Plastids unleashed: their development and their integration in plant development

Derived by endosymbiosis from ancestral cyanobacteria, chloroplasts integrated seamlessly into the biology of their host cell. That integration involved a massive transfer of genes to the cell's nucleus, with the modification of pre-existing processes, like plastid division and the operation of the plastid genetic machinery and the emergence of new ones, like the import of proteins translated in the cytoplasm. The uncovering in molecular detail of several of these processes reveals a merger of mechanisms of symbiont and host origin. Chloroplasts acquired roles as part of the biology of land plants by differentiating into a variety of interconvertible plastid forms according to the cell type. How these conversions take place, or how new problems, like the regulation of the plastid population size in cells, have been solved, is barely starting to be understood. Like the whole plant and as a result of the requirements and dangers associated with photosynthetic activity, chloroplasts in particular are under the control of environmental cues. Far from being passive targets of cellular processes, plastids are sources of signals of plastid-nuclear communication, which regulate activities for their own biogenesis. Plastids are also sources of developmental signals, in whose absence tissue architecture or cell differentiation are aberrant, in a cell-autonomous fashion. Over evolutionary time, plastids also contributed many genes for activities that are no longer directly associated with them (like light perception or hormone function). The overall picture is one in which plastids are at both the receiving and the acting ends in plant development, in both ontogenic and evolutionary terms.     

Mitochondria: Joining forces to thwart cell death

Mitochondria are highly dynamic organelles that undergo constant cycles of fusion and fission. An additional level of regulation of mitochondrial function, which is particularly important in neurons, is their active transport along microtubules. Recent evidence suggests that the mitochondrial fusion/fission machinery as well as the molecular motors responsible for their movement constitute powerful regulatory control points that directly impact metabolism and regulation of cell death. This is true for not only apoptosis, but also for excitotoxicity where calcium overload is a major component of the cell death process. In this review, we will describe the molecular mechanisms regulating fusion and fission and how this impinges on cell survival in the context of acute neuronal injury.     

Joining forces in the quest for orthologs

A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009.     

Joining forces: The interface of gravitropism and plastid protein import

In flowering plants, gravity perception appears to involve the sedimentation of starch-filled plastids, called amyloplasts, within specialized cells (the statocytes) of shoots (endodermal cells) and roots (columella cells). Unfortunately, how the physical information derived from amyloplast sedimentation is converted into a biochemical signal that promotes organ gravitropic curvature remains largely unknown. Recent results suggest an involvement of the Translocon of the Outer Envelope of (Chloro) plastids (TOC) in early phases of gravity signal transduction within the statocytes. This review summarizes our current knowledge of the molecular mechanisms that govern gravity signal transduction in flowering plants and summarizes models that attempt to explain the contribution of TOC proteins in this important behavioral plant growth response to its mechanical environment.Key words: gravitropism, root, amyloplast, TOC complex, TOC132, TOC75     

Auxin cross-talk: integration of signalling pathways to control plant development

Plants sense and respond to endogenous signals and environmental cues to ensure optimal growth and development. Plant cells must integrate the myriad transduction events into a comprehensive network of signalling pathways and responses. The phytohormone auxin occupies a central place within this transduction network, frequently acting in conjunction with other signals, to co-ordinately regulate cellular processes such as division, elongation and differentiation. As a non-cell autonomous signal, auxin also interacts with other signalling pathways to regulate inter-cellular developmental processes. As part of this especially themed edition of Plant Molecular Biology, we will review examples of `cross-talk' between auxin and other signalling pathways. Given the current state of knowledge, we have deliberately focused our efforts reviewing auxin interactions with other phytohormone and light signalling pathways. We conclude by discussing how new genomic approaches and the Arabidopsis genome sequence are likely to impact this area of research in the future.     

植物——土壤反馈研究进展

该文综述了植物—土壤反馈研究的定义、途经、方法和国内外的研究现状以及存在的问题。植物—土壤反馈是指植物改变根际土壤的生物和非生物特征,同时被改变的也能提高或降低该植物的生长,形成正的或负的反馈,从而影响植物群落组成及植物间相互作用。植物—土壤反馈研究对于理解植物群落演替、生态系统多样性与生产力形成与维持机制,认识生态系统对气候变化和生物入侵等全球生态事件的响应具有重要的理论意义。外来物种快速生长和繁殖及其可能的负反馈可能会导致本地种被竞争排除,未来气候变化可能导致物种组成发生变化及生物多样性丢失,但资源互补和植物—土壤反馈效应则可能使植物群落具有较高的生产力和多样性。因此,未来植物—土壤反馈关系应该加强以下几方面研究:(1)开展不同生态系统植物—土壤反馈关系的比较研究;(2)植物—土壤及土壤—植物等群落水平的反馈研究;(3)特别是要加强分子和基因工具在植物土壤—反馈关系中的应用,揭示植物—土壤反馈关系的分子机理。     

Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes

Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies.     

