Cell Defense Responses Research Articles

Callose Synthesis Suppresses Cell Death Induced by Low-Calcium Conditions in Leaves.

Despite the importance of preventing calcium (Ca) deficiency disorders in agriculture, knowledge of the molecular mechanisms underlying plant adaptations to low-Ca conditions is limited. In this study, we provide evidence for a crucial involvement of callose synthesis in the survival of Arabidopsis (Arabidopsis thaliana) under low-Ca conditions. A mutant sensitive to low-Ca conditions, low calcium sensitive3 (lcs3), exhibited high levels of cell death in emerging leaves and had defects in its expanding true leaves under low-Ca conditions. Further analyses showed that the causal mutation was located in a putative β-1,3-glucan (callose) synthase gene, GLUCAN SYNTHASE-LIKE10 (GSL10). Yeast complementation assay results showed that GSL10 encodes a functional callose synthase. Ectopic callose significantly accumulated in wild-type plants under low-Ca conditions, but at a low level in lcs3 The low-Ca sensitivity of lcs3 was phenocopied by the application of callose synthase inhibitors in wild-type plants, which resulted in leaf expansion failure, cell death, and reduced ectopic callose levels under low-Ca conditions. Transcriptome analyses showed that the expression of genes related to cell wall and defense responses was altered in both wild-type plants under low-Ca conditions and in lcs3 under normal-Ca conditions, suggesting that GSL10 is required for the alleviation of both cell wall damage and defense responses caused by low Ca levels. These results suggest that callose synthesis is essential for the prevention of cell death under low-Ca conditions and plays a key role in plants' survival strategies under low-Ca conditions.

Cell wall proteome analysis of banana fruit softening using iTRAQ technology

Softening is important for quality formation in some climacteric fruits. The molecular mechanism underlying fruit softening is, however, not well understood. In this study, we performed a comparative cell wall proteomics analysis on pre-climacteric (P1) and post-climacteric (P2) banana fruit, corresponding to fruit at the mature green stage and softening ripening stage, respectively, using isobaric tags for relative and absolute quantitation (iTRAQ) technology. A total of 5230 proteins were identified in both sample groups, of which 928 were predicted to be secreted proteins. Of the secreted proteins, 162 were differentially expressed in P2 versus P1. The majority of these proteins had catalytic activity, binding activity, electron carrier activity and antioxidant activity. Compared with P1, P2 had 105 and 57 up- and down-regulated proteins, respectively. GO and KEGG-pathway analysis of these differentially expressed secreted proteins revealed that most were implicated in cell wall metabolism, stress and defense response, signaling, and protein metabolism and modification. Quantitative RT-PCR further validated some key differentially expressed secreted proteins associated with cell wall metabolism, stress and defense response, signaling and protein destination. Our results represent the first cell wall proteome of banana fruit and comprehensive proteomic study of banana fruit softening. SignificanceSoftening, which is the consequence of cell wall and turgor modification, is one of the most important factors determining banana fruit quality. The molecular mechanism regulating fruit softening in harvested banana is not currently well understood. In this study, we performed a comparative cell wall proteome analysis for pre-climacteric (P1) and post-climacteric (P2) banana fruit, corresponding to the mature green stage and softening ripening stage, respectively, using iTRAQ technology. We found 162 differentially expressed secreted proteins that were mainly implicated in cell wall metabolism, stress response and defense, signaling, and protein metabolism and modification. We have presented the first cell wall proteome of banana fruit and conducted a comprehensive proteomic study of banana fruit softening that will help to develop strategies to improve the sensorial quality and reduce post-harvest fruit losses.

Renal progenitor cells revert LPS-induced endothelial-to-mesenchymal transition by secreting CXCL6, SAA4, and BPIFA2 antiseptic peptides.

