历久弥新：进化中的代谢工程

20世纪90年代,Bailey及Stephanopoulos等提出了经典代谢工程的理念,旨在利用DNA重组技术对代谢网络进行改造,以达到细胞性能改善,目标产物增加的目的。自代谢工程诞生以来的30年,生命科学蓬勃发展,基因组学、系统生物学、合成生物学等新学科不断涌现,为代谢工程的发展注入了新的内涵与活力。经典代谢工程研究已进入到前所未有的系统代谢工程阶段。组学技术、基因组代谢模型、元件组装、回路设计、动态控制、基因组编辑等合成生物学工具与策略的应用,大大提升了复杂代谢的设计与合成能力;机器学习的介入以及进化工程与代谢工程的结合,为系统代谢工程的未来开辟了新的方向。文中对过去30年代谢工程的发展趋势作了梳理,介绍了代谢工程在发展中不断创新的理论与方法及其应用。     

酿酒酵母代谢工程技术

自20世纪90年代初期诞生以来,代谢工程历经了30年的快速发展。作为代谢工程的首选底盘细胞之一,酿酒酵母细胞工厂已被广泛应用于大量大宗化学品和新型高附加值生物活性物质的生物制造,在能源、医药和环境等领域取得了巨大的突破。近年来,合成生物学、生物信息学以及机器学习等相关技术也极大地促进了代谢工程的技术发展和应用。文中回顾了近30年来酿酒酵母代谢工程重要的技术发展,首先总结了经典代谢工程的常用方法和策略,以及在此基础上发展而来的系统代谢工程和合成生物学驱动的代谢工程技术。最后结合最新技术发展趋势,展望了未来酿酒酵母代谢工程发展的新方向。     

合成生物学开关在代谢工程中的应用

在代谢工程研究领域中合成生物学开关主要用于调控基因的表达。传统的代谢工程改造主要通过敲除和过表达来改变特定基因的表达量。但基因敲除通常会导致菌体生长的下降。因此,我们需要适时的关闭和激活特定基因的表达。合成生物学开关就是解决这一问题的关键工具。目前,在代谢工程中常用的合成生物学开关有光控开关、温度诱导开关、拨动开关和核糖开关。其中,拨动开关和核糖开关在动态调节基因表达上拥有更大优势。介绍了代谢工程中常用的几种合成生物学开关,以及它们在代谢工程的应用。     

2015国际代谢工程峰会圆满落幕

<正>2015年12月2日,国际代谢工程大会(Metabolic Engineering Summit)在北京国际会议中心圆满落幕。这次会议聚集了30多名来自世界各国的顶尖科学家和工业界精英,参会者达到700多名,是中国合成生物学和代谢工程领域举办的规模最大、规格最高的国际学术会议。本次会议的主题是:"合成生物学"时代下的生物制造。国际代谢工程协会(IMES)主席Jens Nielsen高度评价了本次大会:"国际代谢工程大会首次在中国成功     

代谢工程30年专刊序言 (2021)

代谢工程利用重组DNA技术、合成生物学、基因组编辑来改变生物体的细胞网络,包括代谢、基因调控和信号网络等。它可以实现加强包括化学品、燃料、化学原料药和其他生物技术产品等代谢物生产的目标,提升生物制造能力与效率。为了梳理和凝练代谢工程30年来的发展状况,《生物工程学报》特组织出版专刊,从代谢工程总体发展、共性技术以及以什么宿主和做什么产品等4个方面展现该领域的发展动态和趋势,并为代谢工程领域的进一步发展提出建设性的意见与展望。     

合成生物学与代谢工程

随着DNA重组技术的日趋成熟,代谢工程的理论和应用已经得到了迅速发展。合成生物学是近年来蓬勃发展的一门新兴学科,在许多领域都具有重要的应用。以下从改造细胞代谢的关键因子、代谢途径的调节和宿主细胞与代谢途径构建的关系等方面详细讨论了合成生物学的最新进展和合成生物学在代谢工程领域的应用。     

