Phase separation in plants: New insights into cellular compartmentalization

A fundamental challenge for cells is how to coordinate various biochemical reactions in space and time. To achieve spatiotemporal control, cells have developed organelles that are surrounded by lipid bilayer membranes. Further, membraneless compartmentalization, a process induced by dynamic physical association of biomolecules through phase transition offers another efficient mechanism for intracellular organization. While our understanding of phase separation was predominantly dependent on yeast and animal models, recent findings have provided compelling evidence for emerging roles of phase separation in plants. In this review, we first provide an overview of the current knowledge of phase separation, including its definition, biophysical principles, molecular features and regulatory mechanisms. Then we summarize plant-specific phase separation phenomena and describe their functions in plant biological processes in great detail. Moreover, we propose that phase separation is an evolutionarily conserved and efficient mechanism for cellular compartmentalization which allows for distinct metabolic processes and signaling pathways, and is especially beneficial for the sessile lifestyle of plants to quickly and efficiently respond to the changing environment.     

Phosphoproteomics: new insights into cellular signaling

Developments in the field of phosphoproteomics have been fueled by the need simultaneously to monitor many different phosphoproteins within the signaling networks that coordinate responses to changes in the cellular environment. This article presents a brief review of phosphoproteomics with an emphasis on the biological insights that have been derived so far.     

New insights into the interplay between codon bias determinants in plants

Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.     

New insights into the mechanisms of lipid-body biogenesis in plants and other organisms

A comparative approach has been used to study the role of several lipid-body-binding proteins in plants and animals. Caleosins are a newly discovered class of calcium-binding lipid-body proteins found in plants and fungi, which we now report to have separate endoplasmic reticulum- and lipid-body-associated isoforms. We also compare the lipid-body targeting of oleosin from plants and the core protein of the hepatitis C virus when they were expressed separately in lipid-accumulating animal cell lines. This is a novel and powerful approach to investigating the factors that determine the lipid-body targeting of a wide range of proteins.     

Deeper into the maize: new insights into genomic imprinting in plants

Current models for regulation of parent-specific gene expression in plants have been based on a small number of imprinted genes in Arabidopsis. These present repression as the default state, with expression requiring targeted activation. In general, repression is associated with maintenance methylation of cytosines, while no role has been found in Arabidopsis imprinting for de novo methylation--unlike the case in mammals. A recent paper both reinforces and challenges the model drawn from Arabidopsis. Methylation patterns of two imprinted loci in maize were tracked from gametes to offspring, enabling an exploration of the timing of imprinting. For one gene, fie1, the results were as expected: parent-specific methylation patterns were inherited from the three types of gamete: egg, central cell and sperm. The behaviour of fie2, however, was a surprise: no alleles were methylated in the gametes, although paternally contributed fie2 is methylated and silent in the endosperm, indicating that, in some cases, plant imprinting requires de novo DNA methylation. This work significantly broadens our understanding of plant imprinting and points to a greater diversity in imprinting mechanisms than has previously been appreciated.     

Alcoholic liver disease: Current insights into cellular mechanisms

Alcoholic liver disease (ALD) due to chronic alcohol consumption is a significant global disease burden and a leading cause of mortality. Alcohol abuse induces a myriad of aberrant changes in hepatocytes at both the cellular and molecular level. Although the disease spectrum of ALD is widely recognized, the precise triggers for disease progression are still to be fully elucidated. Oxidative stress, mitochondrial dysfunction, gut dysbiosis and altered immune system response plays an important role in disease pathogenesis, triggering the activation of inflammatory pathways and apoptosis. Despite many recent clinical studies treatment options for ALD are limited, especially at the alcoholic hepatitis stage. We have therefore reviewed some of the key pathways involved in the pathogenesis of ALD and highlighted current trials for treating patients.     

Effect of copper on cellular processes in higher plants

Copper (Cu) is a heavy metal which in recent studies has been attributed an increasing role in metabolic processes of plant cells. It is an indispensable component of oxidative enzymes or of particular structural components of cells. At elevated concentrations, Cu can act strongly on chromatin, the photosynthetic apparatus, growth, and senescence processes. The mechanisms of the metal toxicity depending largely on the growth stage of treated plants are presented in this review.     

