Label-free protein quantification for plant Golgi protein localization and abundance

SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii

The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.

A century journey of organelles research in the plant endomembrane system

We are entering an exciting century in the study of the plant organelles in the endomembrane system. Over the past century, especially within the past 50 years, tremendous advancements have been made in the complex plant cell to generate a much clearer and informative picture of plant organelles, including the molecular/morphological features, dynamic/spatial behavior, and physiological functions. Importantly, all these discoveries and achievements in the identification and characterization of organelles in the endomembrane system would not have been possible without: (1) the innovations and timely applications of various state-of-art cell biology tools and technologies for organelle biology research; (2) the continuous efforts in developing and characterizing new organelle markers by the plant biology community; and (3) the landmark studies on the identification and characterization of the elusive organelles. While molecular aspects and results for individual organelles have been extensively reviewed, the development of the techniques for organelle research in plant cell biology is less appreciated. As one of the ASPB Centennial Reviews on "organelle biology," here we aim to take a journey across a century of organelle biology research in plants by highlighting the important tools (or landmark technologies) and key scientists that contributed to visualize organelles. We then highlight the landmark studies leading to the identification and characterization of individual organelles in the plant endomembrane systems.

Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology

The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.

DeepSP: A Deep Learning Framework for Spatial Proteomics

The study of protein subcellular localization (PSL) is a fundamental step toward understanding the mechanism of protein function. The recent development of mass spectrometry (MS)-based spatial proteomics to quantify the distribution of proteins across subcellular fractions provides us a high-throughput approach to predict unknown PSLs based on known PSLs. However, the accuracy of PSL annotations in spatial proteomics is limited by the performance of existing PSL predictors based on traditional machine learning algorithms. In this study, we present a novel deep learning framework named DeepSP for PSL prediction of an MS-based spatial proteomics data set. DeepSP constructs the new feature map of a difference matrix by capturing detailed changes between different subcellular fractions of protein occupancy profiles and uses the convolutional block attention module to improve the prediction performance of PSL. DeepSP achieved significant improvement in accuracy and robustness for PSL prediction in independent test sets and unknown PSL prediction compared to current state-of-the-art machine learning predictors. As an efficient and robust framework for PSL prediction, DeepSP is expected to facilitate spatial proteomics studies and contributes to the elucidation of protein functions and the regulation of biological processes.

Open questions in plant cell wall synthesis

Plant cells are surrounded by strong yet flexible polysaccharide-based cell walls that support the cell while also allowing growth by cell expansion. Plant cell wall research has advanced tremendously in recent years. Sequenced genomes of many model and crop plants have facilitated cataloging and characterization of many enzymes involved in cell wall synthesis. Structural information has been generated for several important cell wall synthesizing enzymes. Important tools have been developed including antibodies raised against a variety of cell wall polysaccharides and glycoproteins, collections of enzyme clones and synthetic glycan arrays for characterizing enzymes, herbicides that specifically affect cell wall synthesis, live-cell imaging probes to track cell wall synthesis, and an inducible secondary cell wall synthesis system. Despite these advances, and often because of the new information they provide, many open questions about plant cell wall polysaccharide synthesis persist. This article highlights some of the key questions that remain open, reviews the data supporting different hypotheses that address these questions, and discusses technological developments that may answer these questions in the future.

TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis

Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with the interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. We extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across data sets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS data sets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.

Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology

In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.

Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin 'egg-box' structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

Physiological Importance of Molybdate Transporter Family 1 in Feeding the Molybdenum Cofactor Biosynthesis Pathway in Arabidopsis thaliana

Molybdate uptake and molybdenum cofactor (Moco) biosynthesis were investigated in detail in the last few decades. The present study critically reviews our present knowledge about eukaryotic molybdate transporters (MOT) and focuses on the model plant Arabidopsis thaliana, complementing it with new experiments, filling missing gaps, and clarifying contradictory results in the literature. Two molybdate transporters, MOT1.1 and MOT1.2, are known in Arabidopsis, but their importance for sufficient molybdate supply to Moco biosynthesis remains unclear. For a better understanding of their physiological functions in molybdate homeostasis, we studied the impact of mot1.1 and mot1.2 knock-out mutants, including a double knock-out on molybdate uptake and Moco-dependent enzyme activity, MOT localisation, and protein–protein interactions. The outcome illustrates different physiological roles for Moco biosynthesis: MOT1.1 is plasma membrane located and its function lies in the efficient absorption of molybdate from soil and its distribution throughout the plant. However, MOT1.1 is not involved in leaf cell imports of molybdate and has no interaction with proteins of the Moco biosynthesis complex. In contrast, the tonoplast-localised transporter MOT1.2 exports molybdate stored in the vacuole and makes it available for re-localisation during senescence. It also supplies the Moco biosynthesis complex with molybdate by direct interaction with molybdenum insertase Cnx1 for controlled and safe sequestering.

Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants

In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?

Plant Trans-Golgi Network/Early Endosome pH regulation requires Cation Chloride Cotransporter (CCC1)

Plant cells maintain a low luminal pH in the trans-Golgi-network/early endosome (TGN/EE), the organelle in which the secretory and endocytic pathways intersect. Impaired TGN/EE pH regulation translates into severe plant growth defects. The identity of the proton pump and proton/ion antiporters that regulate TGN/EE pH have been determined, but an essential component required to complete the TGN/EE membrane transport circuit remains unidentified − a pathway for cation and anion efflux. Here, we have used complementation, genetically encoded fluorescent sensors, and pharmacological treatments to demonstrate that Arabidopsis cation chloride cotransporter (CCC1) is this missing component necessary for regulating TGN/EE pH and function. Loss of CCC1 function leads to alterations in TGN/EE-mediated processes including endocytic trafficking, exocytosis, and response to abiotic stress, consistent with the multitude of phenotypic defects observed in ccc1 knockout plants. This discovery places CCC1 as a central component of plant cellular function.

Extensins: Self-Assembly, Crosslinking, and the Role of Peroxidases

The extensin (EXT) network is elaborated by the covalent intermolecular crosslinking of EXT glycoprotein monomers, and its proper assembly is important for numerous aspects of basic wall architecture and cellular defense. In this review, we discuss new advances in the secretion of EXT monomers and the molecular drivers of EXT network self-assembly. Many of the functions of EXTs are conferred through covalent crosslinking into the wall, so we also discuss the different types of known intermolecular crosslinks, the enzymes that are involved, as well as the potential for additional crosslinks that are yet to be identified. EXTs also function in wall architecture independent of crosslinking status, and therefore, we explore the role of non-crosslinking EXTs. As EXT crosslinking is upregulated in response to wounding and pathogen infection, we discuss a potential regulatory mechanism to control covalent crosslinking and its relationship to the subcellular localization of the crosslinking enzymes.

Mitogen activated protein kinase (MAPK)-regulated genes with predicted signal peptides function in the Glycine max defense response to the root pathogenic nematode Heterodera glycines

Glycine max has 32 mitogen activated protein kinases (MAPKs), nine of them exhibiting defense functions (defense MAPKs) to the plant parasitic nematode Heterodera glycines. RNA seq analyses of transgenic G. max lines overexpressing (OE) each defense MAPK has led to the identification of 309 genes that are increased in their relative transcript abundance by all 9 defense MAPKs. Here, 71 of those genes are shown to also have measurable amounts of transcript in H. glycines-induced nurse cells (syncytia) produced in the root that are undergoing a defense response. The 71 genes have been grouped into 7 types, based on their expression profile. Among the 71 genes are 8 putatively-secreted proteins that include a galactose mutarotase-like protein, pollen Ole e 1 allergen and extensin protein, endomembrane protein 70 protein, O-glycosyl hydrolase 17 protein, glycosyl hydrolase 32 protein, FASCICLIN-like arabinogalactan protein 17 precursor, secreted peroxidase and a pathogenesis-related thaumatin protein. Functional transgenic analyses of all 8 of these candidate defense genes that employ their overexpression and RNA interference (RNAi) demonstrate they have a role in defense. Overexpression experiments that increase the relative transcript abundance of the candidate defense gene reduces the ability that the plant parasitic nematode Heterodera glycines has in completing its life cycle while, in contrast, RNAi of these genes leads to an increase in parasitism. The results provide a genomic analysis of the importance of MAPK signaling in relation to the secretion apparatus during the defense process defense in the G. max-H. glycines pathosystem and identify additional targets for future studies.

