Proteome analysis of fungal and bacterial involvement in leaf litter decomposition

Fungi and bacteria are key players in the decomposition of leaf litter, but their individual contributions to the process and their interactions are still poorly known. We combined semi‐quantitative proteome analyses (1‐D PAGE‐LC‐MS/MS) with qualitative and quantitative analyses of extracellular degradative enzyme activities to unravel the respective roles of a fungus and a bacterium during litter decomposition. Two model organisms, a mesophilic Gram‐negative bacterium (Pectobacterium carotovorum) and an ascomycete (Aspergillus nidulans), were grown in both, pure culture and co‐culture on minimal medium containing either glucose or beech leaf litter as sole carbon source. P. carotovorum grew best in co‐culture with the fungus, whereas growth of A. nidulans was significantly reduced when the bacterium was present. This observation suggests that P. carotovorum has only limited capabilities to degrade leaf litter and profits from the degradation products of A. nidulans at the expense of fungal growth. In accordance with this interpretation, our proteome analysis revealed that most of the extracellular biodegradative enzymes (i.e. proteases, pectinases, and cellulases) in the cultures with beech litter were expressed by the fungus, the bacterium producing only low levels of pectinases.     

蛋白质组学在植物水分胁迫应答中的应用研究进展

水分胁迫是影响植物生长发育的主要生长因子。通过蛋白质组学技术可对水分胁迫下植物差异变化的蛋白和基因进行挖掘,在研究植物抗旱生理机制方面意义重大。总结了植物蛋白质组学的基本方法与关键技术,同时从光合与碳代谢相关蛋白、抗氧化系统、渗透调节蛋白、热激蛋白、胚胎发育晚期丰富蛋白、转录因子等方面综述了近几年国际上在植物水分胁迫蛋白质组研究方面的进展,并展望了今后蛋白质组学技术发展的方向。     

Molecular docking analysis of modified gedunin from neem with snake venom enzymes

Snakebites are a problem due to the increasing number of deaths and permanent disabilities. There is currently a shortage of antidotes for snakebite. The existing antibody antidote, produced from horse/sheep plasma/sera is expensive, species-dependent, and causes fatal side effects. Therefore, it is of interest use of natural flavonoid named gedunin from the Azadirachta indica (Neem) plant species to combat snakebites. Thus, we show the molecular docking analysis of gedunin (C26H31N2O6F) with enzymes (common in snake species) such as 5-nucleotidase, acetyl cholinesterase, L-aao, metalloproteinase, serine, thrombin and phospholipase A2. The modified gedunin in the enzyme pocket showed improved pharmacological properties for further consideration in combating snakebites.     

Proteome analysis of antibody-producing CHO cell lines with different metabolic profiles

Two-dimensional gel electrophoresis and tandem mass spectrometry were used to identify proteins associated with a metabolic shift during fed-batch cultures of two recombinant antibody-producing CHO cell lines. The first cell line underwent a marked change in lactate metabolism during culture, initially producing lactate and then consuming it, while the second cell line produced lactate for a similar duration but did not later consume it. The first cell line displayed a declining specific antibody productivity during culture, correlating to the 2-D gel results and the intracellular antibody concentration determined by HPLC. Several statistical analysis methods were compared during this work, including a fixed fold-change criterion and t-tests using standard deviations determined in several ways from the raw data and mathematically transformed data. Application of a variance-stabilizing transformation enabled the use of a global empirical standard deviation in the t-tests. Most of the protein spots changing in each cell line did not change significantly in the other cell line. A substantial fraction of the changing proteins were glycolytic enzymes; others included proteins related to antibody production, protein processing, and cell structure. Enolase, pyruvate kinase, BiP/GRP78, and protein disulfide isomerase were found in spots that changed over time in both cell lines, and some protein changes differed from previous reports. These data provide a foundation for future investigation of metabolism in industrially relevant mammalian cell culture processes, and suggest that along with differences between cell types, the proteins expressed in cultures with low lactate concentrations may depend on how those conditions were generated.     

