Genosystematics: From E. Chargaff and A.N. Belozersky To the Present

This review considers the history of genosystematics (macromolecular systematics) from early studies of E. Chargaff and A.N. Belozersky up to the present, with emphasis on the most important discoveries in the field. The potential and limitations of genosystematics and possible ways of further development are analyzed using plants as an example. The future of genosystematics depends to a great extent on adequate employment of its methods in studying the problems of phylogeny and taxonomy. Analysis of recent publications shows that this requirement is not always met. It is no less important to design and improve the methods of genosystematics, especially those for comparing complete genomes.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 581–589.Original Russian Text Copyright © 2005 by Antonov.     

From birth to christening

A brief history of comparative studies of nucleic acids for systematic purposes is given. These studies were initiated by a group of Moscow State University scientists headed by A. N. Belozersky. Based mostly on comparative DNA studies, some main dogmas of a new branch of systematics were gradually developed. In Russia, this new branch of systematics is called "genosystematics". Some of the main results obtained by genosystematics since its birth (1957) and up to its "christening" (1974) are described.     

Genosystematics: from E. Chargaff and A. N. Belozersky up to date

A review of history of genosystematics (macromolecular systematics) from E. Chargaff and A. N. Belozersky up to date. The role of A.N. Belozersky and his collaborators in the development of this new branch of systematics is analyzed. Genosystematics was the source of valuable information clarifying some aspects of biological evolution. Its methods were successfully employed in microorganisms--(e.g., discovery of archaebacteria) and in eucaryote systematics (origin of plastids, falcification of "molecular clock" hypothesis, substantial changes in higher plants phylogenetics, etc.). However, attempts to employ some fragmentary and unreliable data obtained by genosystematics for modifying the existing phylogenetic schemes and systems of organisms failed. Nowadays genosystematics is like a newborn child suffering from children's diseases well-known to "classical" systematics. It is rather far from final conclusions describing the evolution of genotypes. Some of its recent achievments, e.g., elaboration of the concept of PhyloCode, allow to believe that this science is able to suggest revolutionary changes in Linnean systematics.     

后基因组时代的工业生物技术

简述了工业生物技术的发展背景和意义,分析了基因组学和功能基因组学发展对工业生物技术的推动作用,重点介绍了本期专刊发表的代谢工程、发酵工程以及工业酶与生物催化领域的17篇论文。     

Gene Flow Happens

Debate over what is a species was already considered old hat when Darwin wrote his seminal abstract (as he called it) more than 150 years ago.¹ Endless papers, workshops, and symposia have been presented in an effort to "solve" the species problem. Yet, here we are, at it again. Has there been any progress? I believe that there has been, and that among the many advances enabled by the genomics revolution, progress on species concepts and species recognition is among them. To quote Feder and colleagues,² we are on the brink of a “unified theory of speciation genomics.”     

Proteomics: general strategies and application to nutritionally relevant proteins

Proteomics as a subset of applied genomics technologies will be a key area of biology during the first decade or two of the new Millennium, and that it will have major impact, both directly and indirectly, on nutritional science. The aim of this review is to summarize information about general strategies of proteome and its application to important food proteins (plant, animal, and microbial). Methods are also described for protein separation, identification and determination. This article covers papers published within the last decade.     

High-throughput reverse genetics: RNAi screens in Caenorhabditis elegans

Two recent chromosome-wide screens for phenotypes caused by RNA-mediated interference (RNAi) in Caenorhabditis elegans have increased our understanding of essential genes in nematodes. These papers represent a major advance in functional genomics.     

RNA targets of the fragile X protein.

Three papers published recently in Cell bring the power of human genetics, Drosophila genetics, and genomics to bear on the understanding of fragile X syndrome. They provide further support for the importance of local protein synthesis within a neuron as a determinant of proper synaptogenesis and the development of cognitive abilities.     

Drosophila genome takes flight

In the March 24 issue of Science, a flurry of papers report on the impending completion of the Drosophila melanogaster genome sequence. This historic achievement is the result of a unique collaboration between the Berkeley Drosophila Genome Project (BDGP), led by Gerry Rubin, and the genomics company Celera, headed by Craig Venter. With its genome almost completely sequenced ahead of schedule, Drosophila is another important model organism to enter the postgenomic age, and represents the largest genome sequenced to date.     

Genomics of forest and ecosystem health in the Fagaceae: meeting report

A summary of 35 keynote, invited and volunteer papers delivered at a recent international conference is provided along with web links to PDFs of those presentations. Major conference themes targeted Genomic Tool Development for the Fagaceae and Application of Genomic Resources. The meeting provided a venue for reviewing the rapidly expanding knowledge base on Fagaceae genomics and for developing collaborations between scientists from Europe and North America.     

Fitting the niche by genomic adaptation

Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms. Many research groups have linked the adaptation of an organism to a niche to large changes in genome size and content. A number of recent papers have underlined the degree to which the genomes of different organisms are a reflection of the opportunities and constraints imposed by their chosen niche.     

Mobile genetic elements: the agents of open source evolution

Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.     

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind’s predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.     