Golgi-localized cyclophilin 21 proteins negatively regulate ABA signalling via the peptidyl prolyl isomerase activity during early seedling development

Plant possesses particular Golgi-resident cyclophilin 21 proteins (CYP21s) and the catalytic isomerase activities have a negative effect on ABA signalling gene expression during early seedling development. Cyclophilins (CYPs) are essential for diverse cellular process, as these catalyse a rate-limiting step in protein folding. Although Golgi proteomics in Arabidopsis thaliana suggests the existence of several CYPs in the Golgi apparatus, only one putative Golgi-resident CYP protein has been reported in rice (Oryza sativa L.; OsCYP21-4). Here, we identified the Golgi-resident CYP21 family genes and analysed their molecular characteristics in Arabidopsis and rice. The CYP family genes (CYP21-1, CYP21-2, CYP21-3, and CYP21-4) are plant-specific, and their appearance and copy numbers differ among plant species. CYP21-1 and CYP21-4 are common to all angiosperms, whereas CYP21-2 and CYP21-3 evolved in the Malvidae subclass. Furthermore, all CYP21 proteins localize to cis-Golgi, trans-Golgi or both cis- and trans-Golgi membranes in plant cells. Additionally, based on the structure, enzymatic function, and topological orientation in Golgi membranes, CYP21 proteins are divided into two groups. Genetic analysis revealed that Group I proteins (CYP21-1 and CYP21-2) exhibit peptidyl prolyl cis-trans isomerase (PPIase) activity and regulate seed germination and seedling growth and development by affecting the expression levels of abscisic acid signalling genes. Thus, we identified the Golgi-resident CYPs and demonstrated that their PPIase activities are required for early seedling growth and development in higher plants.

A Random Forest Sub-Golgi Protein Classifier Optimized via Dipeptide and Amino Acid Composition Features

To gain insight into the malfunction of the Golgi apparatus and its relationship to various genetic and neurodegenerative diseases, the identification of sub-Golgi proteins, both cis-Golgi and trans-Golgi proteins, is of great significance. In this study, a state-of-art random forests sub-Golgi protein classifier, rfGPT, was developed. The rfGPT used 2-gap dipeptide and split amino acid composition for the feature vectors and was combined with the synthetic minority over-sampling technique (SMOTE) and an analysis of variance (ANOVA) feature selection method. The rfGPT was trained on a sub-Golgi protein sequence data set (137 sequences), with sequence identity less than 25%. For the optimal rfGPT classifier with 93 features, the accuracy (ACC) was 90.5%; the Matthews correlation coefficient (MCC) was 0.811; the sensitivity (Sn) was 92.6%; and the specificity (Sp) was 88.4%. The independent testing scores for the rfGPT were ACC = 90.6%; MCC = 0.696; Sn = 96.1%; and Sp = 69.2%. Although the independent testing accuracy was 4.4% lower than that for the best reported sub-Golgi classifier trained on a data set with 40% sequence identity (304 sequences), the rfGPT is currently the top sub-Golgi protein predictor utilizing feature vectors without any position-specific scoring matrix and its derivative features. Therefore, the rfGPT is a more practical tool, because no sequence alignment is required with tens of millions of protein sequences. To date, the rfGPT is the Golgi classifier with the best independent testing scores, optimized by training on smaller benchmark data sets. Feature importance analysis proves that the non-polar and aliphatic residues composition, the (aromatic residues) + (non-polar, aliphatic residues) dipeptide and aromatic residues composition between NH2-termial and COOH-terminal of protein sequences are the three top biological features for distinguishing the sub-Golgi proteins.

Plant cell-surface GIPC sphingolipids sense salt to trigger Ca2+ influx

Salinity is detrimental to plant growth, crop production and food security worldwide. Excess salt triggers increases in cytosolic Ca²⁺ concentration, which activate Ca²⁺-binding proteins and upregulate the Na⁺/H⁺ antiporter in order to remove Na⁺. Salt-induced increases in Ca²⁺ have long been thought to be involved in the detection of salt stress, but the molecular components of the sensing machinery remain unknown. Here, using Ca²⁺-imaging-based forward genetic screens, we isolated the Arabidopsis thaliana mutant monocation-induced [Ca^2+]_i increases 1 (moca1), and identified MOCA1 as a glucuronosyltransferase for glycosyl inositol phosphorylceramide (GIPC) sphingolipids in the plasma membrane. MOCA1 is required for salt-induced depolarization of the cell-surface potential, Ca²⁺ spikes and waves, Na⁺/H⁺ antiporter activation, and regulation of growth. Na⁺ binds to GIPCs to gate Ca²⁺ influx channels. This salt-sensing mechanism might imply that plasma-membrane lipids are involved in adaption to various environmental salt levels, and could be used to improve salt resistance in crops.