药用植物次生代谢工程研究概况

植物次生代谢工程,是通过基因工程技术改变植物体内的合成和代谢途径,以满足人类对天然植物次生代谢产物不断提高的需求。随着对药用植物次生代谢合成途径日渐全面的认识,采取有效的代谢工程策略对植物次生代谢途径进行遗传改良,已经取得了诸多研究成果。但是,对代谢途径的总体调控以及次生代谢途径之间的协调等方面,仍然了解甚少,而利用系统生物学方法开展预见性代谢工程将会成为未来的研究趋势。     

《生物工程学报》2010年“代谢工程”专刊征稿通知

<正>代谢工程自1991年诞生以来,在改造植物、动物、微生物的代谢功能方面得到了广泛的应用。为了展现代谢工程科研工作者取得的最新进展,促进我国代谢工程研究的进步和发展,本刊2009年第9期设立了"代谢工程与细胞工厂"专栏,国内该领域著名学者对代谢工程的技术发展进行了总结,介绍了合成生物学等新理论和新技术,并发表了     

系统代谢工程在微生物定向进化中的应用

系统生物学的迅速发展使人们能够从整体水平上理解细胞的生理生化特性并调控其代谢.系统代谢工程的主要应用之一是以系统生物学为基础对微生物进行定向进化,以期增强细胞对环境胁迫的耐受性,提高目标产品的产量.前者多采用全局转录机制工程和逆代谢工程的方法;后者主要通过设计并导入最优化路径,重构代谢网络及基因的模拟敲除和湿法验证等策略实现.本文综述了利用系统代谢工程解决细胞生物工程几个主要问题的技术及其应用进展.     

从碳代谢流角度新解代谢工程策略

代谢工程通过改造微生物代谢过程,进而利用微生物生产各种有用的医药、化学产品及工业原料.本文从细胞代谢中碳代谢流的角度入手,将代谢工程的传统与新型策略进行分类解析.其中,传统代谢工程手段主要对目标代谢路径的关键酶进行改造,通过过表达或基因敲除增大目的代谢路径碳代谢流.然而,在代谢路径改造需要进行多基因表达的情况下,传统手段在如何最佳表达多种酶使碳流通畅上会受到很大限制.本文提出利用高碳流路径,通过简单基因改造以获得高效目标产物生产的新策略.同时,随着合成生物学与系统生物学的发展,精细调控多基因表达成为可能.本文进一步举例讨论了代谢工程中粗略与精细调控基因表达水平对碳流的影响,以期对教学与前沿科研有助.     

Maps, books and other metaphors for systems biology

We briefly review the use of metaphors in science and progressively focus on fields from biology and molecular biology to genomics and bioinformatics. We discuss how metaphors are both a tool for scientific exploration and a medium for public communication of complex subjects, by various short examples. Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda.     

Building momentum for systems and synthetic biology in India

Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computational and experimental strategy was formally proposed in mid 1990s leading to the re-emergence of Systems Biology. However, soon it became clear that natural systems were far more complex than expected. A new strategy to address biological complexity was proposed at MIT (Massachusetts Institute of Technology) in June 2004, when the first meeting of synthetic biology was held. Though the term ‘synthetic biology’ was proposed during 1970s (Szybalski in Control of gene expression, Plenum Press, New York, 1974), the usage of the original concept found an experimental proof in 2000 with the demonstration of a three-gene circuit called repressilator (Elowitz and Leibler in Nature, 403:335–338, 2000). This encouraged people to think of forward engineering biology from a set of well described parts.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

冷冻电子显微学在结构生物学研究中的现状与展望

冷冻电子显微学近年来在电子显微镜的硬件设备及结构解析的软件算法等方面取得了多个重要的技术突破,正在成为结构生物学研究的重要技术手段,为越来越多的生物学研究者所重视.冷冻电子显微学的技术特点决定了它所具备的一些独特优势和发展方向,同时作为一个正在迅速发展的科学技术领域,需要多学科的交叉促进.本文主要介绍冷冻电子显微学的研究现状及面临的技术挑战,并提出未来可能实现结构生物学与细胞生物学不同尺度的研究在冷冻电子显微学技术上融合的新方法.     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

进化细胞生物学的提出及其任务

作者提出应创建一门源于进化生物学与细胞生物学两者的交叉学科一进化细胞生物学(细胞的进化生物学)。其根本任务在于用进化的观点考察真核细胞的一切方面,从它们的起源和演化来认识它们的现在。文中列举了其具体的研究内容,并分析了其研究方法上的特点,指出在这里需要把进化生物学的综合性分析与细胞生物学的实验研究最紧密地结合起来。文中还论述了真核细胞的细胞器的“不进化”现象,指出其根本原因在于进化焦点的转移。     

Multi-scale modeling in biology: how to bridge the gaps between scales?