不同采集时间野葛不同部位总黄酮和葛根素含量比较

临床常用药材葛根来源于野葛（Pueraria lobata（Willd．）Ohwi]的干燥根,含有多种异黄酮化合物,市场需求量较大,资源比较紧张。过度无序的采挖不仅使其野生资源面临枯竭的危险,也造成了产地区域生态环境的破坏。有研究表明,野葛地上部位含有的成分与葛根基本相同。为寻求利用野葛地上藤茎部位替代葛根药用的可行性,作者用紫外分光光度法和高效液相色谱法分析了不同时间采集的野葛不同部位的总黄酮和葛根素含量,为进一步扩大和开发野葛的药用新资源提供参考依据。     

植物次生代谢产物的生态学意义

概述了植物次生代谢产物的生态学意义,包括增强植物抵御病虫害的侵袭、适应生存环境以及促进植物自身的生存和繁衍等方面的重要作用     

Root exudates and plant secondary metabolites of different plants enhance polychlorinated biphenyl degradation by rhizobacteria

Polychlorinated biphenyls (PCBs) are toxic and persistent compounds that are difficult to break down and biodegrade. Plant secondary metabolites (PSMs) on root exudates can act as inducers of the biphenyl catabolic pathway, enhancing PCB biodegradation. In this study, the authors evaluated the effect of root exudates and PSMs obtained from Avena sativa, Brachiaria decumbens, Medicago sativa, and Brassica juncea on the biodegradation of PCB 44, PCB 66, PCB 118, PCB 138, PCB 153, PCB 170, and PCB 180 by a microbial consortium isolated from the rhizosphere of plants grown on soil contaminated with Aroclor 1260. Microorganisms were identified as Pseudomonas sp. and Stenotrophomonas sp. based on their 16S rRNA sequence. The plant root exudates increased the degradation percentage of PCB 44, PCB 66, and PCB 118, which were used as carbon source by the microorganisms. Flavanone, flavone, isoflavone, 7-hydroxyflavanone, 7-hydroxyflavone, and 6-hydroxyflavone were the PSMs identified in the root exudates, which increased the degradation percentage of all seven PCB congeners; they were also used as growth substrates by microbial consortium. These results showed the importance of the interaction between plants and microorganisms for achieving the removal of persistent pollutants such as PCBs from soil.     

Proteome analysis of human serum proteins adsorbed onto different titanium surfaces used in dental implants

Titanium dental implants are commonly used due to their biocompatibility and biochemical properties; blasted acid-etched Ti is used more frequently than smooth Ti surfaces. In this study, physico-chemical characterisation revealed important differences in roughness, chemical composition and hydrophilicity, but no differences were found in cellular in vitro studies (proliferation and mineralization). However, the deposition of proteins onto the implant surface might affect in vivo osseointegration. To test that hypothesis, protein layers formed on discs of both surface type after incubation with human serum were analysed. Using mass spectrometry (LC/MS/MS), 218 proteins were identified, 30 of which were associated with bone metabolism. Interestingly, Apo E, antithrombin and protein C adsorbed mostly onto blasted and acid-etched Ti, whereas the proteins of the complement system (C3) were found predominantly on smooth Ti surfaces. These results suggest that physico-chemical characteristics could be responsible for the differences observed in the adsorbed protein layer.     

In vitro isoflavonoid production in callus from different organs of Pueraria lobata (Wild.) Ohwi

Pueraria lobata (Wild.) Ohwi is a medicinal plant producing large amounts of isoflavonoid glycosides. Here, the ability of in vitro callus cultures to synthesize isoflavonoids was tested. Callus cultures have been initiated from different explants of in vitro germinated plants using modified MS medium. Roots, leaves and stem segments were the best sources of callus tissue. The isoflavonoid profile and content was determined by means of chromatographic methods. Callus from all organs contained isoflavonoid aglycones: genistein and daidzein and daidzein glycosides: daidzin, puerarin and 3'-methoxypuerarin. The differences between each kind of explant were observed in both the total amount of isoflavonoids and in the proportion of individual compounds. The highest content was in root callus, followed by leaf- and stem callus.     