Glycome and Proteome Components of Golgi Membranes Are Common between Two Angiosperms with Distinct Cell-Wall Structures

The plant endoplasmic reticulum-Golgi apparatus is the site of synthesis, assembly, and trafficking of all noncellulosic polysaccharides, proteoglycans, and proteins destined for the cell wall. As grass species make cell walls distinct from those of dicots and noncommelinid monocots, it has been assumed that the differences in cell-wall composition stem from differences in biosynthetic capacities of their respective Golgi. However, immunosorbence-based screens and carbohydrate linkage analysis of polysaccharides in Golgi membranes, enriched by flotation centrifugation from etiolated coleoptiles of maize (Zea mays) and leaves of Arabidopsis (Arabidopsis thaliana), showed that arabinogalactan-proteins and arabinans represent substantial portions of the Golgi-resident polysaccharides not typically found in high abundance in cell walls of either species. Further, hemicelluloses accumulated in Golgi at levels that contrasted with those found in their respective cell walls, with xyloglucans enriched in maize Golgi, and xylans enriched in Arabidopsis. Consistent with this finding, maize Golgi membranes isolated by flotation centrifugation and enriched further by free-flow electrophoresis, yielded >200 proteins known to function in the biosynthesis and metabolism of cell-wall polysaccharides common to all angiosperms, and not just those specific to cell-wall type. We propose that the distinctive compositions of grass primary cell walls compared with other angiosperms result from differential gating or metabolism of secreted polysaccharides post-Golgi by an as-yet unknown mechanism, and not necessarily by differential expression of genes encoding specific synthase complexes.

Assessing sub-cellular resolution in spatial proteomics experiments

The sub-cellular localisation of a protein is vital in defining its function, and a protein's mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions, including high profile mass spectrometry-based efforts. Here, we present a meta-analysis assessing and comparing the sub-cellular resolution of 29 such mass spectrometry-based spatial proteomics experiments using a newly developed tool termed QSep. Our goal is to provide a simple quantitative report of how well spatial proteomics resolve the sub-cellular niches they describe to inform and guide developers and users of such methods.

Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage

Pectin is a vital component of the plant cell wall and provides the molecular glue that maintains cell-cell adhesion, among other functions. As the most complex wall polysaccharide, pectin is composed of several covalently linked domains, such as homogalacturonan (HG) and rhamnogalacturonan I (RG I). Pectin has widespread uses in the food industry and has emerging biomedical applications, but its synthesis remains poorly understood. For instance, the enzymes that catalyze RG I elongation remain unknown. Recently, a coexpression- and sequence-based MUCILAGE-RELATED (MUCI) reverse genetic screen uncovered hemicellulose biosynthetic enzymes in the Arabidopsis (Arabidopsis thaliana) seed coat. Here, we use an extension of this strategy to identify MUCI70 as the founding member of a glycosyltransferase family essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched RG I. Detailed biochemical and histological characterization of two muci70 mutants and two galacturonosyltransferase11 (gaut11) mutants identified MUCI70 and GAUT11 as required for two distinct RG I domains in seed mucilage. We demonstrate that, unlike MUCI70, GAUT11 catalyzes HG elongation in vitro and, thus, likely is required for the synthesis of an HG region important for RG I elongation. Analysis of a muci70 gaut11 double mutant confirmed that MUCI70 and GAUT11 are indispensable for the production and release of the bulk of mucilage RG I and for shaping the surface morphology of seeds. In addition, we uncover relationships between pectin and hemicelluloses and show that xylan is essential for the elongation of at least one RG I domain.

A broadly conserved NERD genetically interacts with the exocyst to affect root growth and cell expansion

The exocyst, a conserved, octameric protein complex, helps mediate secretion at the plasma membrane, facilitating specific developmental processes that include control of root meristem size, cell elongation, and tip growth. A genetic screen for second-site enhancers in Arabidopsis identified NEW ENHANCER of ROOT DWARFISM1 (NERD1) as an exocyst interactor. Mutations in NERD1 combined with weak exocyst mutations in SEC8 and EXO70A1 result in a synergistic reduction in root growth. Alone, nerd1 alleles modestly reduce primary root growth, both by shortening the root meristem and by reducing cell elongation, but also result in a slight increase in root hair length, bulging, and rupture. NERD1 was identified molecularly as At3g51050, which encodes a transmembrane protein of unknown function that is broadly conserved throughout the Archaeplastida. A functional NERD1-GFP fusion localizes to the Golgi, in a pattern distinct from the plasma membrane-localized exocyst, arguing against a direct NERD1-exocyst interaction. Structural modeling suggests the majority of the protein is positioned in the lumen, in a β-propeller-like structure that has some similarity to proteins that bind polysaccharides. We suggest that NERD1 interacts with the exocyst indirectly, possibly affecting polysaccharides destined for the cell wall, and influencing cell wall characteristics in a developmentally distinct manner.

