the substrate and the fungal cultures displayed much variation, so that it was difficult to quantify performance for this property. The cellobiohydrolase I enzymes are also coded for by a family of genes, and evidence is also presented for allelic variants, for differential expression and for differential splicing. In contrast, the cellobiohydrolase II function is encoded at a unique genetic locus. Approaches to an homologous integrative transformation system are discussed. Some actinomycete bacteria represent an alternative system for lignin solubilisation in which strains differ in their spectra of activities on lignocellulose substrates. The xylanase system of Streptomyces cyaneus is shown to include three enzymes, two of which are inducible by xylan. A novel assay method was developed and used to demonstrate that the third is constitutive and also non-repressible by glucose. It is proposed that this acts as a sensor for xylans in the environment that can yield breakdown products that are taken up and can then act as inducers of the other two enzymes. The studies on microbial lignocellulose degradation from different laboratories have allowed the formulation of specific biotechnological goals, and some of the problems and opportunities in this area are identified.     

Effect of lignocellulose degradation products on microbial biomass and lipid production by the oleaginous yeast Cryptococcus curvatus

This work investigated effects of lignocellulose degradation products on cell biomass and lipid production by Cryptococcus curvatus. Furfural was found to have the strongest inhibitory effect. For the three phenolic compounds tested, vanillin was the most toxic, while PHB and syringaldehyde showed comparable inhibitions in the concentration range of 0–1.0 g/L. Generally little significant differences on the relative cell biomass and lipid contents at the same concentrations of tested compounds were observed between glucose and xylose as a sole carbon source. At 1.0 g/L of furfural, the cell biomass and lipid content decreased by 78.4% and 61.0% for glucose as well as 72.0% and 59.3% for xylose, respectively. C. curvatus ceased to grow at concentrations of PHB over 1.0 g/L or vanillin over 1.5 g/L. The strain could survive in the presence of syringaldehyde up to 2.0 g/L for glucose or 1.5 g/L for xylose. The compounds’ negative impact was reduced by an increase in inoculum size and a 10% (v/v) seed was detected to be optimal for cell biomass and lipid production. The results demonstrated C. curvatus could effectively utilize most of the dominant monosaccharides and cellobiose existing in lignocellulosic biomass hydrolysate in the presence of toxic compounds.     

Aluminum borate whisker-mediated production of transgenic tobacco plants

An aluminum borate whiskers-mediated transformation system for calluses of tobacco (Nicotiana tabacum, cv. SR-1) has been developed. A total of 50 small pieces of calluses were vigorously agitated in a liquid medium containing aluminum borate whiskers, pBI221 plasmid carrying the -glucuronidase (GUS) gene, and pBI222 plasmid carrying the hygromycin phosphotransferase (HPT) gene. After treatment, calluses were cultured to select for hygromycin resistance, and three resistant calluses were obtained. Adventitious shoots were produced from each hygromycin-resistant callus and were transferred to rooting medium. A total of three plantlets obtained from each hygromycin-resistant callus were acclimatized and established in soil. Polymerase chain reaction analysis revealed that all the plantlets were cotransformed with both the GUS and HPT genes. Detached leaves of transgenic individuals showed clear hygromycin resistance when cultured in liquid medium. Histochemical assay for GUS revealed that one of these transgenic plants expressed the GUS gene, indicating coexpression of foreign genes.     

Activities of enzymes involved in the phenylpropanoid pathway in constitutively salicylic acid-producing tobacco plants

Chorismate mutase (CM, EC 5.4.99.5), phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) and chalcone synthase (CHS, EC 2.3.1.74) activities were studied in constitutive salicylic acid-producing (CSA) tobacco plants in relation to the accumulation of flavonoids and chlorogenic acid. The CM, PAL and CHS activities in CSA-tobacco (Nicotiana tabacum cv. Samsun NN) plants were lower than in non-transgenic tobacco plants. Flavonoid and chlorogenic acid accumulation was suppressed in CSA-tobacco plants compared to those of non-transgenic tobacco plants.     

Microbial degradation of lignocellulose: the lignin component

A new procedure was developed for the study of lignin biodegradation by pure or mixed cultures of microorganisms. Natural lignocelluloses were prepared containing C in primarily their lignin components by feeding plants l-[U-C]phenylalanine through their cut stems. Lignin degradation was observed in numerous soils by monitoring evolution of CO(2) from [C]lignin-labeled oak (Quercus albus), maple (Acer rubrum), and cattail (Typha latifola). An organism (Thermonospora fusca ATCC 27730) that is known to degrade cellulose but not lignin was shown to grow on lignocellulose in the presence of [C]lignocelluloses without evolution of CO(2). A known lignin degrader (a white-rot fungus, Polyporus versicolor) was shown to readily evolve CO(2) from damp C-labeled cattail and C-labeled maple.     

