植物响应病原真菌的代谢组学研究进展

代谢组学是对特定条件下的生物体内代谢物进行定性或定量分析,从而得到与特定生理或病理反应相关的代谢物变化的一门新学科,并因此被广泛应用于植物学、微生物学、毒理学及疾病诊断等领域。近年来,代谢组学开始应用到植物–微生物互作研究领域,尤其是在植物响应病原菌胁迫的研究中。该文综述了代谢组学的定义、研究方法及其在植物–病原真菌互作领域中的应用,并讨论了其研究前景和所面临的挑战。     

复杂疾病的离子组学研究进展

离子组学是一个研究特定生物系统中各种元素的组成、分布以及它们在不同生理、病理条件下发生变化的新兴交叉学科。它结合了高通量元素谱检测技术和生物信息学方法,为在系统水平上深入认识这些元素的生物学利用过程与功能提供了重要新思路。越来越多的研究结果表明,离子组学在复杂疾病的病因学研究、早期诊断与筛查和治疗措施制定等方面具有重要的理论与实用价值。本文着重介绍了当前离子组学在一些复杂疾病研究领域取得的新进展,有助于我们进一步探索不同元素及其所构成的动态离子网络对疾病发生与发展的影响和相关重要属性。     

植物响应盐胁迫组学研究进展

盐胁迫对植物生长的影响主要表现在离子毒害、渗透胁迫以及次级氧化胁迫等,植物遭受盐胁迫时迅速启动相关基因,进行转录调控,进而合成相应蛋白质来控制代谢物合成和离子转运以调节渗透平衡。随着现代分子生物学迅速发展,对植物耐盐机理研究也深入到了转录组、蛋白质组、代谢组及离子组等水平,"组学"研究为耐盐基因鉴定及标志性代谢物的挖掘等提供了有力手段。该文对近年来国内外有关转录组学、蛋白质组学、代谢组学、离子组学的主要研究方法及在盐胁迫中的应用研究进展进行综述,以揭示植物耐盐机理,为优良耐盐碱植物的筛选与培育提供支持。     

矿质元素互作及重金属污染的研究进展

随着工农业的发展,重金属污染问题在我国越来越严重。矿质元素互作的研究是理解重金属植物体内迁移规律,解决矿质营养利用和重金属污染治理的矛盾以及重金属复合污染问题的必然要求。本文从几个与重金属关系密切的矿质元素入手,并结合离子组学的发展,简要介绍了矿质元素与重金属的互作方面的主要进展,并对解决重金属污染和重金属复合污染问题进行了探讨。     

代谢组及其在真菌研究中的应用

代谢组学是利用现代分析化学手段对一定条件下生物体内小分子代谢产物（初级和次级代谢产物）定性及定量,从而揭示生命现象及其内在规律的学科。相对于基因组、转录组和蛋白质组,代谢组是一定条件下生物学过程完成后的最终代谢产物的集合,因而是各种组学研究中最接近表型的一种组学,可以直接动态地反映出细胞的生理生化过程,从而有效地检测和发现特定的生化途径,准确地解释生理或者病理现象。代谢组学作为系统生物学中基因组学、转录组学以及蛋白质组学三大组学的延伸和补充,是目前的研究热点之一。目前代谢组学在真菌领域的研究得到日益重视和发展。本文首先从历史发展和技术路线简述了代谢组学的发展历程和常见的代谢组学研究方法。接着从真菌的分类鉴定、生物膜研究、代谢途径、代谢工程、天然产物发现与植物互作这6个方面介绍了代谢组学在真菌研究领域的应用。     

激光扫描共聚焦显微镜在植物学中的应用

激光扫描共聚焦显微镜(LSCM)是普通光学显微镜与激光和计算机及其相应的软件技术组合的产物,实现了连续光学切片,能在亚细胞水平观察细胞骨架的动态变化、细胞内特异蛋白、钙等离子的变化,并结合电生理等技术观察细胞生理活动与细胞形态及运动变化的相互关系。并广泛应用于生物三维结构重组及动态分析。本文综述了应用激光扫描共聚焦显微镜技术在植物细胞学、植物发育、组织化学以及基因表达、检测等领域取得的进展。     

植物硒吸收转化机制及生理作用研究进展

硒是大多微生物、动物及人类的必要微量元素,但其在植物生长发育中的生理作用至今存在争议.较低浓度硒具有促进植物生长、提高植物耐受能力的功能,而大部分植物在高浓度下表现出中毒现象.随着人类对摄入硒及环境硒污染问题的认识加深,作物硒生物强化与硒污染植物修复问题引起重视,推动了对硒在植物中的吸收积累及代谢调控的研究.近年来对植物硒吸收及转化的研究表明,不同硒水平下植物对硒吸收积累及生理响应存在差异,土壤环境因素对植物硒吸收及转化具有重要影响,对高聚硒植物硒代谢研究逐渐揭示出硒在植物体内的转化过程和调控机理等.本文总结了目前硒生物强化与植物修复方面的研究进展,对环境中硒分布特点、植物硒吸收及其影响因素、植物体内硒转化及其过程调控关键酶,以及硒在植物中的生理作用等进行了综述,并对植物硒生理及分子机制未来研究方向进行展望.     