Glycosyltransferases: key players involved in the modification of plant secondary metabolites

Glycosyltransferases are members of the multigene superfamily in plants that can transfer single or multiple activated sugars to a range of plant molecules, resulting in the glycosylation of plant compounds. Although the activities of many glycosyltransferases and their products have been recognized for a long time, only in recent years were some glycosyltransferase genes identified and a few functionally characterized in detail. Glycosylation is thought to be one of the most important modification reactions towards plant secondary metabolites, and plays a key role in maintaining cell homeostasis, thus likely participating in the regulation of plant growth, development and in defense responses to stress environments. With advances in plant genome projects and the development of novel technologies in analyzing gene function, significant progress could be made in gaining new insights into the properties and precise biological roles of plant secondary product glycosyltransferases, and the new knowledge will have extensive application prospects in the catalytic synthesis of glycoconjugates and metabolic engineering of crops. In this review, we summarize the current research, highlighting the possible biological roles, of plant secondary metabolite glycosyltransferases and discuss their potential applications as well as aspects to be further studied in the near future.     

Glycosyltransferases:key players involved in the modification of plant secondary metabolites

Glycosyltransferases are members of the multigene superfamily in plants that can transfer single or multiple activated sugars to a range of plant molecules,resulting in the glycosylation of plant compounds.Although the activities of many glycosyltransferases and their products have been recognized for a long time,only in recent years were some glycosyltransferase genes identified and a few functionally characterized in detail.Glycosylation is thought to be one of the most important modification reactions towards plant secondary metabolites,and plays a key role in maintaining cell homeostasis,thus likely participating in the regulation of plant growth,development and in defense responses to stress environments.With advances in plant genome projects and the development of novel technologies in analyzing gene function,significant progress could be made in gaining new insights into the properties and precise biological roles of plant secondary product glycosyltransferases,and the new knowledge will have extensive application prospects in the catalytic synthesis of glycoconjugates and metabolic engineering of crops.In this review,we summarize the current research,highlighting the possible biological roles,of plant secondary metabolite glycosyltransferases and discuss their potential applications as well as aspects to be further studied in the near future.     

野葛离体培养进展及潜在应用价值

综述了野葛离体培养的研究进展及其利用离体培养进行植物次生代谢物——异黄酮的提取.     

葛根异黄酮的快速分离检测方法研究

以SDS正丁醇-正庚烷-水组成的微乳体系作为展开剂,通过聚酰胺薄层层析,探讨不同类型微乳液对葛根异黄酮分离检测效果的影响。结果表明,选择含水量为70％的微乳液作为展开剂,分离效果明显,一次检测出12个黄酮化合物;与以三氯甲烷-甲醇-水(7:2．5:0．25)为展开剂的硅胶薄层相比,微乳薄层色谱对葛根异黄酮的检测效果和灵敏度显著提高,为实验研究中常规检测提供了简便快捷的方法。     

Quantitative Proteome Analysis of Jatropha curcas L. Genotypes with Contrasting Levels of Phorbol Esters

The phorbol esters in the seeds of Jatropha curcas are a major hindrance to the full exploitation of the potential of this oil crop as a source of raw material for the production of biodiesel. Here, various quantitative proteomic strategies are used to establish the proteomes of roots, leaves, and endosperm of two genotypes of J. curcas with contrasting levels of phorbol esters in the seeds. In total 4532, 1775, and 503 proteins are identified respectively in roots, leaves, and endosperm, comprising 5068 unique proteins; of this total, 185 are differentially abundant in roots, 72 in leaves, and 20 in the endosperm. The biosynthetic pathways for flavonoids and terpenoids are well represented in roots, including the complete set of proteins for the mevalonate and non‐mevalonate/Deoxyxylulose 5‐Phosphate pathways, and proteins involved in the branches which lead to the synthesis tricyclic diterpenoids and gibberellins. Also, casbene synthase which catalyzes the first committed step in the biosynthesis of tigliane‐type diterpenes is identified in roots of both genotypes, but not in leaves and endosperm. This dataset will be a valuable resource to explore the biochemical basis of the low toxicity of Jatropha genotypes with low concentration of phorbol esters in the seeds.     

