IBR5, a dual-specificity phosphatase-like protein modulating auxin and abscisic acid responsiveness in Arabidopsis

Auxin is an important plant hormone that plays significant roles in plant growth and development. Although numerous auxin-response mutants have been identified, auxin signal transduction pathways remain to be fully elucidated. We isolated ibr5 as an Arabidopsis indole-3-butyric acid-response mutant, but it also is less responsive to indole-3-acetic acid, synthetic auxins, auxin transport inhibitors, and the phytohormone abscisic acid. Like certain other auxin-response mutants, ibr5 has a long root and a short hypocotyl when grown in the light. In addition, ibr5 displays aberrant vascular patterning, increased leaf serration, and reduced accumulation of an auxin-inducible reporter. We used positional information to determine that the gene defective in ibr5 encodes an apparent dual-specificity phosphatase. Using immunoblot and promoter-reporter gene analyses, we found that IBR5 is expressed throughout the plant. The identification of IBR5 relatives in other flowering plants suggests that IBR5 function is conserved throughout angiosperms. Our results suggest that IBR5 is a phosphatase that modulates phytohormone signal transduction and support a link between auxin and abscisic acid signaling pathways.     

Innovation at the intersection of synthetic and systems biology

The promises of modern biotechnology hinge upon the hope that we can understand microscopic cellular complexity and in doing so create novel function. In this regard, the fields of systems and synthetic biology are important for accelerating both our understanding of biological systems and our ability to quantitatively engineer cells. At the nexus of these two fields is a unique synergy that can help attain these goals. Thus, the next greatest advances in biology and biotechnology are arising at the intersection of the top-down systems approach and the bottom-up synthetic approach. Collectively, these developments enable the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. This review seeks to highlight this activity as well as provide a perspective for future directions. Combining these efforts can provide novel insights into cellular function and lead to robust, novel synthetic design.     

Plant-insect interactions: molecular approaches to insect resistance

Recent advances in our understanding of induced responses in plants and their regulation, brought about by a revolution in molecular biology, have re-focused attention on the potential exploitation of endogenous resistance mechanisms for crop protection. The future goal of crop biotechnology is thus to engineer a durable, multimechanistic resistance to insect pests through an understanding of the diversity of plant responses to insect attack.     

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.     

And then there were many: MADS goes genomic

During the past decade, MADS-box genes have become known as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by bioinformatics, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Therefore, the recent advances in comparative and functional genomics should enable researchers to identify the full range of MADS-box gene functions, which should help us significantly in developing a better understanding of plant development and evolution.     

Flavonoids act as negative regulators of auxin transport in vivo in arabidopsis

Polar transport of the plant hormone auxin controls many aspects of plant growth and development. A number of synthetic compounds have been shown to block the process of auxin transport by inhibition of the auxin efflux carrier complex. These synthetic auxin transport inhibitors may act by mimicking endogenous molecules. Flavonoids, a class of secondary plant metabolic compounds, have been suggested to be auxin transport inhibitors based on their in vitro activity. The hypothesis that flavonoids regulate auxin transport in vivo was tested in Arabidopsis by comparing wild-type (WT) and transparent testa (tt4) plants with a mutation in the gene encoding the first enzyme in flavonoid biosynthesis, chalcone synthase. In a comparison between tt4 and WT plants, phenotypic differences were observed, including three times as many secondary inflorescence stems, reduced plant height, decreased stem diameter, and increased secondary root development. Growth of WT Arabidopsis plants on naringenin, a biosynthetic precursor to those flavonoids with auxin transport inhibitor activity in vitro, leads to a reduction in root growth and gravitropism, similar to the effects of synthetic auxin transport inhibitors. Analyses of auxin transport in the inflorescence and hypocotyl of independent tt4 alleles indicate that auxin transport is elevated in plants with a tt4 mutation. In hypocotyls of tt4, this elevated transport is reversed when flavonoids are synthesized by growth of plants on the flavonoid precursor, naringenin. These results are consistent with a role for flavonoids as endogenous regulators of auxin transport.     

Towards synthetic microbial consortia for bioprocessing

The use of microbial consortia for bioprocessing has been limited by our ability to reliably control community composition and function simultaneously. Recent advances in synthetic biology have enabled population-level coordination and control of ecosystem stability and dynamics. Further, new experimental and computational tools for screening and predicting community behavior have also been developed. The integration of synthetic biology with metabolic engineering at the community level is vital to our ability to apply system-level approaches to building and optimizing synthetic consortia for bioprocessing applications. This review details new methods, tools and opportunities that together have the potential to enable a new paradigm of bioprocessing using synthetic microbial consortia.     

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commercially-important applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.     