全球气候变化对陆地植物碳氮磷生态化学计量学特征的影响

全球气候变化背景下生物地球化学循环的响应规律和陆地植物适应对策已受到广泛关注.本文在分析气候变暖和降水变化对不同生态系统植物C∶N∶P的影响、CO₂浓度升高对不同光合途径物种元素的影响,以及氮沉降对土壤 植物元素影响的短期和长期效应等基础上,从植物生理特性和土壤有效营养元素变化等方面揭示了其可能存在的内在机理,以期为研究C、N、P化学元素在土壤 植物之间传递与调节机制、陆地生态系统结构和功能,以及生物地球化学元素循环对气候变化的响应提供理论依据.最后提出了该领域研究中存在的问题及对今后研究的展望.     

脂质组学研究方法及其应用

脂质不仅是生物膜的骨架成分和能量贮存物质,越来越多的证据表明,脂质也参与细胞的许多重要功能。脂质组学是代谢组学的一个重要分支,主要研究生物体内所有的脂质分子的特性以及它们在蛋白质表达和基因调控过程中的作用。脂质组学是依赖技术驱动的科学。近年来,随着人们对脂质研究的重视,脂质组学研究方法和策略有了突破性进展,在动物上开发出的脂质组学分析方法已经扩展应用到植物上。该文重点介绍脂质组学的研究方法及其应用,以期推动脂质组学,特别是植物脂质组学的进一步发展。     

脂质组学研究方法及其应用

脂质不仅是生物膜的骨架成分和能量贮存物质, 越来越多的证据表明, 脂质也参与细胞的许多重要功能。脂质组学是代谢组学的一个重要分支, 主要研究生物体内所有的脂质分子的特性以及它们在蛋白质表达和基因调控过程中的作用。脂质组学是依赖技术驱动的科学。近年来, 随着人们对脂质研究的重视, 脂质组学研究方法和策略有了突破性进展, 在动物上开发出的脂质组学分析方法已经扩展应用到植物上。该文重点介绍脂质组学的研究方法及其应用, 以期推动脂质组学,特别是植物脂质组学的进一步发展。     

Plant ionomics: a newer approach to study mineral transport and its regulation

Up to two-thirds of the world population is at risk of deficiency in one or more essential mineral elements. In order to overcome deficiency disorders of mineral nutrients, biofortification approach in crops is an absolute requirement to eliminate the hidden hunger. Hence, the aim of crop biofortification is shifting from food security to nutritional security. In this context, ionomics becomes essential to identify potential gene(s) responsible for the uptake, transport, and storage of ions in plants. It involves the measurement of elemental composition of an organism and change in their composition in relation to physiological, developmental, environmental, and genetic factors. It renders the functional analysis of genes and gene networks that directly or indirectly affect the whole ionome. The present review deals with the study of ionome with special reference to different types of ionic interactions, quantifications, and gene identification.     

Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis

Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomic strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here, we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na(+) from the soil. Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that two coastal populations of Arabidopsis collected from Tossa del Mar, Spain, and Tsu, Japan (Ts-1 and Tsu-1, respectively), accumulate higher shoot levels of Na(+) than do Col-0 and other accessions. We identify AtHKT1, known to encode a Na(+) transporter, as being the causal locus driving elevated shoot Na(+) in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence approximately 5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na(+). Interestingly, and in contrast to the hkt1-1 null mutant, under NaCl stress conditions, this novel AtHKT1 allele not only does not confer NaCl sensitivity but also cosegregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; http://www.purdue.edu/dp/ionomics). Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the casual locus driving the natural variation in shoot Na(+) accumulation we observed in Ts-1 and Tsu-1. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes.     

Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues

Natural variation in the regulation of the accumulation of mineral nutrients and trace elements in plant tissues is crucial to plant metabolism, development, and survival across different habitats. Studies of the genetic basis of natural variation in nutrient metabolism have been facilitated by the development of ionomics. Ionomics is a functional genomic approach for the identification of the genes and gene networks that regulate the elemental composition, or ionome, of an organism. In this study, we evaluated the genetic basis of divergence in elemental composition between an inland annual and a coastal perennial accession of Mimulus guttatus using a recombinant inbred line (RIL) mapping population. Out of 20 elements evaluated, Mo and Cd were the most divergent in accumulation between the two accessions and were highly genetically correlated in the RILs across two replicated experiments. We discovered two major quantitative trait loci (QTL) for Mo accumulation, the largest of which consistently colocalized with a QTL for Cd accumulation. Interestingly, both Mo QTLs also colocalized with the two M. guttatus homologues of MOT1, the only known plant transporter to be involved in natural variation in molybdate uptake.     