AtPAP2, a Unique Member of the PAP Family, Functions in the Plasma Membrane

Purple acid phosphatases (PAPs) play various physiological roles in plants. AtPAP2 was previously shown to localize to both chloroplasts and mitochondria and to modulate carbon metabolism in Arabidopsis. Over-expression of AtPAP2 resulted in faster growth and increased biomass in several plant species, indicating its great potential for crop improvement of phosphate use and yield. Here, we studied the localization of AtPAP2 by transient expression in tobacco leaves. The results showed AtPAP2 was localized to the plasma membrane through the secretory pathway, which is different from previous studies. We also found that AtPAP2 had a close relationship with fungal PAP2-like proteins based on phylogenetic analysis. In addition, the C-terminal transmembrane domain conserved in land plants is unique among other AtPAPs except AtPAP9, which is a close homolog of AtPAP2. Taken together, our results provide information for further study of AtPAP2 in understanding its special function in crop improvement.

Screening Arabidopsis thaliana mutants for low sensitivity to manganese identifies novel alleles of NRAMP1 and PGSIP6

Manganese (Mn) is an essential micronutrient; however, few genes required for growth under low-Mn conditions have been identified. In this study, we isolated Arabidopsis thaliana mutants sensitive to low-Mn conditions from ethyl methanesulfonate-mutagenized seeds. Among them, we identified the causal genes of two mutants. One mutant (35-34) exhibited a short root phenotype and low Mn concentration in the shoots. The other mutant (30-11) exhibited a small shoot phenotype with Mn concentrations similar to the control. Genetic mapping, allelism tests, and gene complementation tests identified the causal genes as At1g80830 (NRAMP1) for 35-34 and At5g18480 (PGSIP6) for 30-11. NRAMP1 was previously reported to be essential for Mn uptake under low-Mn conditions, thus validating our screening method. PGSIP6 encodes inositol phosphorylceramide glucuronosyltransferase, which is involved in glycosyl inositol phosphorylceramide sphingolipid glycosylation. PGSIP6-green fluorescent protein was localized to the Golgi apparatus, which is consistent with its function in the glycosylation of sphingolipids. Our screening identified a novel gene required for low-Mn tolerance, and we also provide new insights towards understanding the physiological function of PGSIP6.

Mass spectrometry approaches to study plant endomembrane trafficking

Intracellular proteins reside in highly controlled microenvironments in which they perform context specific functions. Trafficking pathways have evolved that enable proteins to be precisely delivered to the correct location but also to re-locate in response to environmental perturbation. Trafficking of membrane proteins to their correct endomembrane location is especially important to enable them to carry out their function. Although a considerable amount of knowledge about membrane protein trafficking in plants has been delivered by years of dedicated research, there are still significant gaps in our understanding of this process. Further knowledge of endomembrane trafficking is dependent on thorough characterization of the subcellular components that constitute the endomembrane system. Such studies are challenging for a number of reasons including the complexity of the plant endomembrane system, inability to purify individual constituents, discrimination protein cargo for full time residents of compartments, and the fact that many proteins function at more than one location. In this review, we describe the components of the secretory pathway and focus on how mass spectrometry based proteomics methods have helped elucidation of this pathway. We demonstrate that the combination of targeted and untargeted approaches is allowing research into new areas of the secretory pathway investigation. Finally we describe new enabling technologies that will impact future studies in this area.