Differential effects of mineral and organic acids on the kinetics of arabinose degradation under lignocellulose pretreatment conditions

Sugar degradation occurs during acid-catalyzed pretreatment of lignocellulosic biomass at elevated temperatures, resulting in degradation products that inhibit microbial fermentation in the ethanol production process. Arabinose, the second most abundant pentose in grasses like corn stover and wheat straw, degrades into furfural. This paper focuses on the first-order rate constants of arabinose (5 g/L) degradation to furfural at 150 and 170 °C in the presence of sulfuric, fumaric, and maleic acid and water alone. The calculated degradation rate constants (k_d) showed a correlation with the acid dissociation constant (pK_a), meaning that the stronger the acid, the higher the arabinose degradation rate. However, de-ionized water alone showed a catalytic power exceeding that of 50 mM fumaric acid and equaling that of 50 mM maleic acid. This cannot be explained by specific acid catalysis and the shift in pK_w of water at elevated temperatures. These results suggest application of maleic and fumaric acid in the pretreatment of lignocellulosic plant biomass may be preferred over sulfuric acid. Lastly, the degradation rate constants found in this study suggest that arabinose is somewhat more stable than its stereoisomer xylose under the tested conditions.     

Rhesus monkey TRIM5alpha restricts HIV-1 production through rapid degradation of viral Gag polyproteins

Mammalian cells have developed diverse strategies to restrict retroviral infection. Retroviruses have therefore evolved to counteract such restriction factors, in order to colonize their hosts. Tripartite motif-containing 5 isoform-alpha (TRIM5alpha) protein from rhesus monkey (TRIM5alpharh) restricts human immunodeficiency virus type 1 (HIV-1) infection at a postentry, preintegration stage in the viral life cycle, by recognizing the incoming capsid and promoting its premature disassembly. TRIM5alpha comprises an RBCC (RING, B-box 2 and coiled-coil motifs) domain and a B30.2(SPRY) domain. Sequences in the B30.2(SPRY) domain dictate the potency and specificity of the restriction. As TRIM5alpharh targets incoming mature HIV-1 capsid, but not precursor Gag, it was assumed that TRIM5alpharh did not affect HIV-1 production. Here we provide evidence that TRIM5alpharh, but not its human ortholog (TRIM5alphahu), blocks HIV-1 production through rapid degradation of HIV-1 Gag polyproteins. The specificity for this restriction is determined by sequences in the RBCC domain. Our observations suggest that TRIM5alpharh interacts with HIV-1 Gag during or before Gag assembly through a mechanism distinct from the well-characterized postentry restriction. This finding demonstrates a cellular factor blocking HIV-1 production by actively degrading a viral protein. Further understanding of this previously unknown restriction mechanism may reveal new targets for future anti-HIV-1 therapy.     

Localisation of degradative enzymes in white-rot decay of lignocellulose

The use of immunogold-cytochemical labelling techniques in electron microscopy of wood infected by basidiomycete fungi has assisted in the elucidation of the localisation of enzymes which degrade lignocellulose. The use of specific immunocytochemical techniques is discussed with respect to the authenticity and accuracy of the methods, the use of adequate controls in the gold-labelling procedure, and the immunospecificity of the antibodies.Localisation of the lignin-degrading enzymes, lignin-peroxidase and laccase, has shown that these enzymes do not bind to wood cell walls unless the process of decay has already commenced. Similarly localisation of cellulases Endoglucanase II (EGII) and Cellobiohydrolase I (CBHI) has shown that these enzymes only bind to exposed ends of cellulose fibrils and to partially degraded areas of the wood cell wall. -Glucosidase is always immobilised within the extracellular polysaccharide layer surrounding fungal hyphae.This review postulates that there is regulation of the release sequence of these lignocellulolytic enzymes defining the spatial arrangement between the hyphae and the wood cell wall. This hypothesis is presented diagrammatically.     