镉离子—氨基酸配合物在解释植物体对镉离子解毒机理上的研究

本文研究了重金属离子Cd~(2+)与几种氨基酸配合物合的合成方法,用红外光谱,X射线衍射,元素分析,紫外光谱等检测方法,对配合物的结构进行了分析,并结合生物学的理论,就植物对Cd~(2+)的解毒机理作了探讨。     

Using synchrotron X-ray fluorescence microprobes in the study of metal homeostasis in plants

Background and Aims

This Botanical Briefing reviews the application of synchrotron X-ray fluorescence (SXRF) microprobes to the plant sciences; how the technique has expanded our knowledge of metal(loid) homeostasis, and how it can be used in the future.

Scope

The use of SXRF microspectroscopy and microtomography in research on metal homeostasis in plants is reviewed. The potential use of SXRF as part of the ionomics toolbox, where it is able to provide fundamental information on the way that plants control metal homeostasis, is recommended.

Conclusions

SXRF is one of the few techniques capable of providing spatially resolved in-vivo metal abundance data on a sub-micrometre scale, without the need for chemical fixation, coating, drying or even sectioning of samples. This gives researchers the ability to uncover mechanisms of plant metal homeostasis that can potentially be obscured by the artefacts of sample preparation. Further, new generation synchrotrons with smaller beam sizes and more sensitive detection systems will allow for the imaging of metal distribution within single living plant cells. Even greater advances in our understanding of metal homeostasis in plants can be gained by overcoming some of the practical boundaries that exist in the use of SXRF analysis.Key words: Metal homeostasis, synchrotron X-ray fluorescence, SXRF, microspectroscopy, microtomography, X-ray absorption spectroscopy, XAS, ionomics, Arabidopsis thaliana, hyperaccumulator     

Purdue ionomics information management system. An integrated functional genomics platform

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.     

Imaging techniques for elements and element species in plant science

Revealing the uptake, transport, localization and speciation of both essential and toxic elements in plants is important for understanding plant homeostasis and metabolism, subsequently, providing information for food and nutrient studies, agriculture activities, as well as environmental research. In the last decade, emerging techniques for elemental imaging and speciation analysis allowed us to obtain increasing knowledge of elemental distribution and availabilities in plants. Chemical imaging techniques include mass spectrometric methods such as secondary ionization mass spectrometry (SIMS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and synchrotron-based techniques such as X-ray fluorescence spectroscopy (SRXRF), and so forth. On the other hand, X-ray absorption spectroscopy (XAS) based on synchrotron radiation is capable of in situ investigation of local atomic structure around the central element of interest. This technique can also be operated in tandem with SRXRF to image each element species of interest within plant tissue. In this review, the principles and state-of-the-art of these techniques regarding sample preparation, advantages and limitations, and improvement of sensitivity and spatial resolution are discussed. New results with respect to elemental distribution and speciation in plants revealed by these techniques are presented.     

Biodiversity of mineral nutrient and trace element accumulation in Arabidopsis thaliana

In order to grow on soils that vary widely in chemical composition, plants have evolved mechanisms for regulating the elemental composition of their tissues to balance the mineral nutrient and trace element bioavailability in the soil with the requirements of the plant for growth and development. The biodiversity that exists within a species can be utilized to investigate how regulatory mechanisms of individual elements interact and to identify genes important for these processes. We analyzed the elemental composition (ionome) of a set of 96 wild accessions of the genetic model plant Arabidopsis thaliana grown in hydroponic culture and soil using inductively coupled plasma mass spectrometry (ICP-MS). The concentrations of 17-19 elements were analyzed in roots and leaves from plants grown hydroponically, and leaves and seeds from plants grown in artificial soil. Significant genetic effects were detected for almost every element analyzed. We observed very few correlations between the elemental composition of the leaves and either the roots or seeds. There were many pairs of elements that were significantly correlated with each other within a tissue, but almost none of these pairs were consistently correlated across tissues and growth conditions, a phenomenon observed in several previous studies. These results suggest that the ionome of a plant tissue is variable, yet tightly controlled by genes and gene × environment interactions. The dataset provides a valuable resource for mapping studies to identify genes regulating elemental accumulation. All of the ionomic data is available at www.ionomicshub.org.