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。     

代谢组研究的生物信息学方法

代谢组是细胞新陈代谢过程中小分子代谢物的集合。新陈代谢为细胞提供生理活动必需的物质和能量。代谢组直接反映细胞的新陈代谢过程,对代谢组的研究体现细胞的功能。细胞功能的异常会导致代谢组的异常,因此通过代谢组数据即可分析出细胞的健康状况。对代谢组物质的提取鉴定过程和代谢组数据的分析方法,主要是对代谢组数据整理和代谢网络推断过程进行综述。     

果实风味的代谢基础及其调控机制研究进展

果实风味是重要农艺性状,基因组、代谢组、转录组等多组学联用技术的发展和应用,已相对系统地揭示了风味物质基础。这些物质代谢具有明显的器官、发育以及环境特异性调控的特点,其代谢机制的阐述是果品调控的重要研究热点问题。乙烯是植物生长发育过程中重要的信号分子,对果实风味物质的合成和代谢具有独特的调节作用。在近年来国内外果实风味物质研究的基础上,本文总结了果实风味的代谢基础、调控机制、风味物质对乙烯信号的响应以及生物信息学在果实风味研究中的应用。最后,对该方向未来的发展提出展望,以期为果实风味营养的提高和调控提供理论参考。     

代谢组学及其应用

对代谢组学的概念、特性、发展历史做了简要介绍,综述了当前代谢组学研究中的数据采集、数据分析中采用的技术,及代谢组学在疾病诊断、药物毒性研究、植物和微生物等邻域的应用,并对代谢组学的发展作了展望。     

功能代谢组学技术在微生物研究中的应用

功能代谢组学是以代谢组学技术发现关键代谢物为基础,结合体内体外实验和分子生物学等技术手段,研究差异代谢物及相关蛋白、酶和基因的功能,从而揭示生物体内在的分子调控机制。功能代谢组学技术具有精准识别关键调控代谢物及其相关基因或酶的特性,近年来在微生物相关疾病的防控和工业化生产等方面受到了广泛的关注。本文介绍了功能代谢组学技术的分析流程、相关研究方法与平台及其在微生物研究方面的应用,其中重点阐述了真核、原核以及病毒微生物的代谢特性、调控靶点及相关防控策略等。最后,提出功能代谢组学研究在未来面临的问题与挑战,为后续功能代谢组学的研究与发展提供新的思路。     

功能代谢组学技术在微生物研究中的应用

功能代谢组学是以代谢组学技术发现关键代谢物为基础,结合体内体外实验和分子生物学等技术手段,研究差异代谢物及相关蛋白、酶和基因的功能,从而揭示生物体内在的分子调控机制。功能代谢组学技术具有精准识别关键调控代谢物及其相关基因或酶的特性,近年来在微生物相关疾病的防控和工业化生产等方面受到了广泛的关注。本文介绍了功能代谢组学技术的分析流程、相关研究方法与平台及其在微生物研究方面的应用,其中重点阐述了真核、原核以及病毒微生物的代谢特性、调控靶点及相关防控策略等。最后,提出功能代谢组学研究在未来面临的问题与挑战,为后续功能代谢组学的研究与发展提供新的思路。     

代谢组学在临床研究中的应用及进展

代谢组学是"后基因组学"时期新兴的一门学科,也是系统生物学的重要组成部分。代谢组学通过全面、定量检测生物样本中多种类型小分子化合物,来了解在内在和外界因素作用下生物体内源性物质的变化及规律,特别适合于临床上研究机体因受到遗传、生长、生理、环境因素和异物、病源等刺激的影响而产生的变化。借助于代谢组学技术不仅能够描述疾病发生、发展以及治疗过程中机体代谢机能的状态和变化,为临床疾病的诊断、病理机制的探索、新治疗靶点的发现等提供新的途径和思路,还可以揭示外界干扰因素(药物/毒物、环境、饮食、生活方式等)对机体的影响,为药效评价和疾病病因的筛查提供基础数据。近年来,代谢组学在临床研究方面得到了广泛的应用,取得了巨大的进展并展现了鼓舞人心的应用前景。该文分别就代谢组学在描述疾病发展状态、研究疾病诊断方法、探索疾病发病原因和发病机理、药效学评价等几个方面的应用及进展进行回顾和综述。     

正在蓬勃兴起的“代谢组学”研究技术与方法

<正>1"代谢组学"研究的涵义和科学意义"代谢组学"是研究生命体中所有代谢产物(小分子化合物)变化规律的科学,通过比较实验组和对照组中内源性代谢产物的系统性差异来研究生命现象,并揭示其内在规律。这些"代谢组"水平上的差异与生物体在生理、病理、营养、用药等各种生命过程紧密相关,是生物学过程执行后的最终产物的集合,因而也是各种组学研究中最接近生物表型的一种组学。"代谢组学"是一种典型的用化     