Endothelial dysfunction is a hallmark of LPS-induced acute kidney injury (AKI). Endothelial cells (ECs) acquired a fibroblast-like phenotype and contributed to myofibroblast generation through the endothelial-to-mesenchymal transition (EndMT) process. Of note, human adult renal stem/progenitor cells (ARPCs) enhance the tubular regenerative mechanism during AKI but little is known about their effects on ECs. Following LPS exposure, ECs proliferated, decreased EC markers CD31 and vascular endothelial cadherin, and up-regulated myofibroblast markers, collagen I, and vimentin. The coculture with ARPCs normalized the EC proliferation rate and abrogated the LPS-induced EndMT. The gene expression analysis showed that most of the genes modulated in LPS-stimulated ARPCs belong to cell activation and defense response pathways. We showed that the ARPC-specific antifibrotic effect is exerted by the secretion of CXCL6, SAA4, and BPIFA2 produced after the anaphylatoxin stimulation. Next, we investigated the molecular signaling that underlies the ARPC protective mechanism and found that renal progenitors diverge from differentiated tubular cells and ECs in myeloid differentiation primary response 88-independent pathway activation. Finally, in a swine model of LPS-induced AKI, we observed that activated ARPCs secreted CXCL6, SAA4, and BPIFA2 as a defense response. These data open new perspectives on the treatment of both sepsis- and endotoxemia-induced AKI, suggesting an underestimated role of ARPCs in preventing endothelial dysfunction and novel strategies to protect the endothelial compartment and promote kidney repair.-Sallustio, F., Stasi, A., Curci, C., Divella, C., Picerno, A., Franzin, R., De Palma, G., Rutigliano, M., Lucarelli, G., Battaglia, M., Staffieri, F., Crovace, A., Pertosa, G. B., Castellano, G., Gallone, A., Gesualdo, L. Renal progenitor cells revert LPS-induced endothelial-to-mesenchymal transition by secreting CXCL6, SAA4, and BPIFA2 antiseptic peptides.

LMM24 Encodes Receptor-Like Cytoplasmic Kinase 109, Which Regulates Cell Death and Defense Responses in Rice.

Lesion mimic mutants are excellent models for research on molecular mechanisms of cell death and defense responses in rice. We identified a new rice lesion mimic mutant lmm24 from a mutant pool of indica rice cultivar “ZhongHui8015”. The LMM24 gene was identified by MutMap, and LMM24 was confirmed as a receptor-like cytoplasmic kinase 109 by amino acid sequence analysis. The lmm24 mutant displayed dark brown lesions in leaves and growth retardation that were not observed in wild-type ZH8015. The results of histochemical staining and TUNEL assays showed enhanced ROS accumulation and cell death in lmm24. Chloroplast degradation was observed in lmm24 leaves, with decreased expression of photosynthesis-related genes and increased expression of the senescence-induced STAYGREEN (SGR) gene and other senescence-associated genes. Furthermore, lmm24 exhibited enhanced resistance to rice blast fungus Magnaporthe oryzae (M. oryzae) and up-regulation of defense response genes. Our data demonstrate that LMM24 regulates cell death and defense responses in rice.

A proteomic approach identifies novel proteins and metabolites for lesion mimic formation and disease resistance enhancement in rice

Lesion mimic mutants are ideal genetic materials to study programmed cell death and defense signaling in plants. However, the molecular basis of lesion mimic formation remains largely unknown. Here, we first used a proteomic approach to identify differentially expressed proteins during dynamic lesion mimic formation in the rice oscul3a mutant, then electron microscope observation and physiological assays were used to analyze the mutant. The oscul3a mutant had disrupted cell metabolism balance, and the identified differentially expressed proteins were mainly located in the chloroplast and cytoplasm, which caused enhanced lipid metabolism, but suppressed carbon/nitrogen metabolism with reduced growth and grain quality. The oscul3a mutant had higher salicylic acid (SA) concentration in leaves, and H2O2 was shown to accumulate late in the formation of lesions. The secondary metabolite coumarin induced reactive oxygen species (ROS) and had rice blast resistance activity. Moreover, the cell death initiated lesion mimic formation of oscul3a mutant was light-sensitive, which might be associated with metabolite biosynthesis and accumulation. This study sheds light on the metabolic transition associated with cell death and defense response, which is under tight regulation by OsCUL3a and metabolism-related proteins, and the newly identified chemicals in the secondary metabolic pathway can potentially be used to control disease in crop plants.