单细胞技术进展及其在植物研究中的应用

多细胞生物体的生存依赖于不同类型细胞特异性的功能分工,不同类型的细胞尽管基因组相同,但有其独特的发育过程和应对环境变化的能力。生物学的一大挑战就是揭示基因如何在正确的位置、正确的时间表达到正确的水平,最近出现了很多通过细胞类型特异性方法研究单细胞组学的工具,这些新技术使我们能通过空前分辨率,理解多细胞生物体内不同类型的单个细胞基因表达特点及其适应环境变化的机制。单细胞样品的获取一直是单细胞研究的一大技术瓶颈,因此本文将以如何获得起始材料为重点,探讨单细胞研究的样品标记、单细胞分离及获取、组学数据分析和结果验证等技术方法及其在植物研究中的应用。     

葡萄生长素响应基因家族生物信息学鉴定和表达分析

生长素响应基因家族能调节植物体内生长素平衡和生长素信号途径。文章采用生物信息学方法检索获得葡萄(Vitisvinifera L.)基因组数据库中的生长素响应基因,通过分析其染色体定位、基因共线性和系统进化,发现葡萄基因组含有25个AUX_IAA基因、19个ARF基因、9个GH3基因、42个LBD基因。这些生长素响应基因不均匀分布在葡萄的19条染色体上,部分家族基因在染色体上形成基因簇。葡萄芯片数据结果表明,生长素响应基因在葡萄不同时期的果实和叶芽中均有表达,尤其在果实转色期、叶芽萌发或休眠期表达量急剧变化。研究结果为葡萄生长素响应基因在叶片和果实发育过程中的功能研究提供参考。     

Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products

Plant natural products have been extensively exploited in food,medicine,flavor,cosmetic,renewable fuel,and other industrial sectors.Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products.Compared with engineering microbes for the production of plant natural products,the potential of plants as chassis for producing these compounds is underestimated,largely due to challenges encountered in engineering plants.Knowledge in pl...     

RAC/ROP GTPases and auxin signaling

Auxin functions as a key morphogen in regulating plant growth and development. Studies on auxin-regulated gene expression and on the mechanism of polar auxin transport and its asymmetric distribution within tissues have provided the basis for realizing the molecular mechanisms underlying auxin function. In eukaryotes, members of the Ras and Rho subfamilies of the Ras superfamily of small GTPases function as molecular switches in many signaling cascades that regulate growth and development. Plants do not have Ras proteins, but they contain Rho-like small G proteins called RACs or ROPs that, like fungal and metazoan Rhos, are regulators of cell polarity and may also undertake some Ras functions. Here, we discuss the advances made over the last decade that implicate RAC/ROPs as mediators for auxin-regulated gene expression, rapid cell surface-located auxin signaling, and directional auxin transport. We also describe experimental data indicating that auxin-RAC/ROP crosstalk may form regulatory feedback loops and theoretical modeling that attempts to connect local auxin gradients with RAC/ROP regulation of cell polarity. We hope that by discussing these experimental and modeling studies, this perspective will stimulate efforts to further refine our understanding of auxin signaling via the RAC/ROP molecular switch.     

Auxin: a master regulator in plant root development

The demand for increased crop productivity and the predicted challenges related to plant survival under adverse environmental conditions have renewed the interest in research in root biology. Various physiological and genetic studies have provided ample evidence in support of the role of plant growth regulators in root development. The biosynthesis and transport of auxin and its signaling play a crucial role in controlling root growth and development. The univocal role of auxin in root development has established it as a master regulator. Other plant hormones, such as cytokinins, brassinosteroids, ethylene, abscisic acid, gibberellins, jasmonic acid, polyamines and strigolactones interact either synergistically or antagonistically with auxin to trigger cascades of events leading to root morphogenesis and development. In recent years, the availability of biological resources, development of modern tools and experimental approaches have led to the advancement of knowledge in root development. Research in the areas of hormone signal perception, understanding network of events involved in hormone action and the transport of plant hormones has added a new dimension to root biology. The present review highlights some of the important conceptual developments in the interplay of auxin and other plant hormones and associated downstream events affecting root development.     

Microbial interventions are an easier alternative to engineer higher organisms

Advances in synthetic biology have made microbes easier to engineer than ever before. However, synthetic biology in animals and plants has lagged behind. Since it is now known that the phenotype of higher organisms depends largely on their microbiota, we propose that this is an easier route to achieving synthetic biology applications in these organisms.

A transition from reading to writing biology has blurred the lines between basic science and engineering creating the field of synthetic biology. With an ever‐expanding genetic toolbox, we now manipulate natural biological systems to optimize our anthropocentric activities. From the synthesis of complex aromatic compounds, to the production of safer vaccines, a problem identified may find its solution lying in the metabolism of a single cell. Initially, synthetic biology was largely focused on the production of such commodities at the industrial scale, not only to maximize profitability, but also to minimize energy and resource consumption. Consequently, this paradigm shift has come to alter the notion of a factory by many orders of magnitude and to create a new bridge between the built and natural world, as we employ nature’s evolutionary machinery to address our modern endeavours.Growth of the genetic toolbox and maturation of synthetic biology as a field has led to speculation about increasingly ambitious applications of writing biology with implications beyond biosynthesis. To date, most applications have been developed using microbes because they are less complex, more well understood and easier to manipulate. Single‐celled organisms can be optimized for production of complicated organic molecules; however, other exploits of genetic engineering will target more ambitious feats and thus require engineering of more than a large monoculture of microbes. Applications of synthetic biology outside of the bioreactor can address such issues as health and longevity, challenges in industrial agriculture and farming, the degradation of natural habitats and the reclamation of limited natural resources.Scope and scale of these applications provide obvious obstacles to the development of effective biotechnologies, but a more immediate limitation to realizing these technologies is the relative lack of genetic tools and insights which would allow the tinkering and rewiring of more complex organisms such as animals and plants. However, because of the natural intimate interactions between higher eukaryotes and microbes and the effect of these on phenotype, it is our vision that a faster, more tractable route to the engineering animal and plant phenotypes is via engineering their microbiomes.