Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comparisons of mitochondria purified by density gradients and after further surface charge purification have been used to ensure that the proteins identified copurify with mitochondria and to remove contaminants from the analysis. This rigorous approach to defining a subcellular proteome has yielded 322 nonredundant rice proteins and highlighted contaminants in previously reported rice mitochondrial proteomes. Comparative analysis with the Arabidopsis (Arabidopsis thaliana) mitochondrial proteome reveals conservation of a broad range of known and unknown function proteins in plant mitochondria, with only approximately 20% not having a clear homolog in the Arabidopsis mitochondrial proteome. As in Arabidopsis, only approximately 60% of the rice mitochondrial proteome is predictable using current organelle-targeting prediction tools. Use of the rice protein data set to explore rice transcript data provided insights into rice mitochondrial biogenesis during seed germination, leaf development, and heterogeneity in the expression of nucleus-encoded mitochondrial components in different rice tissues. Highlights include the identification of components involved in thiamine synthesis, evidence for coexpressed and unregulated expression of specific components of protein complexes, a selective anther-enhanced subclass of the decarboxylating segment of the tricarboxylic acid cycle, the differential expression of DNA and RNA replication components, and enhanced expression of specific metabolic components in photosynthetic tissues.

BACKGROUND: The hepatic stellate cell is the primary cell type responsible for the excessive formation and deposition of connective tissue elements during the development of hepatic fibrosis in chronically injured liver. Culturing quiescent hepatic stellate cells on plastic causes spontaneous activation leading to a myofibroblastic phenotype similar to that seen in vivo. This provides a simple model system for studying activation and transdifferentiation of these cells. The introduction of exogenous DNA into these cells is discussed controversially mainly due to the lack of systematic analysis. Therefore, we examined comparatively five nonviral, lipid-mediated gene transfer methods and adenoviral based infection, as potential tools for efficient delivery of DNA to rat hepatic stellate cells and their transdifferentiated counterpart, i.e. myofibroblasts. Transfection conditions were determined using enhanced green fluorescent protein as a reporter expressed under the transcriptional control of the human cytomegalovirus immediate early gene 1 promoter/enhancer. RESULTS: With the use of chemically enhanced transfection methods, the highest relative efficiency was obtained with FuGENE6 gene mediated DNA transfer. Quantitative evaluation of representative transfection experiments by flow cytometry revealed that approximately 6% of the rat hepatic stellate cells were transfected. None of the transfection methods tested was able to mediate gene delivery to rat myofibroblasts. To analyze if rat hepatic stellate cells and myofibroblasts are susceptible to adenoviral infection, we have inserted the transgenic expression cassette into a recombinant adenoviral type 5 genome as replacement for the E1 region. Viral particles of this replication-deficient Ad5-based reporter are able to infect 100% of rat hepatic stellate cells and myofibroblasts, respectively. CONCLUSIONS: Our results indicate that FuGENE6-based methods may be optimized sufficiently to offer a feasible approach for gene transfer into rat hepatic stellate cells. The data further demonstrate that adenoviral mediated transfer is a promising approach for gene delivery to these hepatic cells.

Background: The inflammasomes are cytoplasmic multiprotein complexes that are responsible for activation of inflammatory reactions. In principal, there are four individual inflammasome branches (i.e. NLRP1, NLRP3, NLRC4/NALP4, and AIM2) that mediate the cleavage and activation of caspase-1 and IL-1β that in turn leads to a complex network of cellular reactions that at the end initiate local and systemic inflammatory reactions [1]. We have recently shown that NLRP3 is virtually absent in cultured hepatocytes and that in vitro the stimulation of hepatocytes with lipopolysaccharides (LPS) results in strong activation of NLRP3 expression [2]. In this study we investigated the impact of NF-κB signalling on NLRP3 activation in primary hepatocytes.

