Reprogramming of a defense signaling pathway in rough lemon and sweet orange is a critical element of the early response to‘Candidatus Liberibacter asiaticus’

Huanglongbing(HLB)in citrus infected by Candidatus Liberibacter asiaticus(CLas)has caused tremendous losses to the citrus industry.No resistant genotypes have been identified in citrus species or close relatives.Among citrus varieties,rough lemon(Citrus jambhiri)has been considered tolerant due to its ability to produce a healthy flush of new growth after infection.The difference between tolerance and susceptibility is often defined by the speed and intensity of a plant’s response to a pathogen,especially early defense responses.RNA-seq data were collected from three biological replicates of CLas-and mock-inoculated rough lemon and sweet orange at week 0 and 7 following infection.Functional analysis of the differentially expressed genes(DEGs)indicated that genes involved in the mitogen activated protein kinase(MAPK)signaling pathway were highly upregulated in rough lemon.MAPK induces the transcription of WRKY and other transcription factors which potentially turn on multiple defense-related genes.A Subnetwork Enrichment Analysis further revealed different patterns of regulation of several functional categories,suggesting DEGs with different functions were subjected to reprogramming.In general,the amplitude of the expression of defense-related genes is much greater in rough lemon than in sweet orange.A quantitative disease resistance response may contribute to the durable tolerance level to HLB observed in rough lemon.

Redox proteomics of tomato in response to Pseudomonas syringae infection

Unlike mammals with adaptive immunity,plants rely on their innate immunity based on pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)for pathogen defense.Reactive oxygen species,known to play crucial roles in PTI and ETI,can perturb cellular redox homeostasis and lead to changes of redox-sensitive proteins through modification of cysteine sulfhydryl groups.Although redox regulation of protein functions has emerged as an important mechanism in several biological processes,little is known about redox proteins and how they function in PTI and ETI.In this study,cysTMT proteomics technology was used to identify similarities and differences of protein redox modifications in tomato resistant(PtoR)and susceptible(prf3)genotypes in response to Pseudomonas syringae pv tomato(Pst)infection.In addition,the results of the redox changes were compared and corrected with the protein level changes.A total of 90 potential redox-regulated proteins were identified with functions in carbohydrate and energy metabolism,biosynthesis of cysteine,sucrose and brassinosteroid,cell wall biogenesis,polysaccharide/starch biosynthesis,cuticle development,lipid metabolism,proteolysis,tricarboxylic acid cycle,protein targeting to vacuole,and oxidation–reduction.This inventory of previously unknown protein redox switches in tomato pathogen defense lays a foundation for future research toward understanding the biological significance of protein redox modifications in plant defense responses.

Genome-wide identification and characterization of ACBP gene family in Populus reveal salinity alkali-responsive profiles

Acyl-CoA-binding proteins(ACBPs)are important for the transport of acyl groups for macro molecular biosynthesis involved in plant growth,development,and diverse stress(e.g.,cold,drought,salinity,and heavy metals)responses.Here,we report the phylogeny and characteristics of the ACBP family in the woody plant Populus trichocarpa.Eight genes encoding ACBP proteins were identified,and they are distributed on eight chromosomes in P.trichocarpa.These PtACBP genes were divided into four subgroups according to gene structure,conserved motifs and phylogenetic relationship.Promoter analysis revealed that cis-elements were related to stress response,phytohormone response,and physical and reproductive growth regulation.Expression levels of PtACBP genes varied among different organs,with the highest expression in leaves and the lowest in stems.Quantitative real-time PCR(qRT-PCR)analysis showed that under salinity-alkali stresses(i.e.,200 mM NaCl,75 mM Na2CO3,and 100 mM NaHCO3),four(PtACBP1,PtACBP3,PtACBP4 and PtACBP8)of eight PtACBP genes were significantly induced in roots and leaves.These data provide a comprehensive analysis of the ACBPs family in P.trichocarpa,which could be useful for gene function analyses.

Involvement of Root Hair during <i>Rhizobial</i>Invasion in Cultivated Peanut (<i>Arachis hypogaea</i>L.)

Peanut root invasion by Bradyrhizobia is through a crack entry, which is different from many other legumes applying an infection thread entry in root hair. Understanding the role of root hair in the crack entry of Bradyrhizobia invasion of peanut root and subsequent peanut nodulation would facilitate improvement of biological nitrogen fixation in cultivated peanut. The objective of this study was to investigate the involvement of root hair in Bradyrhizobial invasion of peanut. Seedling roots of a nodulating peanut cultivar were observed for root hair emergence, its life span, and nodule formation at the base of the lateral roots with and without rhizobia inoculation for 14 days after germination (DAG). Scanning electron microscopy (SEM) was utilized to observe rhizobia accumulation at lateral roots at 24 hours after inoculation (HAI) before the emergence of root hair. Root hair emerged at 7 DAG with or without rhizobia inoculation. Two variations of rosette hair (RoH) were observed, the transient-thin RoH had life span of 3 days after root hair emergence and the thick and densely distributed RoH type stayed till the time of nodule emergence (9 days after inoculation). The lateral root devoid of root hair at the top 2 cm region was found to produce nodules. The SEM observation of seedling roots at 24 HAI showed that Bradyrhizobia invaded the roots at epidermis, protoplasm of cortical cell, and cortical cells of the main root near the newly emerged lateral root in the absence of RoH. The observations validated that root hair is not required in the Bradyrhizobia invasion of peanut root in the crack entry mode. Results from this study provided important morphological information for the hypothesis of close relationship between RoH and peanut nodulation for further genetic study of crack entry mechanism and signaling pathway of symbiosis between Bradyrhizobia and peanut.