微生物降解利用木质纤维素的协同作用

木质纤维素复杂的结构组成,是制约高效降解利用这一资源、发展生物炼制的瓶颈。微生物的多酶(菌)体系可有效降解木质纤维素。除好氧微生物的游离酶协同系统之外,主要存在于厌氧细菌中的纤维小体也是有序、高效的协同降解纤维素的复合体系。近年来,在天然纤维小体研究的基础上,研究者们成功设计、构建了人工纤维小体,加深了对这一复合体系的组成单元的理性认识。另外,菌群共培养技术利用各组成菌株代谢途径的协同作用实现了木质纤维素的高效降解。最后,引入异源纤维素酶,可改造现有工程菌株的代谢网络,提高工程菌发酵生产终产物的能力。这些技术有利于实现一步转化生产乙醇的联合生物工艺,有助于提高生物炼制的产率、降低生产成本。     

Industrial production and utilization of enzymes from flowering plants

The papaya tree and barley are the only flowering plants now being utilized to any extent for commercial production of enzymes. The papaya fruit yields papain, a protein-digesting enzyme which can be used to eliminate or modify protein in several industries. Barley is germinated to malt, which contains amylase, necessary for the conversion of starchy materials to fermentable sugars. Malt is used to a great extent in the brewing and distilling industries. Other plants, for example, alfalfa, oranges and beans, are used to a minor extent in the preparation of enzymes for specific industrial purposes.     

The effects of RNA degradation enzymes on antisense RNAI controlling ColE2 plasmid copy number

Replication of the ColE2 plasmid requires a plasmid-coded initiator protein (Rep). Rep expression is controlled by antisense RNA (RNAI), which prevents the Rep mRNA translation. In this paper, we examined the effects of RNA degradation enzymes on the degradation pathways of RNAI of the ColE2 plasmid. In the DeltapcnB strain lacking the poly(A) polymerase I (PAP I) the RNAI degradation intermediate (RNAI(*)) accumulates much more than that in the wt strain. RNAI(*) is produced by the RNase E cleavage. RNase II and PNPase are involved in further degradation of RNAI(*) and PAP I is necessary for efficient degradation. The degradation process of ColE2 RNAI is similar to those of R1 CopA RNA and ColE1 RNAI, although the nucleotide sequences and fine secondary structures of these three RNAs are different. ColE2 RNAI is cleaved at multiple positions in the 5' end region by RNase E. The degradation pathway of ColE2 RNAI shown here is quite different from that of the ColE2 Rep mRNA which we have previously reported. In the DeltapcnB strain used for RNA analysis the copy number of the ColE2 plasmid decreases to about a half as compared with that in the isogenic wt strain.     

Effect of abiotic stresses on the activity of antioxidative enzymes and contents of phytohormones in wild type and AtCKX2 transgenic tobacco plants

The responses of antioxidant enzymes (AOE) ascorbate peroxidase (APX), glutathione reductase (GR), superoxide dismutase (SOD), and catalase (CAT) in soluble protein extracts from leaves and roots of tobacco (Nicotiana tabacum L. cv. Samsun NN) plants to the drought stress, salinity and enhanced zinc concentration were investigated. The studied tobacco included wild-type (WT) and transgenic plants (AtCKX2) harbouring the cytokinin oxidase/dehydrogenase gene under control of 35S promoter from Arabidopsis thaliana (AtCKX2). The transgenic plants exhibited highly enhanced CKX activity and decreased contents of cytokinins and abscisic acid in both leaves and roots, altered phenotype, retarded growth, and postponed senescence onset. Under control conditions, the AtCKX2 plants exhibited noticeably higher activity of GR in leaves and APX and SOD in roots. CAT activity in leaves always decreased upon stresses in WT while increased in AtCKX2 plants. On the contrary, the SOD activity was enhanced in WT but declined in AtCKX2 leaves. In roots, the APX activity prevailingly increased in WT while mainly decreased in AtCKX2 in response to the stresses. Both WT and AtCKX2 leaves as well as roots exhibited elevated abscisic acid content and increased CKX activity under all stresses while endogenous CKs and IAA contents were not much affected by stress treatments in either WT or transgenic plants.     

Synergistic effects of cellulolytic and pectinolytic enzymes in degrading sugar beet pulp

Three cellulases, one hemicellulase and three pectinases were used, separately or in binary and ternary combinations, to hydrolyze dried beet-pulp, a by-product of the sugar industry. By IE-HPLC the compositions and concentrations of the sugars released were determined. The results obtained by enzymatic saccharification were compared to those obtained by acid hydrolysis. The synergistic action of cellulolytic and pectinolytic enzymes in release of total monosaccharides, and of glucose, arabinose and galacturonic acid was also studied. The combination of cellulase, hemicellulase and pectinase, commercially available, was as effective in degrading the beet pulp as the acid hydrolysis. Pectinase appeared to be the most important enzyme, since by hydrolyzing the pectic surface of the lignocellulosic substrate, it favoured the degradation of cellulose and hemicellulose by the respective enzymes.