Cell cycle analysis of Taxus suspension cultures at the single cell level as an indicator of culture heterogeneity

Single cell growth and division was measured via flow cytometry in order to characterize the metabolic variability of Taxus cuspidata suspension cultures, which produce the valuable secondary metabolite Taxol. Good agreement was observed between the cell cycle distribution and biomass accumulation over the batch culture period. Specific growth rates of 0.13 days(-1) by fresh weight and 0.15 days(-1) by dry weight were measured. Elicitation with methyl jasmonate (MJ) significantly decreased both cell cycle progression and biomass accumulation, as the specific growth rate decreased to 0.027 days(-1) by fresh and dry weight. Despite the decrease in biomass accumulation for MJ elicited cultures, sucrose utilization was not significantly different from control cultures. MJ elicitation also increased the accumulation of paclitaxel and other taxanes. The accumulation of upstream taxanes (baccatin III and 10-deactylbaccatin III) increased during exponential growth, reached a maximum around day 12, and then declined throughout the stationary phase. The paclitaxel concentration increased during both exponential growth and stationary phase, reaching a maximum around days 20-25. Throughout the culture period, greater than 70% of the cells were in G(0)/G(1) phase of the cell cycle. Studies using bromodeoxyuridine (BrdU) incorporation showed that approximately 65% of the Taxus cells are noncycling, even during exponential growth. Although the role of these cells is currently unknown, the presence of a large, noncycling subpopulation can have a significant impact on the utilization of plant cell culture technology for the large-scale production of paclitaxel. These results demonstrate that there is a high degree of metabolic heterogeneity in Taxus cuspidata suspension cultures. Understanding this heterogeneity is important for the optimization of plant cell cultures, particularly the reduction of production variability.     

Proteome profiling highlights mechanisms underlying pigment and tocopherol accumulation in red and black rice seeds

Rice is a major component of the human diet and feeds more than 50 million people across the globe. We previously developed two pigmented rice cultivars, Super-hongmi (red seeds) and Super-jami (black seeds), that are highly rich in antioxidants and exhibit high levels of radical scavenging activities. However, the molecular mechanism underlying the accumulation of pigments and different antioxidants in these rice cultivars remains largely elusive. Here, we report the proteome profiles of mature Super-hongmi and Super-jami seeds, and compared them with the Hopum (white seeds) using a label-free quantitative proteomics approach. This approach led to the identification of 5127 rice seed proteins of which 1628 showed significant changes in the pigmented rice cultivar(s). The list of significantly modulated proteins included a phytoene desaturase (PDS3) which suggested accumulation of ζ-carotene in red seeds while the black seeds seem to accumulate more of anthocyanins because of the higher abundance of dihydroflavonol 4-reductase. Moreover, proteins associated with lignin and tocopherol biosynthesis were highly increased in both red and black cultivars. Taken together, these data report the seed proteome of three different colored rice seeds and identify novel components associated with pigment accumulation in rice.     