Activation of hepatic stellate cells is considered to be the main step in the development of liver fibrosis, which is characterized by the transition of quiescent vitamin-A-rich cells to proliferative, fibrogenic and contractile myofibroblasts. The identification of regulatory genes during early cell activation and transdifferentiation is essential to extend our knowledge of hepatic fibrogenesis. In liver, the gene CSRP2 is exclusively expressed by stellate cells, whereas no transcripts are detectable in hepatocytes, sinusoidal endothelial cells or Kupffer cells. The early activation of stellate cells induced by platelet-derived growth factor is accompanied by an enhanced expression of CSRP2. During later stages of transdifferentiation, the expression of CSRP2 in these cells is suppressed in vitro and in vivo. The CSRP2-encoded cysteine- and glycine-rich double-LIM-domain protein (CRP)2 is proposed to function as a molecular adapter, arranging two or more as yet unidentified protein constituents into a macromolecular complex. To identify these proteins and assign a cellular function to CRP2, a human cDNA library was screened with full-length CRP2 as bait in a yeast two-hybrid screen. The protein inhibitor of activated STAT1 ('PIAS1') was shown to associate selectively with the C-terminal LIM domain of CRP2. Physical interaction of both proteins in the cellular environment was confirmed by co-localization experiments with confocal laser scanning microscopy and co-immunoprecipitation analysis. These results establish CRP2 as a potential new factor in the JAK/STAT-signalling pathway and suggest that the suppression of CSRP2 might be a prerequisite for the myofibroblastic transition of hepatic stellate cells.

Understanding the metal ion content of plant mitochondria and metal ion interactions with the proteome are vital for insights into both normal respiratory function and the process of protein damage during oxidative stress. We have analyzed the metal content of isolated Arabidopsis (Arabidopsis thaliana) mitochondria, revealing a 26:8:6:1 molar ratio for iron:zinc:copper:manganese and trace amounts of cobalt and molybdenum. We show that selective changes occur in mitochondrial copper and iron content following in vivo and in vitro oxidative stresses. Immobilized metal affinity chromatography charged with Cu(2+), Zn(2+), and Co(2+) was used to identify over 100 mitochondrial proteins with metal-binding properties. There were strong correlations between the sets of immobilized metal affinity chromatography-interacting proteins, proteins predicted to contain metal-binding motifs, and protein sets known to be oxidized or degraded during abiotic stress. Mitochondrial respiratory chain pathways and matrix enzymes varied widely in their susceptibility to metal-induced loss of function, showing the selectivity of the process. A detailed study of oxidized residues and predicted metal interaction sites in the tricarboxylic acid cycle enzyme aconitase identified selective oxidation of residues in the active site and showed an approach for broader screening of functionally significant oxidation events in the mitochondrial proteome.

Clover and special‐purpose legumes (not including alfalfa, Medicago sativa L.) constitute the primary genetic resource of legumes for grass‐legume based pasture and hay systems. The group is diverse and contains species from the genera Trifolium, Lotus, Lespedeza, Vicia , and others. Although species in these genera have been the subject of research for at least six decades no systematic scheme for genetic nomenclature has been adopted and a variety of conventions and gene symbols have been used. Absense of a centralized repository for genetic marker stocks has contributed to the loss of seed stocks of named genes. This paper (i) outlines a set of rules for uniform nomenclature and symbolization for the clovers and special purpose legumes, (ii) defines the membership of a permanent committee on gene symbolism and designates a central repository for named genes, and (iii) tabulates gene symbols published to date for red clover ( Trifolium pratense L.) and white clover ( T. repens L.) and attempts to clarify cases of duplicate nomenclature with establishment of a list of recommended gene symbols. The inheritance and gene symbols are tabulated for 61 previously published red clover genes and 28 previously published white clover genes. The genetic behavior of 27 other traits in red clover for which gene symbols were not published is summarized. Gene nomenclature and symbols according to the rules outlined are proposed for 27 genes in red clover and 28 genes in white clover. Two linkage groups are described for white clover.

