Determining the structure of a biosynthetic pathway from incorporation measurements

Incorporation data, collected judiciously from a biosynthetic tracer experiment, can be processed to yield a considerable body of detailed information     

Effects of pulsed magnetic field treatment of soybean seeds on calli growth,cell damage,and biochemical changes under salt stress

The effects of magnetic field (MF) treatments of soybean seeds on calli growth, cell damage, and biochemical changes under salt stress were investigated under controlled conditions. Soybean seeds were exposed to a 1.0 Hz sinusoidal uniform pulsed magnetic field (PMF) of 1.5 µT for 5 h/day for 20 days. Non‐treated seeds were considered as controls. For callus regeneration, the embryonic axis explants were taken from seeds and inoculated in a saline medium with a concentration of 10 mM NaCl for calli growth analysis and biochemical changes. The combined treatment of MF and salt stress was found to significantly increase calli fresh weight, total soluble sugar, total protein, and total phenol contents, but it decreased the ascorbic acid, lipid peroxidation, and catalase activity of calli from magnetically exposed seeds compared to the control calli. PMF treatment significantly improved calli tolerance to salt stress in terms of an increase in flavonoid, flavone, flavonole, alkaloid, saponin, total polyphenol, genistein, and daidzein contents under salt stress. The results suggest that PMF treatment of soybean seeds has the potential to counteract the adverse effects of salt stress on calli growth by improving primary and secondary metabolites under salt stress conditions. Bioelectromagnetics 33:670–681, 2012. © 2012 Wiley Periodicals, Inc.     

二噁(口英)的生物降解及其机理

利用微生物降解二口恶口英是一种具有广阔前景的治理二口恶口英污染的方法。近年来利用微生物降解二口恶口英已经引起众多研究者的重视,国外在这方面的研究已取得了一定成果。介绍了能降解二口恶口英的微生物种类及其所能降解的二口恶口英类型,对近年来提出的微生物降解(包括氧化降解和还原降解)的可能途径,中间产物及其降解效果进行了综述。并对土壤在被污染后如何进行生物修复等方面进行了探讨。     

Detection and structure determination of an equilibrium unfolding intermediate of Rd-apocytochrome b562: native fold with non-native hydrophobic interactions

The absence of detectable kinetic and equilibrium folding intermediates by optical probes is commonly taken to indicate that protein folding is a two-state process. However, for some small proteins with apparent two-state behavior, unfolding intermediates have been identified in native-state hydrogen exchange or kinetic unfolding experiments monitored by nuclear magnetic resonance. Rd-apocytochrome b(562), a four-helix bundle, is one such protein. Here, we found another unfolding intermediate for Rd-apocytochrome b(562). It is based on a cooperative transition of (15)N chemical shifts of amide protons as a function of urea concentrations before the global unfolding. We have solved the high-resolution structure of the protein at 2.8 M urea, which is after this cooperative transition but before the global unfolding. All four helices remained intact, but a number of hydrophobic core residues repacked. This intermediate provides a possible structural interpretation for the kinetic unfolding intermediates observed using nuclear magnetic resonance methods for several proteins and has important implications for theoretical studies of protein folding.     

真菌次生代谢产物多样性及其潜在应用价值

从生物间的协同进化和微生物次生代谢产物的功能意义原理出发,本文侧重介绍了与植物和昆虫密切相关的一些真菌及其次生代谢产物在医药和农用新药物开发应用中的潜在价值。     

毛状根培养与植物次生代谢物的生产

综述了发根土壤杆菌诱导植物产生毛状根的方法及毛状根的特点,重点介绍了国内利用毛状根培养技术生产植物次生代谢物的最新研究进展。     

曲霉无性发育及其与次级代谢相关性研究进展

曲霉(Aspergillus)是应用于工业生产的一类重要微生物,它与人类生活及医药卫生等方面密切相关。分生孢子的形成是曲霉无性繁殖的主要方式,它是个复杂的过程,需要多个基因参与调控,且分生孢子的形成与次级代谢产物的生物合成有密切的关系。本文综述了曲霉分生孢子形成的调控模式,简述了曲霉中连接无性发育和曲霉毒素生物合成的G-蛋白信号通路,及既参与发育调控又参与曲霉次级代谢调控的Velvet蛋白家族,可为其他丝状真菌的研究提供理论指导,对工业生产也有很重要的意义。     

The biosynthetic pathway of crucifer phytoalexins and phytoanticipins: De novo incorporation of deuterated tryptophans and quasi-natural compounds

