Identification of low abundance polyA-binding proteins in Arabidopsis chloroplast using polyA-affinity column

Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na₂CO₃ stress were conducted. In addition, Western blot, real-time PCR, and transgenic techniques were applied to validate the proteomic results and test the functions of the Na₂CO₃-responsive proteins. A total of 104 and 102 Na₂CO₃-responsive proteins were identified in leaves and chloroplasts, respectively. In addition, 84 Na₂CO₃-responsive phosphoproteins were identified, including 56 new phosphorylation sites in 56 phosphoproteins from chloroplasts, which are crucial for the regulation of photosynthesis, ion transport, signal transduction, and energy homeostasis. A full-length PtFBA encoding an alkaligrass chloroplastic fructose-bisphosphate aldolase (FBA) was overexpressed in wild-type cells of cyanobacterium Synechocystis sp. Strain PCC 6803, leading to enhanced Na₂CO₃ tolerance. All these results indicate that thermal dissipation, state transition, cyclic electron transport, photorespiration, repair of photosystem (PS) II, PSI activity, and ROS homeostasis were altered in response to Na₂CO₃ stress, which help to improve our understanding of the Na₂CO₃-responsive mechanisms in halophytes.

Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications

In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.

AtOMA1 Affects the OXPHOS System and Plant Growth in Contrast to Other Newly Identified ATP-Independent Proteases in Arabidopsis Mitochondria

Compared with yeast, our knowledge on members of the ATP-independent plant mitochondrial proteolytic machinery is rather poor. In the present study, using confocal microscopy and immunoblotting, we proved that homologs of yeast Oma1, Atp23, Imp1, Imp2, and Oct1 proteases are localized in Arabidopsis mitochondria. We characterized these components of the ATP-independent proteolytic system as well as the earlier identified protease, AtICP55, with an emphasis on their significance in plant growth and functionality in the OXPHOS system. A functional complementation assay demonstrated that out of all the analyzed proteases, only AtOMA1 and AtICP55 could substitute for a lack of their yeast counterparts. We did not observe any significant developmental or morphological changes in plants lacking the studied proteases, either under optimal growth conditions or after exposure to stress, with the only exception being retarded root growth in oma1-1, thus implying that the absence of a single mitochondrial ATP-independent protease is not critical for Arabidopsis growth and development. We did not find any evidence indicating a clear functional complementation of the missing protease by any other protease at the transcript or protein level. Studies on the impact of the analyzed proteases on mitochondrial bioenergetic function revealed that out of all the studied mutants, only oma1-1 showed differences in activities and amounts of OXPHOS proteins. Among all the OXPHOS disorders found in oma1-1, the complex V deficiency is distinctive because it is mainly associated with decreased catalytic activity and not correlated with complex abundance, which has been observed in the case of supercomplex I + III₂ and complex I deficiencies. Altogether, our study indicates that despite the presence of highly conservative homologs, the mitochondrial ATP-independent proteolytic system is not functionally conserved in plants as compared with yeast. Our findings also highlight the importance of AtOMA1 in maintenance of proper function of the OXPHOS system as well as in growth and development of Arabidopsis thaliana.

Protein import into plant mitochondria: signals, machinery, processing, and regulation

The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.

Plant proteomics methods to reach low-abundance proteins

The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.

RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa

RNA binding proteins (RBPs) play an important role not only in nuclear gene expression, but also in cytosolic events, including RNA transport, localization, translation, and stability. Although over 200 RBPs are predicted from the Arabidopsis genome alone, relatively little is known about these proteins in plants as many exhibit no homology to known RBPs in other eukaryotes. Furthermore, RBPs likely have low expression levels making them difficult to identify and study. As part of our continuing efforts to understand plant cytosolic gene expression and the factors involved, we employed a combination of affinity chromatography and proteomic techniques to enrich for low abundance RBPs in developing rice seed. Our results have been compiled into RiceRBP (http://www.bioinformatics2.wsu.edu/RiceRBP), a database that contains 257 experimentally identified proteins, many of which have not previously been predicted to be RBPs. For each of the identified proteins, RiceRBP provides information on transcript and protein sequence, predicted protein domains, details of the experimental identification, and whether antibodies have been generated for public use. In addition, tools are available to analyze expression patterns for the identified genes, view phylogentic relationships and search for orthologous proteins. RiceRBP is a valuable tool for the community in the study of plant RBPs.

Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium sativum and Arabidopsis thaliana seed germination

Germination of endospermic seeds is partly regulated by the micropylar endosperm, which acts as constraint to radicle protrusion. Gibberellin (GA) signalling pathways control coat-dormancy release, endosperm weakening, and organ expansion during seed germination. Three GIBBERELLIN INSENSITIVE DWARF1 (GID1) GA receptors are known in Arabidopsis thaliana: GID1a, GID1b, and GID1c. Molecular phylogenetic analysis of angiosperm GID1s reveals that they cluster into two eudicot (GID1ac, GID1b) groups and one monocot group. Eudicots have at least one gene from each of the two groups, indicating that the different GID1 receptors fulfil distinct roles during plant development. A comparative Brassicaceae approach was used, in which gid1 mutant and whole-seed transcript analyses in Arabidopsis were combined with seed-tissue-specific analyses of its close relative Lepidium sativum (garden cress), for which three GID1 orthologues were cloned. GA signalling via the GID1ac receptors is required for Arabidopsis seed germination, GID1b cannot compensate for the impaired germination of the gid1agid1c mutant. Transcript expression patterns differed temporarily, spatially, and hormonally, with GID1b being distinct from GID1ac in both species. Endosperm weakening is mediated, at least in part, through GA-induced genes encoding cell-wall-modifying proteins. A suppression subtraction hybridization (SSH) cDNA library enriched for sequences that are highly expressed during early germination in the micropylar endosperm contained expansins and xyloglucan endo-transglycosylases/hydrolases (XTHs). Their transcript expression patterns in both species strongly suggest that they are regulated by distinct GID1-mediated GA signalling pathways. The GID1ac and GID1b pathways seem to fulfil distinct regulatory roles during Brassicaceae seed germination and seem to control their downstream targets distinctly.

The RNA-recognition motif in chloroplasts

Chloroplast RNA metabolism is characterized by multiple RNA processing steps that require hundreds of RNA binding proteins. A growing number of RNA binding proteins have been shown to mediate specific RNA processing steps in the chloroplast, but little do we know about their regulatory importance or mode of molecular action. This review summarizes knowledge on chloroplast proteins that contain an RNA recognition motif, a classical RNA binding domain widespread in pro- and eukaryotes. Several members of this family respond to external and internal stimuli by changes in their expression levels and protein modification state. They therefore appear as ideal candidates for regulating chloroplast RNA processing under shifting environmental conditions.

Physiological and proteomic analysis of salinity tolerance in Puccinellia tenuiflora

Soil salinity poses a serious threat to agriculture productivity throughout the world. Studying mechanisms of salinity tolerance in halophytic plants will provide valuable information for engineering plants for enhanced salt tolerance. Monocotyledonous Puccinellia tenuiflora is a halophytic species that widely distributed in the saline-alkali soil of the Songnen plain in northeastern China. Here we investigate the molecular mechanisms underlying moderate salt tolerance of P. tenuiflora using a combined physiological and proteomic approach. The changes in biomass, inorganic ion content, osmolytes, photosynthesis, defense-related enzyme activities, and metabolites in the course of salt treatment were analyzed in the leaves. Comparative proteomic analysis revealed 107 identities (representing 93 unique proteins) differentially expressed in P. tenuiflora leaves under saline conditions. These proteins were mainly involved in photosynthesis, stress and defense, carbohydrate and energy metabolism, protein metabolism, signaling, membrane, and transport. Our results showed that reduction of photosynthesis under salt treatment was attributed to the down-regulation of the light-harvesting complex (LHC) and Calvin cycle enzymes. Selective uptake of inorganic ions, high K(+)/Na(+) ratio, Ca(2+) concentration changes, and an accumulation of osmolytes contributed to ion balance and osmotic adjustment in leaf cells. Importantly, P. tenuiflora plants developed diverse reactive oxygen species (ROS) scavenging mechanisms in their leaves to cope with moderate salinity, including enhancement of the photorespiration pathway and thermal dissipation, synthesis of the low-molecular-weight antioxidant α-tocopherol, and an accumulation of compatible solutes. This study provides important information toward improving salt tolerance of cereals.

Proteomics-based analysis of novel genes involved in response toward soybean mosaic virus infection

Soybean mosaic virus (SMV) is one of the most serious virus diseases of soybean. However, little is known about the molecular basis of the soybean defense mechanism against this pathogen. We identified differentially expressed proteins in soybean leaves infected with SMV by proteomic approaches. Twenty-eight protein spots that showed ≥2-fold difference in intensity were identified between mock-inoculated and SMV-infected samples. Among them, 16 spots were upregulated and 12 spots were downregulated in the SMV-infected samples. We recovered 25 of the 28 differentially expressed proteins from two-dimensional electrophoresis (2-DE) gels. These spots were identified as 16 different proteins by Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and tandem TOF/TOF MS, and were potentially involved in protein degradation, defense signal transfer, reactive oxygen, cell wall reinforcement, and energy and metabolism regulation. Gene expression analysis of 13 genes by quantitative real time polymerase chain reaction (qRT-PCR) showed that metabolism genes and photosynthesis genes were downregulated at all time points. One energy gene was downregulated, whereas another energy gene was upregulated at five of the six time points. The other interesting genes that were altered by SMV infection showed changes in transcription over time. This is the first extensive application of proteomics to the SMV-soybean interaction. These results contribute to a better understanding of the molecular basis of soybean's responses to SMV.