Effect of copper on cellular processes in higher plants

Copper (Cu) is a heavy metal which in recent studies has been attributed an increasing role in metabolic processes of plant cells. It is an indispensable component of oxidative enzymes or of particular structural components of cells. At elevated concentrations, Cu can act strongly on chromatin, the photosynthetic apparatus, growth, and senescence processes. The mechanisms of the metal toxicity depending largely on the growth stage of treated plants are presented in this review.     

New insights into the biological effects of anthrax toxins: linking cellular to organismal responses

The anthrax toxins lethal toxin (LT) and edema toxin (ET) are essential virulence factors produced by Bacillus anthracis. These toxins act during two distinct phases of anthrax infection. During the first, prodromal phase, which is often asymptomatic, anthrax toxins act on cells of the immune system to help the pathogen establish infection. Then, during the rapidly progressing (or fulminant) stage of the disease bacteria disseminate via a hematological route to various target tissues and organs, which are typically highly vascularized. As bacteria proliferate in the bloodstream, LT and ET begin to accumulate rapidly reaching a critical threshold level that will cause death even when the bacterial proliferation is curtailed by antibiotics. During this final phase of infection the toxins cause an increase in vascular permeability and a decrease in function of target organs including the heart, spleen, kidney, adrenal gland, and brain. In this review, we examine the various biological effects of anthrax toxins, focusing on the fulminant stage of the disease and on mechanisms by which the two toxins may collaborate to cause cardiovascular collapse. We discuss normal mechanisms involved in maintaining vascular integrity and based on recent studies indicating that LT and ET cooperatively inhibit membrane trafficking to cell-cell junctions we explore several potential mechanisms by which the toxins may achieve their lethal effects. We also summarize the effects of other potential virulence factors secreted by B. anthracis and consider the role of toxic factors in the evolutionarily recent emergence of this devastating disease.     

New insights into reactive oxygen species and nitric oxide signalling under low oxygen in plants

Plants produce reactive oxygen species (ROS) when exposed to low oxygen (O₂). Much experimental evidence has demonstrated the existence of an oxidative burst when there is an O₂ shortage. This originates at various subcellular sites. The activation of NADPH oxidase(s), in complex with other proteins, is responsible for ROS production at the plasma membrane. Another source of low O₂‐dependent ROS is the mitochondrial electron transport chain, which misfunctions when low O₂ limits its activity. Arabidopsis mutants impaired in proteins playing a role in ROS production display an intolerant phenotype to anoxia and submergence, suggesting a role in acclimation to stress. In rice, the presence of the submergence 1A (SUB1A) gene for submergence tolerance is associated with a higher capacity to scavenge ROS. Additionally, the destabilization of group VII ethylene responsive factors, which are involved in the direct O₂ sensing mechanism, requires nitric oxide (NO). All this evidence suggests the existence of a ROS and NO – low O₂ mechanism interplay which likely includes sensing, anaerobic metabolism and acclimation to stress. In this review, we summarize the most recent findings on this topic, formulating hypotheses on the basis of the latest advances.     

Neodiptera: New insights into the adult morphology and higher level phylogeny of Diptera (Insecta)

This paper outlines several aspects of the skeleto-muscular organization of the adult prothorax and cervix pertaining to the ground pattern of Diptera, which in turn leads to the characterization of Neodiptera, a higher level dipterous taxon which includes Brachycera and bibionomorph Nematocera ( sensu Hennig). The monophyly of Neodiptera is firmly supported by four skeleto-muscular modifications of the pronoto-cervical region. The bibionomorph Nematocera are shown to be paraphyletic in terms of Brachycera. On more preliminary evidence it is argued that the fundamental dichotomy of the extant Diptera lies between a 'polyneuran' clade which includes Trichoceridae, Tipuloidea, Tanyderidae, and Ptychopteridae and an 'oligoneuran' clade which includes all the remaining groups. Preliminary evidence for a sister group relationship between Blephariceroidea and Culicomorpha is also provided. The possible adaptational significance of the cervical specializations in Neodiptera is discussed.