Although several biosynthetic intermediates in pathways to cruciferous phytoalexins and phytoanticipins are common, questions regarding the introduction of substituents at N-1 of the indole moiety remain unanswered. Toward this end, we investigated the potential incorporations of several perdeuterated d- and l-1′-methoxytryptophans, d- and l-tryptophans and other indol-3-yl derivatives into pertinent phytoalexins and phytoanticipins (indolyl glucosinolates) produced in rutabaga (Brassica napus L. ssp. rapifera) roots. In addition, we probed the potential transformations of quasi-natural compounds, these being analogues of biosynthetic intermediates that might lead to “quasi-natural” products (products similar to natural products but not produced under natural conditions). No detectable incorporations of deuterium labeled 1′-methoxytryptophans into phytoalexins or glucobrassicin were detected. l-tryptophan was incorporated in a higher percentage than d-tryptophan into both phytoalexins and phytoanticipins. However, in the case of the phytoalexin rapalexin A, both d- and l-tryptophan were incorporated to the same extent. Furthermore, the transformations of both 1′-methylindolyl-3′-acetaldoxime and 1′-methylindolyl-3′-acetothiohydroxamic acid (quasi-natural products) into 1′-methylglucobrassicin but not into phytoalexins suggested that post-aldoxime enzymes in the biosynthetic pathway of indolyl glucosinolates are not substrate-specific. Hence, it would appear that the 1-methoxy substituent of the indole moiety is introduced downstream from tryptophan and that the post-aldoxime enzymes of the glucosinolate pathway are different from the enzymes of the phytoalexin pathway. A higher substrate specificity of some enzymes of the phytoalexin pathway might explain the relatively lower structural diversity among phytoalexins than among glucosinolates.     

The past,present and future of secondary metabolite research in the Dothideomycetes

The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over‐represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field.     

青霉属真菌次级代谢产物的结构类型及其药用活性的研究进展

青霉属(Penicillium)真菌属于腐生类真菌,是自然界中一类重要的分解者。其可以产生多种多样的次级代谢产物。这些结构新颖、功能特殊的次级代谢产物在抗菌、抗氧化、抗肿瘤等药物开发中发挥重要作用,主要由聚酮类、生物碱、萜类、大环内酯等化学结构类型组成。本文综述了青霉属真菌次级代谢产物的结构类型以及丰富的生物药用活性,该内容可为后续青霉属真菌新型天然药物的开发提供研究思路。     

Cryopreservation and post freeze molecular and biosynthetic stability in transformed roots of Beta vulgaris and Nicotiana rustica

Crypopreservation methods were firstly developed for root-tips from hairy root cultures of Beta vulgaris, established after transformation by Agrobacterium rhizogenes. The effects of culture age, pre-growth, cryoprotection, freezing rate and post-freeze culture conditions were determined. The resulting freezing protocol was then used to cryopreserve transformed root cultures of Nicotiana rustica. Both species were viable after freezing (ca. 80%), according to fluorescein diacetate vital staining. However, on average the regeneration of proliferating roots from surviving root-tips was low (<20%). Growth rates, secondary metabolite production and T-DNA structure of a number of hairy root lines were examined and found to be unchanged after cryopreservation.Abbreviations DMSO dimethyl sulphoxide - 2,4-D dichlorophenoxyacetic acid - FDA fluoroscein diacetate - IAA indole-3-acetic acid - NAA -napthalene acetic acid     

In the light of new greenhouse technologies: 1. Plant-mediated effects of artificial lighting on arthropods and tritrophic interactions

This review describes the effects of the current and emerging lighting technologies on plants, and the plant-mediated effects on herbivorous and beneficial arthropods in high-technology year-round greenhouse production, where light quality, quantity and photoperiod differ from the natural environment. The spectrum provided by the current lighting technology, high-pressure sodium lamp (HPSL), differs considerably from that of solar radiation. The major plant-mediated effects on arthropods were predicted to result from (a) extended photoperiods and lower light integrals, (b) the attenuation of ultraviolet (UV) wavelengths, particularly UV-B, (c) the high red: far-red (R : FR) ratio and lower blue : red (B : R) in comparison with solar radiation and (d) the high proportion of yellow wavelengths during winter months. Of these light factors (a–d) (ceteris paribus), (a) and (b) were hypothesised to result in increased performance of herbivores in winter months, whereas the high R : FR ratio decreased herbivore performance or not affected it, at least when interlights are used. The predictions obtained on the basis of this review are also discussed in relation to the modifying factors prevailing in these production environments: enriched CO₂ levels, high nutrient amounts, optimised irrigation and temperatures optimal for plants' needs. Based on the carbon/nitrogen and growth/differentiation balance theories, these modifying factors tend to produce plants that allocate most resources to growth at the expense of defensive secondary metabolism and physicochemical defensive structures. At the end, this review discusses knowledge gaps and future research prospects, in which light-emitting diodes, the emerging lighting technology, play an important role by enabling the targeted manipulation of plant responses to different wavelengths.     