Infection process and host responses to Elsinoë ampelina, the causal organism of grapevine anthracnose

Grape anthracnose, caused by Elsinoe ampelina, is an important fungal disease during grape production. Little is known about the interactions of grape-E.ampelina compared with other grapevine fungal diseases. This study used potted seedlings of Vitis vinifera ‘Red Globe’ and E. ampelina to investigate their interactions under greenhouse conditions. The infection process of E. ampelina in the young leaves of grape was observed from 0 to 6 days post-inoculation (dpi) under microscope. Results showed that the first symptom on grape leaves were observed at 3 dpi. The rates of conidial germination on grape leaves were 23.4, 73.2, and 85.6% at 1, 2, and 3 dpi, respectively. Early penetration occurred in the epidermal cells with or without forming appressoria at 2 dpi. E. ampelina enlarged in intercellular spaces at 2–3 dpi and began to enter intracellular spaces from 3 dpi. New conidia were produced in acervuli on the leaf surface from 6 dpi. The ultrastructural observation revealed defense responses in infected host cells, including collapse of cell walls and chloroplasts, changes in the number of mitochondria, plasmolysis, and cell death. Overall, these results provide a detailed understanding of the grape-E.ampelina interaction and theoretical bases for infection pathway of grape anthracnose.

Genome-wide mining of respiratory burst homologs and its expression in response to biotic and abiotic stresses in Triticum aestivum.

Membrane-bound NADPH oxidases (Nicotinamide adenine ainucleotide phosphate oxidase) also called respiratory burst oxidase homologs (Rboh) play an essential role in ROS production under normal as well as environmental stress conditions in plants. To identify and study respiratory burst homologs (Rboh) from the wheat genome as well as characterize their role in various biological and molecular processes along with expression in response to biotic and abiotic stresses. The Rboh homologs in the wheat genome were predicted based on data processing, alignment of sequences and phylogenetic analysis of sequences in numerous plant species and wheat. The conserved motifs were known followed by domain design study. The 3-D structure prediction and similarity modeling were administered for NADPH enzyme domain. Gene ontology and a functional study were done in addition to expression analysis of Triticum aestivum respiratory burst oxidase (TaRboh) gene family in response to biotic as well as abiotic stress. Phylogenetic analysis of Rboh gene family members among seven plant species including wheat, classified the family into four subfamilies. Rboh genes are mainly involved in various biological processes such as Response to oxidative stress, Superoxide anion generation, Hydrogen peroxide biosynthetic process. Among the molecular functions, calcium ion binding, peroxidase activity, oxidoreductase activity, superoxide-generating NADPH oxidase activity are essential. Enzyme annotation of the family and superfamily revealed that it encodes to five structural clusters and coding to enzymes NAD(P)H oxidase (H2O2-forming) (EC:1.6.3.1), Ferric-chelate reductase (NADH) (EC: 1.16.1.7), Peroxidase (EC: 1.11.1.7), Ribose-phosphate diphosphokinase (EC: 2.7.6.1). The enzymes contain six membrane-spanning domains, two hemes, and conserved motifs associated with NADPH, EF-hand and FAD binding. The outcomes additionally reflect a distinct role of this enzyme in different molecular functions which are responsible for the stress signaling. Further, the transcripts of TaRboh found expressed in various plant parts such as stem, leaves, spike, seed, and roots. We also observed expression of these gene family members under drought/combination of drought + heat and important wheat pathogens such as Puccinia striformis, Blumeria graminis f.sp. tritici, Fusarium graminiarum, F. pseudograminiarum, and Zymoseptoria tritici. The investigation demonstrated that identified respiratory burst homologs (Rboh) in T. aestivum were involved in pathogen activated ROS production and have regulatory functions in cell death and defense responses.