生态代谢组学研究进展

代谢组学指某一生物系统中产生的或已存在的代谢物组的研究,以质谱和核磁共振技术为分析平台,以信息建模与系统整合为目标。随着代谢组学中的研究方法与技术成为生态学研究的有力工具,生态代谢组学概念应运而生,即研究某一个生物体对环境变化的代谢物组水平的响应。理清代谢组学与生态代谢组学学科发展的脉络,综述代谢组学研究中的常用技术及其优势与局限性,论述代谢组学技术在生态学研究中的应用现状,展望代谢组学技术与其他系统生物学组学技术的结合在生态学中的应用前景,提出生态代谢组学研究者未来要完成的任务和面对的挑战。     

基元模式分析在生物网络和途径分析中的应用

基元模式分析是应用最广泛的代谢途径分析方法。基元模式分析的研究对象从代谢网络发展到信号传导网络;研究尺度从细胞到生物反应器,甚至生态系统;数学描述从稳态分解到动态解析;研究领域从微生物代谢到人类疾病。以下综述了基元模式分析的算法和软件开发现状,以及其在代谢途径与鲁棒性、代谢通量分解、稳态代谢通量分析、动态模型与生物过程模拟、网络结构与调控、菌株设计和信号传导网络等方面的应用。开发新的算法解决组合爆炸问题,探索基元模式与代谢调控的关系以及提高菌株设计算法效率是今后基元模式的重要发展方向。     

Changes in biosynthesis of exopolysaccharide in Lactococcus lactis subspecies cremoris treated by moderate pulsed electric field treatment

Metabolome analysis and physicochemical analyses were executed with cell extracts of a Lactococcus lactis subspecies cremoris strain treated by moderate pulsed electric field (PEF) to elucidate the mechanism of enhanced production of exopolysaccharide (EPS) by the treatment. Metabolome analysis by capillary electrophoresis time of flight mass spectrometry annotated 224 metabolites from the cytoplasmic extract of the strain, which, however, showed no significant changes in metabolites related to the EPS production. Electron microscopic observation and chemical analysis of undecaprenoids as carrier of EPS biosynthetic intermediates suggested that PEF treatment dissociated immature EPSs from the intermediates due to the focal electro-condensation of hydrogen ions at the cell surface. Thus, liberated undecaprenyl phosphates were recycled efficiently, which resulted in mass increase of EPS with smaller molecular weight. The study suggested the feasibility of moderate PEF treatment as a food processing technique and revealed the mechanism of enhanced production of EPS by the treatment.     

ORF355 confers enhanced salinity stress adaptability to S-type cytoplasmic male sterility maize by modulating the mitochondrial metabolic homeostasis

Moderate stimuli in mitochondria improve wide-ranging stress adaptability in animals, but whether mitochondria play similar roles in plants is largely unknown. Here, we report the enhanced stress adaptability of S-type cytoplasmic male sterility (CMS-S) maize and its association with mild expression of sterilizing gene ORF355. A CMS-S maize line exhibited superior growth potential and higher yield than those of the near-isogenic N-type line in saline fields. Moderate expression of ORF355 induced the accumulation of reactive oxygen species and activated the cellular antioxidative defense system. This adaptive response was mediated by elevation of the nicotinamide adenine dinucleotide concentration and associated metabolic homeostasis. Metabolome analysis revealed broad metabolic changes in CMS-S lines, even in the absence of salinity stress. Metabolic products associated with amino acid metabolism and galactose metabolism were substantially changed, which underpinned the alteration of the antioxidative defense system in CMS-S plants. The results reveal the ORF355-mediated superior stress adaptability in CMS-S maize and might provide an important route to developing salt-tolerant maize varieties.     

Identification of the first glyphosate transporter by genomic adaptation

The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.     

mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics

Background  

Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other relevant data, e.g. formulas, chemical structures, identification numbers to other databases etc. Since existing solutions are either commercial and therefore only available for certain instruments or not capable of storing such information, there is need to provide a software tool for the management of such data.     

Metabolomics in agriculture

Metabolome refers to the complete set of metabolites synthesized through a series of multiple enzymatic steps from various biochemical pathways processing the information encrypted in the plant genome. Knowledge about synthesis and regulation of various plant metabolic substances has improved substantially with availability of Omics data originating from sequencing of plant genomes. Metabolic profiling of crops is increasingly becoming popular in assessing plant phenotypes and genetic diversity. Metabolic compositional changes vividly reflect the changes occurring during plant growth, development, and in response to stress. Hence, study of plant metabolic pathways, the interconnections between them in context of systems biology is increasingly becoming popular in identification of candidate genes. The present article reviews recent developments in analysis of plant metabolomics, available bioinformatics techniques and databases employed for comparative pathway analysis, metabolic QTLs, and their application in plants.