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome

The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specific and sensitive antibodies. One method that provides a global picture of the cell is localization of organelle proteins by isotope tagging (LOPIT), which combines biochemical cell fractionation using density gradient ultracentrifugation with multiplexed quantitative proteomics mass spectrometry, allowing simultaneous determination of the steady-state distribution of hundreds of proteins within organelles. Proteins are assigned to organelles based on the similarity of their gradient distribution to those of well-annotated organelle marker proteins. We have substantially re-developed our original LOPIT protocol (published by Nature Protocols in 2006) to enable the subcellular localization of thousands of proteins per experiment (hyperLOPIT), including spatial resolution at the suborganelle and large protein complex level. This Protocol Extension article integrates all elements of the hyperLOPIT pipeline, including an additional enrichment strategy for chromatin, extended multiplexing capacity of isobaric mass tags, state-of-the-art mass spectrometry methods and multivariate machine-learning approaches for analysis of spatial proteomics data. We have also created an open-source infrastructure to support analysis of quantitative mass-spectrometry-based spatial proteomics data (http://bioconductor.org/packages/pRoloc) and an accompanying interactive visualization framework (http://www. bioconductor.org/packages/pRolocGUI). The procedure we outline here is applicable to any cell culture system and requires ∼1 week to complete sample preparation steps, ∼2 d for mass spectrometry data acquisition and 1-2 d for data analysis and downstream informatics.

The Glycosyltransferase QUA1 Regulates Chloroplast-Associated Calcium Signaling During Salt and Drought Stress in Arabidopsis

Cytoplasmic Ca2+ ([Ca2+]cyt) elevation induced by various signals is responsible for appropriate downstream responses. Through a genetic screen of Arabidopsis thaliana mutants defective in stress-induced [Ca2+]cyt elevation, the glycosyltransferase QUASIMODO1 (QUA1) was identified as a regulator of [Ca2+]cyt in response to salt stress. Compared with the wild type, the qua1-4 mutant exhibited a dramatically greater increase in [Ca2+]cyt under NaCl treatment. Functional analysis showed that QUA1 is a novel chloroplast protein that regulates cytoplasmic Ca2+ signaling. QUA1 was detected in chloroplast thylakoids, and the qua1-4 mutant exhibited irregularly stacked grana. The observed greater increase in [Ca2+]cyt was inhibited upon recovery of chloroplast function in the qua1-4 mutant. Further analysis showed that CAS, a thylakoid-localized calcium sensor, also displayed irregularly stacked grana, and the chloroplasts of the qua1-4 cas-1 double mutant were similar to those of cas-1 plants. In QUA1-overexpressing plants, the protein level of CAS was decreased, and CAS was readily degraded under osmotic stress. When CAS was silenced in the qua1-4 mutant, the large [Ca2+]cyt increase was blocked, and the higher expression of PLC3 and PLC4 was suppressed. Under osmotic stress, the qua1-4 mutant showed an even greater elevation in [Ca2+]cyt and was hypersensitive to drought stress. However, this sensitivity was inhibited when the increase in [Ca2+]cyt was repressed in the qua1-4 mutant. Collectively, our data indicate that QUA1 may function in chloroplast-dependent calcium signaling under salt and drought stresses. Additionally, CAS may function downstream of QUA1 to mediate these processes.

Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions

Lipid droplets (LDs) are cell compartments specialized for oil storage. Although their role and biogenesis are relatively well documented in seeds, little is known about their composition, structure and function in senescing leaves where they also accumulate. Here, we used a label free quantitative mass spectrometry approach to define the LD proteome of aging Arabidopsis leaves. We found that its composition is highly different from that of seed/cotyledon and identified 28 proteins including 9 enzymes of the secondary metabolism pathways involved in plant defense response. With the exception of the TRIGALACTOSYLDIACYLGLYCEROL2 protein, we did not identify enzymes implicated in lipid metabolism, suggesting that growth of leaf LDs does not occur by local lipid synthesis but rather through contact sites with the endoplasmic reticulum (ER) or other membranes. The two most abundant proteins of the leaf LDs are the CALEOSIN3 and the SMALL RUBBER PARTICLE1 (AtSRP1); both proteins have structural functions and participate in plant response to stress. CALEOSIN3 and AtSRP1 are part of larger protein families, yet no other members were enriched in the LD proteome suggesting a specific role of both proteins in aging leaves. We thus examined the function of AtSRP1 at this developmental stage and found that AtSRP1 modulates the expression of CALEOSIN3 in aging leaves. Furthermore, AtSRP1 overexpression induces the accumulation of triacylglycerol with an unusual composition compared to wild-type. We demonstrate that, although AtSRP1 expression is naturally increased in wild type senescing leaves, its overexpression in senescent transgenic lines induces an over-accumulation of LDs organized in clusters at restricted sites of the ER. Conversely, atsrp1 knock-down mutants displayed fewer but larger LDs. Together our results reveal that the abundancy of AtSRP1 regulates the neo-formation of LDs during senescence. Using electron tomography, we further provide evidence that LDs in leaves share tenuous physical continuity as well as numerous contact sites with the ER membrane. Thus, our data suggest that leaf LDs are functionally distinct from seed LDs and that their biogenesis is strictly controlled by AtSRP1 at restricted sites of the ER.