Human physiological functions are regulated across many orders of magnitude in space and time. Integrating the information and dynamics from one scale to another is critical for the understanding of human physiology and the treatment of diseases. Multi-scale modeling, as a computational approach, has been widely adopted by researchers in computational and systems biology. A key unsolved issue is how to represent appropriately the dynamical behaviors of a high-dimensional model of a lower scale by a low-dimensional model of a higher scale, so that it can be used to investigate complex dynamical behaviors at even higher scales of integration. In the article, we first review the widely-used different modeling methodologies and their applications at different scales. We then discuss the gaps between different modeling methodologies and between scales, and discuss potential methods for bridging the gaps between scales.     

Reproductive biology of Trichocentrum pumilum: an orchid pollinated by oil-collecting bees

The reproductive biology, reward production and pollination mechanism of Trichocentrum pumilum were studied in a gallery forest in the interior of the State of São Paulo, southeast Brazil. The floral visitors and pollination mechanism were recorded, and experimental pollinations were carried out in order to determine the breeding system of this species. Trichocentrum pumilum blooms in spring. Each paniculate inflorescence bears an average of 85 flowers that present a central yellow callus and finger‐like trichomes on the lateral lobes of the lip. A lipoidal substance is produced and stored among these trichomes. In the studied population, T. pumilum is exclusively visited and pollinated by two bee species (Tetrapedia diversipes and Lophopedia nigrispinis). Pollinaria are deposited on mouthparts of bees during collection of the lipoidal substance from the lateral lobes of the labellum. Trichocentrum pumilum is self‐incompatible and pollinator‐limited. Natural fruit set was low (9%, compared to 45% in experimentally cross‐pollinated flowers). Potentially viable seed exceed 97% in fruits obtained through cross‐pollination and in natural conditions (open pollination).     

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Large‐scale proteomic approaches have been used to study signaling pathways. However, identification of biologically relevant hits from a single screen remains challenging due to limitations inherent in each individual approach. To overcome these limitations, we implemented an integrated, multi‐dimensional approach and used it to identify Wnt pathway modulators. The LUMIER protein–protein interaction mapping method was used in conjunction with two functional screens that examined the effect of overexpression and siRNA‐mediated gene knockdown on Wnt signaling. Meta‐analysis of the three data sets yielded a combined pathway score (CPS) for each tested component, a value reflecting the likelihood that an individual protein is a Wnt pathway regulator. We characterized the role of two proteins with high CPSs, Ube2m and Nkd1. We show that Ube2m interacts with and modulates β‐catenin stability, and that the antagonistic effect of Nkd1 on Wnt signaling requires interaction with Axin, itself a negative pathway regulator. Thus, integrated physical and functional mapping in mammalian cells can identify signaling components with high confidence and provides unanticipated insights into pathway regulators.     

A computational framework for the design of optimal protein synthesis

Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework for the identification of a set of mutant codon sequences for optimized heterologous protein production, which uses a codon-sequence mechanistic model of protein synthesis. Through a sensitivity analysis on the optimal steady state configuration of protein synthesis we are able to identify the set of codons, that are the most rate limiting with respect to steady state protein synthesis rate, and we replace them with synonymous codons recognized by charged tRNAs more efficient for translation, so that the resulting codon-elongation rate is higher. Repeating this procedure, we iteratively optimize the codon sequence for higher protein synthesis rate taking into account multiple constraints of various types. We determine a small set of optimized synonymous codon sequences that are very close to each other in sequence space, but they have an impact on properties such as ribosomal utilization or secondary structure. This limited number of sequences can then be offered for further experimental study. Overall, the proposed method is very valuable in understanding the effects of the different properties of mRNA sequences on the final protein yield in heterologous protein production and it can find applications in synthetic biology and biotechnology.