Isobaric Tags for Relative and Absolute Quantificationbased Comparative Proteomics Reveals the Features of Plasma Membrane-Associated Proteomes of Pollen Grains and Pollen Tubes from Lilium davidii

Mature pollen grains （PGs） from most plant species are metabolically quiescent. However, once pollinated onto stigma, they quickly hydrate and germinate. A PG can give rise to a vegetative cell-derived polarized pollen tube （PT）, which represents a specialized polar cell. The polarized PT grows by the tip and requires interaction of different signaling molecules localized in the apical plasma membrane and active membrane trafficking. The mechanisms underlying the interaction and membrane trafficking are not well understood. In this work, we purified PG and PT plasma-membrane vesicles from Lilium davidii Duch. using the aqueous two-phase partition technique, then enriched plasma membrane proteins by using Brij58 and KCl to remove loosely bound contaminants. We identified 223 integral and membrane-associated proteins in the plasma membrane of PGs and PTs by using isobaric tags for relative and absolute quantification （iTRAQ） and 2-D high-performance liquid chromatography-tandem mass spectrometry. More than 68% of the proteins have putative transmembrane domains and/or lipid-modified motifs. Proteins involved in signal transduction, membrane trafficking and transport are predominant in the plasma-membrane proteome. We revealed most components of the clathrin-dependent endocytosis pathway. Statistical analysis revealed 14 proteins differentially expressed in the two development stages： in PTs, six upregulated and eight downregulated are mainly involved in signaling, transport and membrane trafficking. These results provide novel insights into polarized PT growth.

Liver Characterization of a Cohort of Alpha-1 Antitrypsin Deficiency Patients with and without Lung Disease

Background and Aims:Alpha-1 antitrypsin deficiency(AATD)is a genetic disorder characterized by the misfolding and accumulation of the mutant variant of alpha-1 antitrypsin(AAT)within hepatocytes,which limits its access to the circulation and exposes the lungs to protease-mediated tissue damage.This results in progressive liver disease secondary to AAT polymerization and accumulation,and chronic obstructive pulmonary disease(COPD)due to deficient levels of AAT within the lungs.Our goal was to characterize the unique effects of COPD secondary to AATD on liver disease and gene expression.Methods:A subcohort of AATD individuals with COPD(n=33)and AATD individuals without COPD(n=14)were evaluated in this study from our previously reported cross-sectional cohort.We used immunohistochemistry to assess the AATD liver phenotype,and RNA sequencing to explore liver transcriptomics.We observed a distinct transcriptomic profile in liver tissues from AATD individuals with COPD compared to those without.Results:A total of 339 genes were differentially expressed.Canonical pathways related to fibrosis,extracellular matrix remodeling,collagen deposition,hepatocellular damage,and inflammation were significantly upregulated in the livers of AATD individuals with COPD.Histopathological analysis also revealed higher levels of fibrosis and hepatocellular damage in these individuals.Conclusions:Our data supports a relationship between the development of COPD and liver disease in AATD and introduces genes and pathways that may play a role in AATD liver disease when COPD is present.We believe addressing lung impairment and airway inflammation may be an approach to managing AATD-related liver disease.

Sugar-Hormone Cross-Talk in Seed Development： Two Redundant Pathways of IAA Biosynthesis Are Regulated Differentially in the Invertase- Deficient miniature 1 （mn 1） Seed Mutant in Maize

The miniature1 （mn1） seed phenotype is a loss-of-function mutation at the Mnl locus that encodes a cell wall invertase; its deficiency leads to pleiotropic changes including altered sugar levels and decreased levels of IAA throughout seed development. To understand the molecular details of such a sugar-hormone relationship, we have initiated studies on IAA biosynthesis genes in developing seeds of maize. Two tryptophan-dependent pathways of IAA biosynthesis, tryptamine （TAM） and indole-3-pyruvic acid （IPA）, are of particular interest. We report on molecular isolation and characterization of an endosperm-specific ZmTARelatedl （ZmTarl） gene of the IPA branch; we have also reported recently on ZmYucl gene in the TAM branch. Comparative gene expression analyses here have shown that （1） the ZmTarl transcripts were approximately 10-fold higher levels than the ZmYucl; （2） although both genes showed the highest level of expression at 8-12 d after pollination （DAP） coincident with an early peak in IAA levels, the two showed highly divergent （antagonistic） response at 12 and 16 DAP but similar patterns at 20 and 28 DAP in the Mnl and ran1 endosperm. The Western blot analyses for the ZmTAR1 protein, however, displayed disconcordant protein/transcript expression patterns. Overall, these data report novel observations on redundant trp-dependent pathways of auxin biosynthesis in developing seeds of maize, and suggest that homeostatic control of IAA in this important sink is highly complex and may be regulated by both sucrose metabolism and developmental signals.