Extraction and Characterization of Extracellular Proteins and Their Post-Translational Modifications from Arabidopsis thaliana Suspension Cell Cultures and Seedlings: A Critical Review

Proteins secreted by plant cells into the extracellular space, consisting of the cell wall, apoplastic fluid, and rhizosphere, play crucial roles during development, nutrient acquisition, and stress acclimation. However, isolating the full range of secreted proteins has proven difficult, and new strategies are constantly evolving to increase the number of proteins that can be detected and identified. In addition, the dynamic nature of the extracellular proteome presents the further challenge of identifying and characterizing the post-translational modifications (PTMs) of secreted proteins, particularly glycosylation and phosphorylation. Such PTMs are common and important regulatory modifications of proteins, playing a key role in many biological processes. This review explores the most recent methods in isolating and characterizing the plant extracellular proteome with a focus on the model plant Arabidopsis thaliana, highlighting the current challenges yet to be overcome. Moreover, the crucial role of protein PTMs in cell wall signalling, development, and plant responses to biotic and abiotic stress is discussed.

Comparative "Golgi" Proteome Study of Lolium multiflorum and Populus trichocarpa

The Golgi apparatus (GA) is a crucial organelle in the biosynthesis of non-cellulosic polysaccharides, glycoproteins and proteoglycans that are primarily destined for secretion to the cell surface (plasma membrane, cell wall and apoplast). Only a small proportion of the proteins involved in these processes have been identified in plants, with the majority of their functions still unknown. The availability of a GA proteome would greatly assist plant biochemists, cell and molecular biologists in determining the precise function of the cell wall-related proteins. There has been some progress towards defining the GA proteome in the model plant system Arabidopsis thaliana, yet in commercially important species, such as either the cereals or woody species there has been relatively less progress. In this study, we applied discontinuous sucrose gradient centrifugation to partially enrich GA from suspension cell cultures (SCCs) and combined this with stable isotope labelling (iTRAQ) to determine protein sub-cellular locations. Results from a representative grass species, Italian ryegrass (Lolium multiflorum) and a dicot species, black cottonwood (Populus trichocarpa) are compared. The results confirm that membrane fractionation approaches that provide effective GA-enriched fractions for proteomic analyses in Arabidopsis are much less effective in the species examined here and highlight the complexity of the GA, both within and between species.

Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis

As the most abundant biopolymer on Earth, cellulose is a key structural component of the plant cell wall. Cellulose is produced at the plasma membrane by cellulose synthase (CesA) complexes (CSCs), which are assembled in the endomembrane system and trafficked to the plasma membrane. While several proteins that affect CesA activity have been identified, components that regulate CSC assembly and trafficking remain unknown. Here we show that STELLO1 and 2 are Golgi-localized proteins that can interact with CesAs and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. Hence, we have uncovered proteins that regulate CSC assembly in the plant Golgi apparatus.

Visualization of proteomics data using R and bioconductor

Data visualization plays a key role in high-throughput biology. It is an essential tool for data exploration allowing to shed light on data structure and patterns of interest. Visualization is also of paramount importance as a form of communicating data to a broad audience. Here, we provided a short overview of the application of the R software to the visualization of proteomics data. We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.

A set of GFP-based organelle marker lines combined with DsRed-based gateway vectors for subcellular localization study in rice (Oryza sativa L.)

In the post-genomic era, many useful tools have been developed to accelerate the investigation of gene functions. Fluorescent proteins have been widely used as protein tags for studying the subcellular localization of proteins in plants. Several fluorescent organelle marker lines have been generated in dicot plants; however, useful and reliable fluorescent organelle marker lines are lacking in the monocot model rice. Here, we developed eight different GFP-based organelle markers in transgenic rice and created a set of DsRed-based gateway vectors for combining with the marker lines. Two mitochondrial-localized rice ascorbate peroxidase genes fused to DsRed and successfully co-localized with mitochondrial-targeted marker lines verified the practical use of this system. The co-localization of GFP-fusion marker lines and DsRed-fusion proteins provide a convenient platform for in vivo or in vitro analysis of subcellular localization of rice proteins.