Quantitative proteomics analysis reveals resistance differences of banana cultivar ‘Brazilian’ to Fusarium oxysporum f. sp. cubense races 1 and 4

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in banana production. Foc is classified into three physiological races. However, the resistance mechanisms of banana against different Foc races are poorly understood. In this study, we performed a comparative proteomics analysis to investigate the resistance mechanisms of ‘Brazilian’ against Foc1 and Foc4. The proteomes of ‘Brazilian’ roots inoculated with Foc1 and Foc4 and mock inoculated control at 48 h were analyzed using TMT based quantitative analysis technique. A total of 7325 unique protein species were identified, of which 689, 744, and 1222 protein species were differentially accumulated in Foc1 vs. CK, Foc4 vs. CK, and Foc1 vs. Foc4, respectively. The differential accumulations of candidate protein species were further confirmed by RT-qPCR, PRM, and physiological and biochemical assays. Bioinformatics analysis revealed that the differentially abundance protein species (DAPS) related to pattern recognition receptors, plant cell wall modification, redox homeostasis, and defense responses were differentially accumulated after Foc1 and Foc4 infection, suggesting that ‘Brazilian’ differed in resistance to the two Foc races. Our study lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level. SignificanceThe banana fusarium wilt disease is one of the most destructive disease of banana and is caused by Fusarium oxysporum f. sp. cubense (Foc). Foc is classified into three physiological races, namely, Foc1, Foc2, and Foc4. Among these races, Foc1 and Foc4 are widely distributed in south China and significantly lose yield. Although both physiological races (Foc1 and Foc4) can invade the Cavendish banana cultivar ‘Brazilian’, they have significant pathogenicity differences. Unfortunately, how the resistance differences are produced between two races is still largely unclear to date. In this study, we addressed this issue by performing TMT-based comparative quantitative proteomics analysis of ‘Brazilian’ roots after inoculation with Foc1 and Foc4 as well as sterile water as the control. We revealed that the series of protein species associated with pattern recognition receptors, plant cell wall modification, redox homeostasis, pathogenesis, phytohormones and signal transduction, plant secondary metabolites and programmed cell death etc. were involved in the response to Foc infection. Notably, the potential role of lipid signaling in banana defense against Foc are not reported previously but rather unveiled for the first time in this study. The current study represents the most extensive analysis of the protein profile of ‘Brazilian’ in response to Foc inoculation and includes for the first time the results from comparison quantitative proteomics analysis between plants inoculated with a pathogenic strain Foc4 and a nonpathogenic strain Foc1 of ‘Brazilian’, which will lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level.

Disruption of gene SPL35, encoding a novel CUE domain-containing protein, leads to cell death and enhanced disease response in rice.

SummaryLesion mimic mutants that exhibit spontaneous hypersensitive response (HR)‐like necrotic lesions are ideal experimental systems for elucidating molecular mechanisms involved in plant cell death and defence responses. Here we report identification of a rice lesion mimic mutant, spotted leaf 35 (spl35), and cloning of the causal gene by TAIL‐PCR strategy. spl35 exhibited decreased chlorophyll content, higher accumulation of H2O2, up‐regulated expression of defence‐related marker genes, and enhanced resistance to both fungal and bacterial pathogens of rice. The SPL35 gene encodes a novel CUE (coupling of ubiquitin conjugation to ER degradation) domain‐containing protein that is predominantly localized in cytosol, ER and unknown punctate compartment(s). SPL35 is constitutively expressed in all organs, and both overexpression and knockdown of SPL35 cause the lesion mimic phenotype. SPL35 directly interacts with the E2 protein OsUBC5a and the coatomer subunit delta proteins Delta‐COP1 and Delta‐COP2 through the CUE domain, and down‐regulation of these interacting proteins also cause development of HR‐like lesions resembling those in spl35 and activation of defence responses, indicating that SPL35 may be involved in the ubiquitination and vesicular trafficking pathways. Our findings provide insight into a role of SPL35 in regulating cell death and defence response in plants.