Proteomics and Metabolomics of Arabidopsis Responses to Perturbation of Glucosinolate Biosynthesis

To understand plant molecular networks of glucosinolate metabolism, perturbation of aliphatic glucosinolate biosynthesis was established using inducible RNA interference （RNAi） in Arabidopsis. Two RNAi lines were chosen for examining global protein and metabolite changes using complementary proteomics and metabolomics approaches. Pro- teins involved in metabolism including photosynthesis and hormone metabolism, protein binding, energy, stress, and defense showed marked responses to glucosinolate perturbation. In parallel, metabolomics revealed major changes in the levels of amino acids, carbohydrates, peptides, and hormones. The metabolomics data were correlated with the pro- teomics results and revealed intimate molecular connections between cellular pathways/processes and glucosinolate me- tabolism. This study has provided an unprecedented view of the molecular networks of glucosinolate metabolism and laid a foundation towards rationale glucosinolate engineering for enhanced defense and quality.

The stomata frontline of plant interaction with the environment-perspectives from hormone regulation

Plants have evolved elaborate mechanisms to perceive and integrate signals from various environmental conditions. On leaf surface, stomata formed by pairs of guard cells mediate gas exchange, water transpiration as well as function in response to abiotic and biotic stresses. Stomatal closure could be induced by drought, salt, pathogen and other adverse conditions. This constitutes an instant defense response to prevent further damage to plants. Abscisic acid （ABA） is a major plant hormone involved in stress responses. Stress-activated ABA synthesis causes stomatal closure and prevents opening to reduce water loss and cell dehydration. Key regulatory receptor complex and other important components in the ABA signaling pathway have been identified. However, our knowledge of ABA signal transduction in guard cells is far from complete. Jasmonates are a group of phytohormones generally known to be important for plant defense against insects and necrotrophic pathogens. The increased levels of methyl jasmonate （MeJA） induced by herbivory and pathogen invasion show a similar effect on stomatal movement associated with ROS production as ABA. Investigation of guard cell signaling networks involving the two important phytohormones is significant and exciting. Information about protein and metabolite components and how they interact in guard cells is lacking. Here we review recent advances on hormone signaling networks in guard cells and how the networks integrate environmental signals to plant physiological output.

Advances in quantitative proteomics

Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research.During the past years,different techniques have been developed,including gel-based such as differential in-gel electrophoresis(DIGE)and liquid chromatography-based such as isotope labeling and labelfree quantification.These quantitative proteomics tools hold significant promise for biomarker discovery,diagnostic and therapeutic applications.They are also important for research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions.In this review,we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies.

Na_(2)CO_(3)-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics

Alkali-salinity exerts severe osmotic,ionic,and high-p H 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 Na_(2)CO_(3)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 Na_(2)CO_(3)-responsive proteins.A total of 104 and 102 Na_(2)CO_(3)-responsive proteins were identified in leaves and chloroplasts,respectively.In addition,84 Na_(2)CO_(3)-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 Pt FBA encoding an alkaligrass chloroplastic fructosebisphosphate aldolase(FBA)was overexpressed in wild-type cells of cyanobacterium Synechocystis sp.Strain PCC 6803,leading to enhanced Na_(2)CO_(3)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 Na_(2)CO_(3)stress,which help to improve our understanding of the Na_(2)CO_(3)-responsive mechanisms in halophytes.

Proteomics characteristics of rice leaves in response to environmental factors

Rice is an important food crop worldwide.Its productivity has been influenced by various abiotic and biotic factors including temperature,drought,salt,microbe,ozone,hormone and glyphosate.The responses of plants to stress are regulated by multiple signaling pathways,and the mechanisms of leaf growth and development in response to stress remain unclear to date.Recently,proteomics studies have provided new evidence for better understanding the mechanisms.The proteins in response to different stress conditions are mainly involved in photosynthesis,signal transduction,transcription,protein synthesis and destination,defense response,cytoskeleton,energy,cell wall and other metabolism.In addition,some stress type-specific proteins have been identified,such as small heat shock proteins under temperature stress,S-like RNase homolog and actin depolymerizing factor under drought stress,ascorbate peroxidase and lipid peroxidation under salt stress,probenazole-inducible protein and rice pathogenesis-related proteins under blast fungus.Many of the proteins including ribulose-1,5-bisphosphate carboxylase/oxygenase(RuBisCO),molecular chaperones,antioxidases and S-adenosylmethionine synthetase play very important roles in leaves.This paper reviews the proteomic characterization of rice leaves in response to various environmental factors.