EDITORIAL article Front. Plant Sci., 26 February 2014Sec. Plant Proteomics and Protein Structural Biology Volume 5 - 2014 | https://doi.org/10.3389/fpls.2014.00055

Plant mitochondria are highly responsive organelles that vary their metabolism in response to a wide range of chemical and environmental conditions. Quantitative proteomics studies have begun to allow the analysis of these large-scale protein changes in mitochondria. However studies of the integral membrane proteome of plant mitochondria, arguably the site responsible for the most fundamental mitochondrial processes of oxidative phosphorylation, protein import and metabolite transport, remain a technical challenge. Here we have investigated the changes in protein abundance in response to a number of chemical stresses and cold. In addition to refining the subcellular localization of 66 proteins, we have been able to characterize 596 protein × treatment combinations following a range of stresses. To date it has been assumed that the main mitochondrial response to stress involved the induction of alternative respiratory proteins such as AOX, UCPs, and alternative NAD(P)H dehydrogenases; we now provide evidence for a number of very specific protein abundance changes that have not been highlighted previously by transcript studies. This includes both previously characterized stress responsive proteins as well as major components of oxidative phosphorylation, protein import/export, and metabolite transport.

Factor VII activating protease (FSAP) is a multifunctional serine protease that is mainly synthesized and secreted by hepatocytes. This enzyme is highly evolutionarily conserved and contains three epidermal growth factor like domains, a kringle domain and a trypsin-like serine protease signature at its C-terminus. Animal experimentation and clinical findings indicate that FSAP influences a range of inflammatory fibroproliferative diseases. In particular, recent work demonstrated that FSAP is anti-fibrotic and influences liver fibrosis progression. The relative high physiological concentration, occurrence of gene variants affecting the proteolytic activity of FSAP and eclectic substrate specificity should in principal presuppose this protease to be frequently found in studies in which quantitative proteomics is performed. However, presently there are only a few studies available that have identified FSAP in applications using 2D gels, MS or other proteomic-associated techniques. We summarize here the actual knowledge about FSAP functions in initiation and progression of hepatic fibrosis and comment on proteome studies in which altered expression or activity of FSAP was reported.

In reverse genetic knockout (KO) studies that aim to assign function to specific genes, confirming the reduction in abundance of the encoded protein will often aid the link between genotype and phenotype. However, measuring specific protein abundance is particularly difficult in plant research, where only a limited number of antibodies are available. This problem is enhanced when studying gene families or different proteins derived from the same gene (isoforms), as many antibodies cross react with more than one protein. We show that utilizing selected reaction monitoring (SRM) mass spectrometry allows researchers to confirm protein abundance in mutant lines, even when discrimination between very similar proteins is needed. Selecting the best peptides for SRM analysis to ensure that protein- or gene-specific information can be obtained requires a series of steps, aids, and interpretation. To enable this process in Arabidopsis (Arabidopsis thaliana), we have built a Web-based tool, the Arabidopsis Proteotypic Predictor, to select candidate SRM transitions when no previous mass spectrometry evidence exists. We also provide an in-depth analysis of the theoretical Arabidopsis proteome and its use in selecting candidate SRM peptides to establish assays for use in determining protein abundance. To test the effectiveness of SRM mass spectrometry in determining protein abundance in mutant lines, we selected two enzymes with multiple isoforms, aconitase and malate dehydrogenase. Selected peptides were quantified to estimate the abundance of each of the two mitochondrial isoforms in wild-type, KO, double KO, and complemented plant lines. We show that SRM protein analysis is a sensitive and rapid approach to quantify protein abundance differences in Arabidopsis for specific and highly related enzyme isoforms.

The subcellular energy organelles (chloroplast, mitochondria, and peroxisome) in plants are responsible for major metabolic processes including photosynthesis, photorespiration, oxidative phosphorylation, β-oxidation, and the tricarboxylic acid cycle. Arabidopsis thaliana provides a considerable challenge to organellar researchers that have traditionally focused their methods on the use of larger plants and storage organs from which organelles are relatively easy to isolate. In contrast, the small size and lack of abundant heterotrophic organs in Arabidopsis thaliana means that many traditional techniques have required significant modification to yield enough isolated organelles for experimentation. However, these challenges are balanced by the advantages of working in an organism that has such a wide array of publically available genetic resources. Here we present methods for the isolation of chloroplasts, mitochondria and peroxisomes from Arabidopsis thaliana plants and heterotrophic cell cultures as well as a number of commonly used assays to assess their functional integrity and purity.