Exposure in vitro to an Environmentally Isolated Strain TC09 of Cladosporium sphaerospermum Triggers Plant Growth Promotion, Early Flowering, and Fruit Yield Increase.

A growing number of bacteria and fungi have been found to promote plant growth through mutualistic interactions involving elements such as volatile organic compounds (VOCs). Here, we report the identification of an environmentally isolated strain of Cladosporium sphaerospermum (herein named TC09), that substantially enhances plant growth after exposure in vitro beyond what has previously been reported. When cultured on Murashige and Skoog (MS) medium under in vitro conditions, tobacco seedlings (Nicotiana tabacum) exposed to TC09 cultures for 20 days increased stem height and whole plant biomass up to 25- and 15-fold, respectively, over controls without exposure. TC09-mediated growth promotion required >5 g/L sucrose in the plant culture medium and was influenced by the duration of exposure ranging from one to 10 days, beyond which no differences were detected. When transplanted to soil under greenhouse conditions, TC09-exposed tobacco plants retained higher rates of growth. Comparative transcriptome analyses using tobacco seedlings exposed to TC09 for 10 days uncovered differentially expressed genes (DEGs) associated with diverse biological processes including cell expansion and cell cycle, photosynthesis, phytohormone homeostasis and defense responses. To test the potential efficacy of TC09-mediated growth promotion on agricultural productivity, pepper plants (Capsicum annuum L.) of two different varieties, Cayenne and Minisweet, were pre-exposed to TC09 and planted in the greenhouse to monitor growth, flowering, and fruit production. Results showed that treated pepper plants flowered 20 days earlier and yielded up to 213% more fruit than untreated controls. Altogether the data suggest that exposure of young plants to C. sphaerospermum produced VOCs may provide a useful tool to improve crop productivity.

Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz)

Drought stress is one of the potent abiotic stress limiting cassava (Manihot esculenta) yield globally, but studies addressing both physiological and proteomic responses that how cassava crops can adjust their growth and metabolism under drought conditions are lacking. Combining leaf physiological and proteomic characteristics strongly allied with drought tolerance should results in enhanced drought tolerance in cassava crop. Therefore, the aims of this study were to explore the plant physiological and proteomic mechanisms involved in drought adaptation in cassava. Xinxuan 048 (XX048) was exposed to well-watered control (CK, relative soil water content (RSWC) as 80 ± 5%), mild drought stress (LD, RSWC as 65 ± 5%), moderate drought stress (MD, RSWC as 50 ± 5%) and severe drought stress (SD, RSWC as 35 ± 5%) from 30 days after planting. Under drought stress conditions, cassava plant showed a substantial decline in plant height, stem diameter, leaf number, leaf water content, the ratio of free water content to bound water content of leaf (FW/BW), net photosynthetic rate (Pn), intercellular CO2 concentration (Ci), stomatal conductance (Gs) and transpiration rate (Tr) compared with well watered plants. However, compared with control, leaf water content, SPAD value, cell membrane permeability, malondialdehyde (MDA), soluble sugar, protein proline content SOD and CAT activity were at peak under drought stress. The proteomic analysis revealed that among 3 339 identified proteins, drought stress increased and decreased abundance of 262 and 296 proteins, respectively, compared with control condition. These proteins were involved in carbohydrate energy metabolism, protein homeostasis, transcription, cell structure, cell membrane transport, signal transduction, stress and defense responses. These data not only provides a comprehensive dataset on overall proteomic changes in cassava leaves under drought stress, but also highlights the mechanisms by which euphorbiaceae plants can adapt to drought conditions.