多组学前沿技术专刊序言

后基因组时代,基因组学、转录组学、蛋白质组学及代谢组学等技术应用日趋广泛,功能注释成为生命科学研究的中心任务,多组学整合分析成为全面解析生物学机理的主要手段。本专刊邀请了国内多组学领域的相关专家学者介绍了基因组学、转录组学、蛋白质组学及代谢组学等领域最新进展和应用成果,收录了相关文章28篇,以供从事多组学研究的科研工作者参考。     

Genomics: Applications,Challenges, and Opportunities for the U.S. Environmental Protection Agency

Genomics information has great potential to enhance assessment of risks to human health and the environment. Although understanding genomic responses with respect to adverse ecological and human health outcomes is not, as yet, established, it is important to consider the likely future impacts of genomics technologies on risk assessment and decision-making. Four areas are identified as those likely to be influenced by the generation of genomics information within, and the submission of such information to, the U.S. Environmental Protection Agency (USEPA): risk assessment, prioritization of contaminants and contaminated sites, monitoring, and reporting provisions. For each of these risk assessment and regulatory applications, representative activities are presented to illustrate the application. Three major challenges for the USEPA associated with genomics are also identified in the areas of research, technical development, and capacity. The USEPA's initial activities to address these challenges are discussed. The Agency recognizes it must be prepared to use genomics information, and that many scientific, policy, ethical, and legal concerns will need to be addressed. The USEPA also recognizes it is essential to continue to collaborate with other federal agencies, academia, the regulated community, and other stakeholders in order to benefit from ongoing advances in genomics in the wider scientific and regulatory communities.     

On the Epistemological Crisis in Genomics

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.     

代谢组学：一个迅速发展的新兴学科

对代谢组学的含义,中心任务,研究方法,样品要求,应用及其发展方向进行了简要综述. 系统生物学概念的诞生标志着研究哲学由“还原论”向“整体论”的变化. 系统生物学的中心任务就是要针对生物系统整体 (无论它是生物细胞,多细胞组织,器官还是生物整体),建立定量,普适,整体和可预测 (QUIP) 的认知. 具体而言,系统生物学研究就是要将给定生物系统的基因,转录,蛋白质和代谢水平所发生的事件,相关性及其对所涉及生物过程的意义进行整体性认识. 从而出现了许多的“组”和“组学”的新概念. 但是现已提出的一百多个“组”和“组学”,可以大体归纳为“基因组”/“基因组学”,“转录组”/“转录组学”,“蛋白质组”/“蛋白质组学”和“代谢组”/“代谢组学”四个方面. 显而易见,DNA,mRNA 以及蛋白质的存在为生物过程的发生提供了物质基础 (但这个过程有可能不发生!),而代谢物质所反映的是已经发生了的生物学事件. 因此代谢组学是对一个生物系统进行全面认识的不可缺少的一部分,是全局系统生物学 (global systems biology) 的重要基础,也是系统生物学的一个重要组成部分. 在现有的英文表述中,代谢组学同时存在两个不同的词汇和概念,即metabonomics 和 metabolomics. 尽管前者多用在动物系统而后者多用于植物和微生物系统,但这些概念的本质从他们的定义中能够得到较细致的了解. Metabonomics 的最初定义是就生物系统对生理和病理刺激以及基因改变的代谢应答的定量测定(“the quantitative measurement of the multi-parametric metabolic response of living systems to pathophysiological stimuli or geneticmodifications”). 我们认为这个定义现在可以更广泛地表述为:代谢组学是关于定量描述生物内源性代谢物质的整体及其对内因和外因变化应答规律的科学 (“Metabonomics is the branch of science concerned with the quantitative understandings of themetabolite complement of integrated living systems and its dynamic responses to the changes of both endogenous factors (such asphysiology and development) and exogenous factors (such as environmental factors and xenobiotics).”). 其中心任务包括 (1) 对内源性代谢物质的整体及其动态变化规律进行检测,量化和编录,(2) 确定此变化规律和生物过程的有机联系. Metabolomics 存在多个定义,但其精髓是:对一个生物系统的细胞在给定时间和给定条件下所有小分子代谢物质的定量分析(the quantitativemeasurement of all low molecular weight metabolites in an organism's cells at a specified time under specific environmentalconditions). 因此,metabolomics 可以译作“代谢物组学”. 不难看出,前者是对生物系统进行的整体和动态的认识 (不仅关心代谢物质的整体也关注其动态变化规律),而后者强调分析而且是个静态的认识概念. 因此可以认为,metabolomics 是metabonomics 的一个组成部分 (参看定义). 近年又有人提出了“dynamic metabolomics”的概念,这个概念所表达的含义十分接近“metabonomics”本身的含义. 所以,可以预见,随着这门新兴学科的发展和更深入讨论,这两个概念必将趋向一致. 因此我们建议,在中文表述中将“代谢组学”一词和英文中的 metabonomics 相对应,以避免不必要的混淆和争议. 就细胞系统而言,不仅存在细胞自身的代谢物质组成问题,存在细胞之间代谢物质交换的问题,也存在代谢过程所发生的位点问题. 因此,简单地分析代谢物质的总组成 (即代谢组) 缺乏“整体论”所要求的全面性,其意义有一定局限. 代谢组学属于全局系统生物学 (Global systems biology) 研究方法,便于对复杂体系的整体进行认识. 譬如,一个正常工作的人体包括“人体”本身和与之共同进化而来且共生的消化道微生物群体 (或称菌群),孤立地研究“人体”本身的基因,转录子以及蛋白质当然可以为人们认识人体生物学提供重要信息,但无法提供使人体正常工作不可缺少的菌群的信息. 人体血液和尿液的代谢组却携带着包括菌群在内的每一个细胞的信息,因此代谢组学方法对研究如人体这样复杂的进化杂合体十分有效. 正因如此,代谢组学已经广泛地应用到了包括药物研发,分子生理学,分子病理学,基因功能组学,营养学,环境科学等重要领域. 在代谢组学诞生的过去 6 年里,有关代谢组学的研究论文和专利以指数的形式逐年增长. 可以预见,这门新兴学科将应用到更为广泛的领域.