Recent developments in the use of transgenic plants for the production of human therapeutics and biopharmaceuticals

In recent years there has been a dramatic increase in the application of plant biotechnology for the production of a variety of commercially valuable simple and complex biological molecules (biologics) for use in human and animal healthcare. Transgenic whole plants and plant cell culture systems have been developed that have the capacity to economically produce large-scale quantities of antibodies and antibody fragments, antigens and/or vaccine epitopes, metabolic enzymes, hormones, (neuro)peptides and a variety of biologically active complexes and secondary metabolites for direct use as therapeutic agents or diagnostic tools in the medical healthcare industry. As the products of genetically modified plants make their way from concept to commercialization the associated risks and acceptance by the public has been become a focal point. In this paper, we summarize the recent advances made in the use of transgenic plants and plant cell cultures as biological factories for the production of human therapeutics and biopharmaceuticals and discuss the long-term potential of `molecular farming' as a low-cost, efficient method for the production of biological materials with demonstrated utility to the pharmaceutical industry or medical community.     

The secondary metabolism glycosyltransferases UGT73B3 and UGT73B5 are components of redox status in resistance of Arabidopsis to Pseudomonas syringae pv. tomato

Secondary metabolism plant glycosyltransferases (UGTs) ensure conjugation of sugar moieties to secondary metabolites (SMs) and glycosylation contributes to the great diversity, reactivity and regulation of SMs. UGT73B3 and UGT73B5, two UGTs of Arabidopsis thaliana (Arabidopsis), are involved in the hypersensitive response (HR) to the avirulent bacteria Pseudomonas syringae pv. tomato (Pst‐AvrRpm1), but their function in planta is unknown. Here, we report that ugt73b3, ugt73b5 and ugt73b3 ugt73b5 T‐DNA insertion mutants exhibited an accumulation of reactive oxygen species (ROS), an enhanced cell death during the HR to Pst‐AvrRpm1, whereas glutathione levels increased in the single mutants. In silico analyses indicate that UGT73B3 and UGT73B5 belong to the early salicylic acid (SA)‐induced genes whose pathogen‐induced expression is co‐regulated with genes related to cellular redox homeostasis and general detoxification. Analyses of metabolic alterations in ugt mutants reveal modification of SA and scopoletin contents which correlate with redox perturbation, and indicate quantitative modifications in the pattern of tryptophan‐derived SM accumulation after Pst‐AvrRpm1 inoculation. Our data suggest that UGT73B3 and UGT73B5 participate in regulation of redox status and general detoxification of ROS‐reactive SMs during the HR to Pst‐AvrRpm1, and that decreased resistance to Pst‐AvrRpm1 in ugt mutants is tightly linked to redox perturbation.     

植物PDR型ABC转运蛋白的结构及功能

ATP-结合盒(ATP-binding cassette,ABC)转运蛋白是目前已知最大、功能最广泛的蛋白质家族。多向耐药性(pleiotropic drug resistance,PDR)蛋白是该家族中仅存于植物和真菌中的一个亚族,结构域与其他亚族相反,即核苷酸结合域(nucleotide-binding domain,NBD)位于跨膜结构域(trans-membrane domain,TMD)的N端。目前已发现PDR型转运蛋白具有转运次生代谢产物和参与胁迫反应等方面的功能。植物PDR基因分为5个亚族:I族基因涉及多种生物和非生物胁迫反应,II￣V族基因功能研究甚少。植物PDR基因在器官水平、化学及环境因素影响下具有特异性较好的表达谱。本文系统阐述了植物PDR型转运蛋白基因的进化、结构及其功能,为理解植物PDR型转运蛋白在生物分子转运和复杂生理功能方面提供一个基础框架。     

A 3D building blocks approach to analyzing and predicting structure of proteins

A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of C alpha coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set of standard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can "replace" about 76% of all hexamers in well-refined known proteins with an error of less than 1 A, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.