Effects of fungal volatile organic compounds on Arabidopsis thaliana growth and gene expression

Abstract Many microorganisms produce volatile organic compounds (VOCs) with biological effects on plants. In this study, Arabidopsis seeds or 14-day-old vegetative plants were exposed to 0.5 μg/l of chemical standards of 26 VOCs previously identified from the biocontrol fungus Trichoderma. Seven compounds (1-decene, 2-heptylfuran, 2-methyl-1-propanol, 2-methyl-1-butanol, 3-methyl-1- butanol, 2-heptanone, and 1-octen-3-ol) were further tested at the physiological concentration (10 ng/l) and 3-methyl-1-butanol, 1-decene, and 2-heptylfuran induced significant increases in fresh weight and total chlorophyll content. Plants exposed to 1-decene had the greatest increase in plant fresh shoot weight (38.9%) and chlorophyll content (67.8%). An RNA sequencing analysis was performed on plants treated with vapors of 1-decene. The expression of 123 genes was differentially affected, encompassing genes involved in cell wall modification, auxin induction, stress, and defense responses, with several major classes of stress-related genes showing down-regulation. To our knowledge, this is the first report of the effect of a plant growth promoting VOC on gene expression in Arabidopsis thaliana. As the role of fungal VOCs in biocontrol moves from correlative studies to more hypothesis driven approaches, our findings can guide both basic and applied studies in agricultural research.

Identification of potential whole blood MicroRNA biomarkers for the blood stage of adult imported falciparum malaria through integrated mRNA and miRNA expression profiling

Correlating aberrant miRNA levels with imported malaria during the blood stage is required to better understand the in vivo biological and molecular processes that are involved in the response to Plasmodium falciparum infection and to find new biomarkers and diagnosis tools. We used a parallel microarray-based approach to investigate an integrated view of how the host miRNA expression profile changes in response to P. falciparum infection in whole blood obtained from six subjects with adult imported falciparum malaria (AIFM) and six normal subjects. We first investigated the functions of 1007 significantly differentially expressed genes from microarrays and predicted 56 putative pathways participating in malaria pathogenesis, which reflected systemic changes in the host under falciparum infection. Then, we validated the in silico-predicted targets of 50 differentially modulated miRNAs (7 upregulated and 43 downregulated) by examining the actual mRNA expression of these particular genes in our gene expression profile database; putative target gene sets were grouped into functional categories to investigate the roles of differentially expressed miRNAs. We considered 36 intersecting putative pathways, most of which were involved in multiple immune response processes, such as cell defense response, immune response, TNF signaling pathway, and T cell receptor signaling pathway, which may actually be regulated by differentially expressed miRNAs. Additionally, we identified five enriched upregulated miRNA sets (miR-3135b, miR-6780b-5p, miR-1246, miR-6126, and miR-3613-5p) as potential blood biomarkers of immunopathological status and prediction of early host responses, disease prognosis, and severe outcomes in AIFM.

Biocompatibility, hemocompatibility and antimicrobial properties of xyloglucan-based hydrogel film for wound healing application

Crosslinked xyloglucan-poly(vinyl alcohol) based hydrogel films are interesting materials for wound healing applications. This work focuses on the hydrolytic degradation and consequent morphological modification of a XG-PVA film and on its interaction with cells, blood, bacteria. Biocompatibility of the film was assessed in vitro by investigating different aspects, such as cell viability, oxidative stress level, mitochondrial dysfunction and specific stress biomarkers. Partial adhesiveness was demonstrated by performing different attaching assays and phalloidin staining. Hemocompatibility of XG-PVA film after interaction with blood was evaluated by using a multi-parametric approach, including human Red Blood Cells (RBC) count, hemolytic response and platelets activation. Thrombin and fibrinogen concentrations were examined as marker of the coagulation cascade. After direct contact with human blood and peripheral blood mononuclear cells (PBMC), no evidence of cell defense response was observed. Antimicrobial activity of XG-PVA film was tested against Escherichia coli (E.coli). XG-PVA film promotes bacterial retentivity and provides mechanical protection against bacterial infiltration. After loading the film with ampicillin, an inhibitory E. coli growth zone was observed. All together these results indicate that the XG-PVA system is a promising material to be tested in vivo for wound healing applications.

Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus

SUMMARYRhinovirus is a leading cause of acute respiratory infections and asthma attacks, but infections are also frequently cleared from the nasal mucosa without causing symptoms. We sought to better understand host defense against rhinovirus by investigating antiviral defense in primary human nasal and bronchial airway epithelial cells cultured ex vivo. Surprisingly, upon rhinovirus infection or RIG-I stimulation, nasal-derived epithelial cells exhibited much more robust antiviral responses than bronchial-derived cells. Conversely, RIG-I stimulation triggered more robust activation of the NRF2-dependent oxidative stress response in bronchial cells compared to nasal cells. NRF2 activation dampened epithelial antiviral responses, whereas NRF2 knockdown enhanced antiviral responses and was protective during rhinovirus infection. These findings demonstrate a tradeoff in epithelial defense against distinct types of airway damage, namely, viral versus oxidative, and reveal differential calibration of defense responses in cells derived from different airway microenvironments.

Long-term cadmium exposure influences the abundance of proteins that impact the cell wall structure in Medicago sativa stems.

Cadmium (Cd) is a non‐essential, toxic heavy metal that poses serious threats to both ecosystems and human health. Plants employ various cellular and molecular mechanisms to minimise the impact of Cd toxicity and cell walls function as a defensive barrier during Cd exposure.In this study, we adopted a quantitative gel‐based proteomic approach (two‐dimensional difference gel electrophoresis) to investigate changes in the abundance of cell wall and soluble proteins in stems of Medicago sativa L. upon long‐term exposure to Cd (10 mg·Cd·kg−1 soil as CdSO 4). Obtained protein data were complemented with targeted gene expression analyses.Plants were affected by Cd exposure at an early growth stage but seemed to recover at a more mature stage as no difference in biomass was observed. The accumulation of Cd was highest in roots followed by stems and leaves. Quantitative proteomics revealed a changed abundance for 179 cell wall proteins and 30 proteins in the soluble fraction upon long‐term Cd exposure. These proteins are involved in cell wall remodelling, defence response, carbohydrate metabolism and promotion of the lignification process.The data indicate that Cd exposure alters the cell wall proteome and underline the role of cell wall proteins in defence against Cd stress. The identified proteins are linked to alterations in cell wall structure and lignification process in stems of M. sativa, underpinning the function of the cell wall as an effective barrier against Cd stress.

Genome-Wide Identification and Functional Analysis of NADPH Oxidase Family Genes in Wheat During Development and Environmental Stress Responses.

As the key producers of reactive oxygen species (ROS), NADPH oxidases (NOXs), also known as respiratory burst oxidase homologs (RBOHs), play crucial roles in various biological processes in plants with considerable evolutionary selection and functional diversity in the entire terrestrial plant kingdom. However, only limited resources are available on the phylogenesis and functions of this gene family in wheat. Here, a total of 46 NOX family genes were identified in the wheat genome, and these NOXs could be classified into three subgroups: typical TaNOXs, TaNOX-likes, and ferric reduction oxidases (TaFROs). Phylogenetic analysis indicated that the typical TaNOXs might originate from TaFROs during evolution, and the TaFROs located on Chr 2 might be the most ancient forms of TaNOXs. TaNOXs are highly expressed in wheat with distinct tissue or organ-specificity and stress-inducible diversity. A large-scale expression and/or coexpression analysis demonstrated that TaNOXs can be divided into four functional groups with different expression patterns under a broad range of environmental stresses. Different TaNOXs are coexpressed with different sets of other genes, which widely participate in several important intracellular processes such as cell wall biosynthesis, defence response, and signal transduction, suggesting their vital but diversity of roles in plant growth regulation and stress responses of wheat.