不同寄主植物继代饲养后草地贪夜蛾幼虫生理酶活性差异

为了明确继代饲喂不同寄主植物对草地贪夜蛾幼虫体内生理酶活性的影响,在室内分别用3种寄主植物叶片饲养草地贪夜蛾多代,测定其F3代5龄幼虫体内保护酶（SOD,POD,CAT）、消化酶（脂肪酶、胃蛋白酶和α-淀粉酶）和解毒酶（GSTs,CarEs,CYP450s）活性差异,并分析不同寄主植物次生代谢物含量与幼虫体内酶活及其生长发育的相关性。结果表明,取食马铃薯叶片的F3代幼虫总发育历期最长,取食小麦的最短,两者间差异显著;小麦叶片中的单宁、总酚、类黄酮和生物碱含量均显著低于玉米和马铃薯;草地贪夜蛾幼虫体内保护酶活性均为取食小麦叶片的最低,取食马铃薯叶片的最高,其中取食马铃薯叶片的草地贪夜蛾体内POD和SOD酶活性达取食小麦的1.34和1.26倍;以3种寄主为食的F3代幼虫脂肪酶和α-淀粉酶活性变化不大,但持续饲喂马铃薯叶片3个世代可导致草地贪夜蛾幼虫体内胃蛋白酶活性显著升高,达10.502 U/mg. prot,为持续饲喂玉米叶片幼虫（1.508 U/mg. prot）的6.96倍以上。连续饲喂3种寄主叶片后的幼虫GSTs和CarEs活性无显著性差异,但取食玉米叶片的幼虫体内细胞色素P450s（CYP450s）活性显著高于取食小麦和马铃薯的幼虫。可见,连续多代取食次生物质含量不同的寄主植物会使草地贪夜蛾体内部分酶活性发生变化,并对幼虫的生长发育产生影响。     

Regulation of isoflavone production in hydroponically grown Pueraria montana (kudzu) by cork pieces, XAD-4, and methyl jasmonate

A mini-hydroponic growing system was employed for seedlings of kudzu vine (Pueraria montana) and contents of isoflavones (daidzein, genistein, daidzin, genistin, and puerarin) from shoot and root parts of seedlings were analyzed quantitatively. In addition, exogenous cork pieces, polymeric adsorbent, XAD-4, and universal elicitor, methyl jasmonate (MeJA), were used to regulate the production of these isoflavones. It was shown that cork pieces up-regulate the production of daidzein and genistein up to seven- and eight-fold greater than the levels obtained for control roots. In contrast, levels of glucosyl conjugates, daidzin and genistin, decrease up to five- and eight-fold, respectively. Cork treatment also induces the excretion of the root isoflavone constituents into the growth medium. Minimal levels of isoflavones are absorbed by the cork pieces. XAD-4 stimulates the production of glucosyl conjugates, daidzin and genistin, in root parts about 1.5-fold greater than that obtained in control roots. These are the highest amounts of daidzin and genistin that are observed (5.101 and 6.759 mg g⁻¹ dry weight, respectively). In contrast to these two adsorbents, MeJA increases the accumulation of isoflavones in shoot rather than in root parts of seedlings, about three- to four-fold over control levels, with the exception of genistein. These studies reveal new observations on the regulation of isoflavone production in hydroponically grown Pueraria montana plants by two adsorbents (cork pieces and XAD-4) and MeJA elicitor.     

The antimicrobial effects of hops (Humulus lupulus L.) on ruminal hyper ammonia-producing bacteria

Aim:  To assess the antimicrobial effects of hops ( Humulus lupulus L.) on hyper ammonia producing-bacteria (HAB), which catabolize amino acids and peptides in the bovine rumen.
Methods and Results:  When media were amended with dried hops or hops extract (30·7% lupulone), ammonia production by mixed rumen bacteria was inhibited. The growth and ammonia production of pure cultures ( Peptostreptococcus anaerobius, Clostridium aminophilum, or Clostridium sticklandii ) was inhibited by 30 ppm lupulone at pH 6·7, and bactericidal activity was observed at pH 5·6. When hops extract was added to energized cell suspensions, the intracellular pH rapidly decreased and intracellular potassium was lost.
Conclusions:  The three HAB species were sensitive to the antimicrobial components in hops, and the inhibition of ammonia production by mixed rumen bacteria indicates that similar effects could be expected in the rumen.
Significance and Impact of the Study:  As much as half of the amino acids consumed by ruminants can be lost due to microbial degradation in the rumen. This study supports the idea that biologically active plant metabolites can be used to mitigate this wasteful process.