Mycorrhizal traits and plant communities: perspectives for integration

Plant functional type‐ and trait‐based approaches to understanding vegetation dynamics are gradually gaining popularity. However, plant mycorrhizal traits are rarely considered in plant trait databases and are almost totally neglected in trait‐based plant community studies, despite more than 90% of the land flora being mycorrhizal. In this paper I describe and define the mycorrhizal traits of plant species, notably mycorrhizal type, mycorrhizal status, mycorrhizal flexibility and mycorrhizal dependency, which potentially influence plant distribution and community structure. I propose ways of using these traits for large‐scale synthetic studies for understanding the role of mycorrhizal symbiosis in vegetation dynamics. I suggest considering plant community mycorrhization – community means of mycorrhizal traits weighted by plant species abundances – and suggest an index of mycorrhization to describe the mycorrhizal trait composition of plant communities.     

Applied plant genomics: the secret is integration

Although concerted efforts to understand selected botanical models have been made, the resulting basic knowledge varies in its applicability to other diverse species including the major crops. Recent advances in high-throughput genomics are offering new avenues through which to exploit model systems for the study of botanical diversity, providing prospects for crop improvement. In particular, whole-genome sequencing has provided opportunities for the broader application of reverse genetics, expression profiling, and molecular mapping in diverse species.     

Transfection of plant mitochondria and in organello gene integration

Investigation and manipulation of mitochondrial genetics in animal and plant cells remains restricted by the lack of an efficient in vivo transformation methodology. Mitochondrial transfection in whole cells and maintenance of the transfected DNA are main issues on this track. We showed earlier that isolated mitochondria from different organisms can import DNA. Exploiting this mechanism, we assessed the possibility to maintain exogenous DNA in plant organelles. Whereas homologous recombination is scarce in the higher plant nuclear compartment, recombination between large repeats generates the multipartite structure of the plant mitochondrial genome. These processes are under strict surveillance to avoid extensive genomic rearrangements. Nevertheless, following transfection of isolated organelles with constructs composed of a partial gfp gene flanked by fragments of mitochondrial DNA, we demonstrated in organello homologous recombination of the imported DNA with the resident DNA and integration of the reporter gene. Recombination yielded insertion of a continuous exogenous DNA fragment including the gfp sequence and at least 0.5 kb of flanking sequence on each side. According to our observations, transfection constructs carrying multiple sequences homologous to the mitochondrial DNA should be suitable and targeting of most regions in the organelle genome should be feasible, making the approach of general interest.     

Measuring the multi-scale integration of mechanical forces during morphogenesis

The elaborate changes in morphology of an organism during development are the result of mechanical contributions that are a mixture of those generated locally and those that influence from a distance. We would like to know how chemical and mechanical information is transmitted and transduced, how work is done to achieve robust morphogenesis and why it sometimes fails. We introduce a scheme for separating the influence of two classes of forces. Active intrinsic forces integrate up levels of scale to shape tissues. Counter-currently, extrinsic forces exert influence from higher levels downwards and feed back directly and indirectly upon the intrinsic behaviours. We identify the measurable signatures of different kinds of forces and identify the frontiers where work is most needed.     

miSSING LINKS: miRNAs and plant development

The discovery of hundreds of plant micro RNAs (miRNAs) has triggered much speculation about their potential roles in plant development. The search for plant genes involved in miRNA processing has revealed common factors such as DICER, and new molecules, including HEN1. Progress is also being made toward identifying miRNA target genes and understanding the mechanisms of miRNA-mediated gene regulation in plants. This work has lead to a reexamination of many previously characterized mutations that are now known to affect components or targets of miRNA-mediated pathways.     

Fluid flows and forces in development: functions, features and biophysical principles

Throughout morphogenesis, cells experience intracellular tensile and contractile forces on microscopic scales. Cells also experience extracellular forces, such as static forces mediated by the extracellular matrix and forces resulting from microscopic fluid flow. Although the biological ramifications of static forces have received much attention, little is known about the roles of fluid flows and forces during embryogenesis. Here, we focus on the microfluidic forces generated by cilia-driven fluid flow and heart-driven hemodynamics, as well as on the signaling pathways involved in flow sensing. We discuss recent studies that describe the functions and the biomechanical features of these fluid flows. These insights suggest that biological flow determines many aspects of cell behavior and identity through a specific set of physical stimuli and signaling pathways.     

Sensory feedback in a bump attractor model of path integration

Mammalian spatial navigation systems utilize several different sensory information channels. This information is converted into a neural code that represents the animal’s current position in space by engaging place cell, grid cell, and head direction cell networks. In particular, sensory landmark (allothetic) cues can be utilized in concert with an animal’s knowledge of its own velocity (idiothetic) cues to generate a more accurate representation of position than path integration provides on its own (Battaglia et al. The Journal of Neuroscience 24(19):4541–4550 (2004)). We develop a computational model that merges path integration with feedback from external sensory cues that provide a reliable representation of spatial position along an annular track. Starting with a continuous bump attractor model, we explore the impact of synaptic spatial asymmetry and heterogeneity, which disrupt the position code of the path integration process. We use asymptotic analysis to reduce the bump attractor model to a single scalar equation whose potential represents the impact of asymmetry and heterogeneity. Such imperfections cause errors to build up when the network performs path integration, but these errors can be corrected by an external control signal representing the effects of sensory cues. We demonstrate that there is an optimal strength and decay rate of the control signal when cues appear either periodically or randomly. A similar analysis is performed when errors in path integration arise from dynamic noise fluctuations. Again, there is an optimal strength and decay of discrete control that minimizes the path integration error.