Proteomic Characterization of Golgi Membranes Enriched from Arabidopsis Suspension Cell Cultures

The plant Golgi apparatus has a central role in the secretory pathway and is the principal site within the cell for the assembly and processing of macromolecules. The stacked membrane structure of the Golgi apparatus along with its interactions with the cytoskeleton and endoplasmic reticulum has historically made the isolation and purification of this organelle difficult. Density centrifugation has typically been used to enrich Golgi membranes from plant microsomal preparations, and aside from minor adaptations, the approach is still widely employed. Here we outline the enrichment of Golgi membranes from an Arabidopsis cell suspension culture that can be used to investigate the proteome of this organelle. We also provide a useful workflow for the examination of proteomic data as the result of multiple analyses. Finally, we highlight a simple technique to validate the subcellular localization of proteins by fluorescent tags after their identification by tandem mass spectrometry.

MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage

Plants invest a lot of their resources into the production of an extracellular matrix built of polysaccharides. While the composition of the cell wall is relatively well characterized, the functions of the individual polymers and the enzymes that catalyze their biosynthesis remain poorly understood. We exploited the Arabidopsis (Arabidopsis thaliana) seed coat epidermis (SCE) to study cell wall synthesis. SCE cells produce mucilage, a specialized secondary wall that is rich in pectin, at a precise stage of development. A coexpression search for MUCILAGE-RELATED (MUCI) genes identified MUCI10 as a key determinant of mucilage properties. MUCI10 is closely related to a fenugreek (Trigonella foenumgraecum) enzyme that has in vitro galactomannan α-1,6-galactosyltransferase activity. Our detailed analysis of the muci10 mutants demonstrates that mucilage contains highly branched galactoglucomannan (GGM) rather than unbranched glucomannan. MUCI10 likely decorates glucomannan, synthesized by CELLULOSE SYNTHASE-LIKE A2, with galactose residues in vivo. The degree of galactosylation is essential for the synthesis of the GGM backbone, the structure of cellulose, mucilage density, as well as the adherence of pectin. We propose that GGM scaffolds control mucilage architecture along with cellulosic rays and show that Arabidopsis SCE cells represent an excellent model in which to study the synthesis and function of GGM. Arabidopsis natural varieties with defects similar to muci10 mutants may reveal additional genes involved in GGM synthesis. Since GGM is the most abundant hemicellulose in the secondary walls of gymnosperms, understanding its biosynthesis may facilitate improvements in the production of valuable commodities from softwoods.

The biochemical properties of the Arabidopsis ecto-nucleoside triphosphate diphosphohydrolase AtAPY1 contradict a direct role in purinergic signaling

The Arabidopsis E-NTPDase (ecto-nucleoside triphosphate diphosphohydrolase) AtAPY1 was previously shown to be involved in growth and development, pollen germination and stress responses. It was proposed to perform these functions through regulation of extracellular ATP signals. However, a GFP-tagged version was localized exclusively in the Golgi and did not hydrolyze ATP. In this study, AtAPY1 without the bulky GFP-tag was biochemically characterized with regard to its suggested role in purinergic signaling. Both the full-length protein and a soluble form without the transmembrane domain near the N-terminus were produced in HEK293 cells. Of the twelve nucleotide substrates tested, only three--GDP, IDP and UDP--were hydrolyzed, confirming that ATP was not a substrate of AtAPY1. In addition, the effects of pH, divalent metal ions, known E-NTPDase inhibitors and calmodulin on AtAPY1 activity were analyzed. AtAPY1-GFP extracted from transgenic Arabidopsis seedlings was included in the analyses. All three AtAPY1 versions exhibited very similar biochemical properties. Activity was detectable in a broad pH range, and Ca(2+), Mg(2+) and Mn(2+) were the three most efficient cofactors. Of the inhibitors tested, vanadate was the most potent one. Surprisingly, sulfonamide-based inhibitors shown to inhibit other E-NTPDases and presumed to inhibit AtAPY1 as well were not effective. Calmodulin stimulated the activity of the GFP-tagless membranous and soluble AtAPY1 forms about five-fold, but did not alter their substrate specificities. The apparent Km values obtained with AtAPY1-GFP indicate that AtAPY1 is primarily a GDPase. A putative three-dimensional structural model of the ecto-domain is presented, explaining the potent inhibitory potential of vanadate and predicting the binding mode of GDP. The found substrate specificity classifies AtAPY1 as a nucleoside diphosphatase typical of N-terminally anchored Golgi E-NTPDases and negates a direct function in purinergic signaling.