林木蛋白质组学研究进展

近年来,应用新的基因组学技术来研究林木生长发育以及林木对生物与非生物胁迫的反应已使得人们对林木生物学有了相当大的了解。蛋白质组学是林木生物学的重要内容。本文综述了林木蛋白质组学在群体遗传、遗传作图、逆境生理、组织器官以及木材形成等方面的研究进展,并简要介绍了林木蛋白质组数据库。最后展望了林木蛋白质组学的发展前景。     

非模式植物蛋白质组学研究进展

蛋白质组学研究是对基因组学研究的重要补充,它是在蛋白质水平定量、动态、整体性研究生物体。该文简要介绍了蛋白质组学的含义,蛋白质组学及植物蛋白质组学产生的科学背景,蛋白质组学的研究内容。概述了非模式植物蛋白质组学的研究进展,主要包括非模式植物个体及群体蛋白质组学,组织和器官蛋白质组学,亚细胞蛋白质组学,响应环境变化的蛋白质组学以及非模式植物生物环境因子的蛋白质组学的研究情况,同时对植物蛋白质组学的发展前景进行了展望。     

Proteomic approaches to uncover MMP function

Proteomics has revolutionized protease research and particularly contributed to the identification of novel substrates and their sites of cleavage as key determinants of protease function. New technologies and rapid advancements in development of powerful mass spectrometers allowed unprecedented insights into activities of matrix metalloproteinases (MMPs) within their complex extracellular environments. Mass spectrometry-based proteomics extended our knowledge on MMP cleavage specificities and will help to develop more specific inhibitors as new therapeutics. Quantitative proteomics and N-terminal enrichment strategies have revealed numerous novel MMP substrates and shed light on their modes of action in vitro and in vivo. In this review, we provide an overview of current proteomic technologies in protease research and their application to the functional characterization of MMPs.     

Protein extraction from plant tissues for 2DE and its application in proteomic analysis

Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction before 2DE in plant proteomics. We briefly describe the history, development, and feature of major sample preparation methods for the 2DE analysis of plant tissues, that is, trichloroacetic acid/acetone precipitation and phenol extraction. We introduce the interfering compounds in plant tissues and the general guidelines for tissue disruption, protein precipitation and resolubilization. We describe in details the advantages, limitations, and application of the trichloroacetic acid/acetone precipitation and phenol extraction methods to enable the readers to select the appropriate method for a specific species, tissue, or cell type. The current applications of the sample preparation methods in plant proteomics in the literature are analyzed. A comparative proteomic analysis between male and female plants of Pistacia chinensis is used as an example to represent the sample preparation methodology in 2DE‐based proteomics. Finally, the current limitations and future development of these sample preparation methods are discussed. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP17).     

Advances in fungal proteomics

Proteomics, the global analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. This review summarizes recent developments in fungal proteomics and also generalizes protocols for sample preparation from plant pathogenic fungi. Challenges and future perspectives of proteomics are discussed as well.     

植物响应病原菌胁迫的蛋白质组学研究进展

随着拟南芥、水稻等模式植物基因组测序的完成,植物基因组学的研究重点已经转变为功能基因组学研究。蛋白质组学成为后基因组时代的重要研究手段,它有助于从分子水平上了解植物功能。主要介绍了双向电泳技术、生物质谱、蛋白质质谱数据的生物信息学分析等蛋白质组学研究的主要技术手段及植物应答病原菌胁迫的蛋白质组学研究进展,并对蛋白质组学在研究植物抗病机制方面的应用前景做出展望。     

First Systematic Plant Proteomics Workshop in Botany Department,University of Delhi: Transferring Proteomics Knowledge to Next‐generation Researchers and Students

International Plant Proteomics Organization (INPPO) outlined ten initiatives to promote plant proteomics in each and every country. With greater emphasis in developing countries, one of those was to “organize workshops at national and international levels to train manpower and exchange information”. This third INPPO highlights covers the workshop organized for the very first time in a developing country, India, at the Department of Botany in University of Delhi on December 26–30, 2013 titled – “1^st Plant Proteomics Workshop / Training Program” under the umbrella of INPPO India‐Nepal chapter. Selected 20 participants received on‐hand training mainly on gel‐based proteomics approach along with manual booklet and parallel lectures on this and associated topics. In house, as well as invited experts drawn from other Universities and Institutes (national and international), delivered talks on different aspects of gel‐based and gel‐free proteomics. Importance of gel‐free proteomics approach, translational proteomics, and INPPO roles were presented and interactively discussed by a group of three invited speakers Drs. Ganesh Kumar Agrawal (Nepal), Randeep Rakwal (Japan), and Antonio Masi (Italy). Given the output of this systematic workshop, it was proposed and thereafter decided to be organized every alternate year; the next workshop will be held in 2015. Furthermore, possibilities on providing advanced training to those students / researchers / teachers with basic knowledge in proteomics theory and experiments at national and international levels were discussed. INPPO is committed to generating next‐generation trained manpower in proteomics, and it would only happen by the firm determination of scientists to come forward and do it.     