Prediction of Molecular Signature, Potential Biomarkers, and Molecular Pathways Associated with Membranous Nephropathy Based on Protein Protein Interactions

Membranous nephropathy (MN) is one of the causes of nephrotic syndrome in adults that lead to end-stage renal disease with an unknown molecular signature. The current diagnosis is based on renal biopsy, which is an invasive method and has several complications and challenges. Thus, identification of the novel biomarker candidates, as well as impaired pathways, will be helpful for non-invasive molecular-based diagnosis. We aimed to study the molecular signature of MN and facilitate the systematic discovery of diagnostic candidate biomarkers, molecular pathway, and potential therapeutic targets using bioinformatics predictions. The protein-protein interaction (PPI) network of an integrated list of downloaded microarray data, differential proteins from a published proteomic study, and a list of retrieved scientific literature mining was constructed and analyzed in terms of functional modules, enriched biological pathways, hub genes, master regulator, and target genes. These network analyses revealed several functional modules and hub genes including Vitamin D3 receptor, retinoic acid receptor RXR-alpha, interleukin 8, and SH3GL2. TEAD4 and FOXA1 were identified as the regulatory master molecules. LRP1 and ITGA3 were identified as the important target genes. Extracellular matrix organization, cell surface receptor signaling pathway, and defense and inflammatory response were found to be impaired in MN using functional analyses. A specific subnetwork for MN was suggested using PPI approach. Omics data integration and systems biology analysis on the level of interaction networks provide a powerful approach for identification of pathway-specific biomarkers for MN.

Whole-genome re-sequencing reveals molecular mechanisms of biomass changes in 11-year-old Bt transgenic poplar

Genome-wide insertions/deletions were identified in Bt transgenic poplar through whole-genome re-sequencing, revealing the molecular mechanisms underlying changes in the growth and wood characteristics of Bt transgenic poplar. Poplar is a fast-growing tree that relieves the wood demand in China. Previously, we found growth and wood characteristics differed in some lines of insect-resistant Bt transgenic poplar. Here, we selected five Bt transgenic lines (#12, #153, #172, #208 and #209), one untransformed control (CK2), one comparable control (CK3), and one native cultivar (JY, Populus × euramericana ‘Robusta’) in Xinjiang, China, for further study. Based on breast diameter, tree height, chemical content, and fibre morphology analyses, these transgenic lines showed fast growth and high-lignin and low-cellulose contents in the cell wall. In addition, genome-wide insertions/deletions (InDels) were compared between two transgenic lines (#12 and #153) and the untransformed control via whole-genome re-sequencing. GO enrichment and protein–protein interaction networks indicated the genes affected by differential InDels were related to programmed cell death and defence responses. This study provides new insight into the molecular mechanisms underlying changes in biomass characteristics in Bt transgenic poplar.

In vivo monitoring of plant small GTPase activation using a F\xf6rster resonance energy transfer biosensor

BackgroundSmall GTPases act as molecular switches that regulate various plant responses such as disease resistance, pollen tube growth, root hair development, cell wall patterning and hormone responses. Thus, to monitor their activation status within plant cells is believed to be the key step in understanding their roles.ResultsWe have established a plant version of a Förster resonance energy transfer (FRET) probe called Ras and interacting protein chimeric unit (Raichu) that can successfully monitor activation of the rice small GTPase OsRac1 during various defence responses in cells. Here, we describe the protocol for visualizing spatiotemporal activity of plant Rac/ROP GTPase in living plant cells, transfection of rice protoplasts with Raichu-OsRac1 and acquisition of FRET images.ConclusionsOur protocol should be adaptable for monitoring activation for other plant small GTPases and protein–protein interactions for other FRET sensors in various plant cells.