Proteomic dissection of plant responses to various pathogens

During their growth and development, plants are vulnerable to the effects of a variety of pathogens. Proteomics technology plays an important role in research studies of plant defense mechanisms by mining the expression changes of proteins in response to various biotic stresses. This review article provides a comprehensive overview of the latest developments in international proteomic research on plant biotic stress. It summarizes the methods commonly used in plant proteomic research to investigate biotic stress, analyze the protein responses of plants in adverse conditions, and reviews the applications of proteomics combined with transgenic technology in plant protection.     

2014蛋白质组学专刊序言

蛋白质组学研究是后基因组学时代最重要的功能基因组学研究之一,与医学生物学、化学、物理学、信息学以及现代技术等关系十分密切。为了检阅近年来国内外蛋白质组学某些重要研究进展,探索其可能的应用范围,讨论其存在的问题,展望其发展前景,特组织出版"蛋白质组学专刊"。本期专刊包括综述和研究论文两部分,内容主要涉及不同物种(包括人类、哺乳类动物、原核生物、放线菌等)蛋白质组学研究、蛋白质组学重要方法学与技术研究(包括串联质谱分析、尿蛋白膜保存法、定量蛋白质组学分折、meta分析等)和蛋白质组功能与应用研究(包括蜘蛛毒素蛋白质组、磷酸化蛋白质组、卵母细胞和早期胚胎蛋白质组、肝脏纤维化蛋白质组、分枝杆菌耐药的蛋白质组等)。     

Protecting our environment,a motivating outdoor game for proteomics!

The global Earth ecosystem faces many intertwined threats, primarily anthropogenic pollution, drastic reduction of wild spaces, faster spread of pathogens, and global climate warming. Ecotoxicology, the integration of toxicology and ecology, aims to describe the effects of toxicants on organisms, whether at the level of the population, the community, the ecosystem, or the biosphere. Sentinel species are employed to assess threats to life, giving advance warning of danger. In this issue of Proteomics, Wilde and collaborators (Proteomics 2022, 22, https://doi.org/10.1002/pmic.202100289 ) present a comprehensive coverage of the proteome of the crustacean Daphnia magna, a species used to evaluate aquatic pollution. This study illustrates how current shotgun proteomics technology allows straightforward quantitation of any protein for whole animals or dissected organs, making global molecular phenotyping a reality for animals. Tandem mass spectrometry operated in data-independent acquisition can be used to compare the response of sentinels to various environmental conditions. The current low number of well-annotated animal or plant genomes, the high diversity of genetic backgrounds of each species, and the paucity of knowledge about protein functions for most of the relevant sentinels pose huge challenges for data interpretation. As a result, ecology and ecotoxicology today constitute an exceptional field for proteomics.     

Recent insights into Mycobacterium tuberculosis through proteomics and implications for the clinic

Introduction: This review aimed at providing an update on the application of proteomics-based approaches to gain recent insights of Mycobacterium tuberculosis (M.tb) and its relevance to clinic. Proteomics and bioinformatics approaches helped in the identification and characterization of novel proteins. Studying M.tb, causative agent of tuberculosis (TB), at the proteomic level can contribute to the identification of proteins which can be considered as potential targets for developed drugs and can help us in better understanding the pathogen physiology.

Areas covered: In this review we have presented a comprehensive literature pertaining to role of proteomics in understanding M.tb. We have also focused on how the development and advancement in technology in the field of proteomics has augmented the research and played a pivotal role in answering many unexplored questions. Lastly, the application of proteomics to clinic has also been discussed.

Expert commentary: We envisage that proteomics has gained remarkable momentum over the years. Proteomics can play an important role in the discovery of biomarkers for TB and other diseases. Also, it can aid in development of effective vaccines and simple, rapid and cost-effective test for the diagnosis of TB which is crucial for the management and control of the disease.     

蛋白质组学的进展

蛋白质组学是在细胞的整体蛋白质水平上进行研究、从蛋白质整体活动的角度来认识生命活动规律的一门新学科.简要介绍蛋白质组学的科学背景及其最新发展.     

A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district,eastern Japan

To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and C_MH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.     

Translational plant proteomics: a perspective

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.     

Changes in plant community of Seasonally Semideciduous Forest after invasion by Schizolobium parahyba at southeastern Brazil

The recognition of a species as invasive is generally accepted when it comes from another continent or even from another country, but requires strong evidences of negative impacts to support control actions when the invasive species comes from another region in the same country. Schyzolobium parahyba – the ‘guapuruvu’, is a Brazilian tree native from the evergreen type of the Atlantic Forest, which has been recorded as invader in a number of remnants of the Seasonally Semideciduous Forest – SSF. We hypothesized that this giant and fast growing invasive tree changes the structure and composition of the understory, thus impairing the forest dynamics. We assessed the invasive population in the whole fragment, and, within the portion invaded, we sampled the regenerating plant community 1) under the largest alien trees, 2) under a native species with similar ecology (Peltophorum dubium), and 3) randomly in the forest. Density, basal area and richness under S. parahyba were remarkably lower than under the equivalent native species or in the understory as a whole. Floristic composition of the plant community was also distinct under S. parahyba, possibly due to increased competition for soil water. Even though the alien species has occupied, as yet, a small proportion of the forest fragment, it dominates the overstory and threatens the regeneration processes under its canopy. In view of our findings, we recommend extirpation of the species from SSF, as well as avoiding cultivation of the species away from its native range.     

Mass Spectrometry and Proteomics 2018: the Mass Spectrometry Society of Japan,Japanese Proteomics Society,and Asia-Oceania Human Proteome Organization

ABSTRACT

Introduction: The mass spectrometry society of Japan, Japanese proteomics society, and Asia–Oceania human proteome organization held the conference ‘Mass Spectrometry and Proteomics 2018’ in Osaka, Japan, on May 15–18, 2018. This international conference focused on cutting edge technologies and their applications in a variety of research fields such as agriculture, material science, environmental factors, and clinical applications. An overview of the conference and a summary of the major lectures are reported here.

Expert commentary: The meeting will facilitate the development of fundamental technologies and the multi-disciplinary applications of proteomics.     

粤东桥溪村风水林群落特征初探

在粤东梅州市桥溪村风水林设立样方,对其乔木层、灌木层和草本层植物进行调查,分析该风水林的群落特征及植物多样性。结果表明:该风水林3 000 m2的样方内,共有维管植物67种,隶属于37个科54个属,其中蕨类植物4科4属4种,裸子植物3科3属3种,被子植物30科47属60种。群落分布型以热带性分布占优势,热带属所占比例为74.08%。群落主要优势科为樟科、壳斗科、金缕梅科,优势种为细柄阿丁枫、刺毛杜鹃、鼠刺、阿丁枫。群落为常绿阔叶林,生活型以高位芽为主,占73.13%,其中又以中高位芽类型最多,约占43%。乔木层可分为三层,但以株高6~9.9 m的个体数为最多;藤本的比例高达17.91%。马尾松、杉木、细柄阿丁枫以及阿丁枫都缺少幼苗贮备,其种群属于衰退状态;而刺毛杜鹃、越南山龙眼幼苗贮备较充足,且刺毛杜鹃种群是典型的增长型种群。该风水林群落比周边其他群落有较高的物种丰富度、植物多样性,且物种分布较为均匀,种间相遇率较大。在群落不同层中,物种丰富度、Margalef指数、Shannon-Winer指数、Simpson指数、种间相遇机率乔木层均为最高,均匀度指数以灌木层较高,草本层的优势度指数最高。桥溪村风水林与粤东和华南地区的其他常绿阔叶林有很大的相似性。该风水林在粤东地区是一种典型的地带性森林,其树种组成是经过长时间对当地环境适应而形成的,具有稳定性和多功能性,对其研究可为华南地区的植物资源保护、生态公益林的保护和营造提供科学依据。     

Holocene forest development along the Setesdal valley, southern Norway, reconstructed from macrofossil and pollen evidence

The Setesdal valley in South Norway runs north to south for 200 km, from alpine vegetation at 1200 m, passing the tree-line at around 1000 m, through Boreal forests, to Nemoral forest at sea level. The Holocene vegetation history and its altitudinal differentiation were reconstructed using pollen percentages and influx and plant macrofossil concentration records from four lakes along an altitudinal transect. During the early Holocene (c. 10500–8000 cal b.p.) Betula pubescens, Pinus sylvestris, Alnus, and Corylus expanded in the lowlands. Only Pinus and B. pubescens reached 1000 m asl (Lille Kjelavatn). Only B. pubescens reached Holebudalen (1144 m asl) at about the same time as it arrived in the lowlands. Between c. 8000–3000 cal b.p. mixed deciduous forest developed around Dalane (40 m asl) and to a lesser extent around Grostjørna (180 m asl), birch woodland with pine surrounded Lille Kjelavatn and birch woodland occurred at Holebudalen. From c. 3000 cal b.p. to present, the vegetation at Dalane hardly changed except for slight human impact and the immigration of Picea abies. At Grostjørna Pinus expanded. At Lille Kjelavatn Pinus disappeared and Betula became sparse as at the tree-line today. Betula retreated from Holebudalen thus leaving it above the tree-line in low-alpine vegetation. The strengths and weaknesses of pollen and plant macrofossil data were assessed for forest reconstructions. Where local pollen production is low, as near the tree-line, percentages of long-distance tree pollen can be misleadingly high. Pollen influxes of Betula and Pinus were much smaller near their altitudinal limits than at lower altitudes, although their macrofossils were equally abundant. The limited dispersal capacity of macrofossils documents the local presence of species and the character of the local vegetation, although macrofossils of some tree taxa are rarely found. Pollen and plant macrofossil evidence complement each other to provide a more complete reconstruction of Holocene tree-limits and tree-lines and hence climate changes, than either form of evidence alone.