International Journal of Molecular Sciences

Editorial

Jump to: Research, Review

7 pages, 764 KiB

Open AccessEditorial

Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era

by Xuchu Wang

Int. J. Mol. Sci. 2019, 20(20), 5222; https://doi.org/10.3390/ijms20205222 - 21 Oct 2019

Cited by 11 | Viewed by 4269

Abstract

In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more [...] Read more.

In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

Research

Jump to: Editorial, Review

21 pages, 4461 KiB

Open AccessArticle

Heat-Responsive Proteomics of a Heat-Sensitive Spinach Variety

by Shanshan Li, Juanjuan Yu, Ying Li, Heng Zhang, Xuesong Bao, Jiayi Bian, Chenxi Xu, Xiaoli Wang, Xiaofeng Cai, Quanhua Wang, Pengcheng Wang, Siyi Guo, Yuchen Miao, Sixue Chen, Zhi Qin and Shaojun Dai

Int. J. Mol. Sci. 2019, 20(16), 3872; https://doi.org/10.3390/ijms20163872 - 8 Aug 2019

Cited by 25 | Viewed by 4878

Abstract

High temperatures seriously limit plant growth and productivity. Investigating heat-responsive molecular mechanisms is important for breeding heat-tolerant crops. In this study, heat-responsive mechanisms in leaves from a heat-sensitive spinach (Spinacia oleracea L.) variety Sp73 were investigated using two-dimensional gel electrophoresis (2DE)-based and [...] Read more.

High temperatures seriously limit plant growth and productivity. Investigating heat-responsive molecular mechanisms is important for breeding heat-tolerant crops. In this study, heat-responsive mechanisms in leaves from a heat-sensitive spinach (Spinacia oleracea L.) variety Sp73 were investigated using two-dimensional gel electrophoresis (2DE)-based and isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics approaches. In total, 257 heat-responsive proteins were identified in the spinach leaves. The abundance patterns of these proteins indicated that the photosynthesis process was inhibited, reactive oxygen species (ROS) scavenging pathways were initiated, and protein synthesis and turnover, carbohydrate and amino acid metabolism were promoted in the spinach Sp73 in response to high temperature. By comparing this with our previous results in the heat-tolerant spinach variety Sp75, we found that heat inhibited photosynthesis, as well as heat-enhanced ROS scavenging, stress defense pathways, carbohydrate and energy metabolism, and protein folding and turnover constituting a conservative strategy for spinach in response to heat stress. However, the heat-decreased biosynthesis of chlorophyll and carotenoid as well as soluble sugar content in the variety Sp73 was quite different from that in the variety Sp75, leading to a lower capability for photosynthetic adaptation and osmotic homeostasis in Sp73 under heat stress. Moreover, the heat-reduced activities of SOD and other heat-activated antioxidant enzymes in the heat-sensitive variety Sp73 were also different from the heat-tolerant variety Sp75, implying that the ROS scavenging strategy is critical for heat tolerance. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

22 pages, 4111 KiB

Open AccessArticle

Comparative Proteomics Indicates That Redox Homeostasis Is Involved in High- and Low-Temperature Stress Tolerance in a Novel Wucai (Brassica campestris L.) Genotype

by Lingyun Yuan, Jie Wang, Shilei Xie, Mengru Zhao, Libing Nie, Yushan Zheng, Shidong Zhu, Jinfeng Hou, Guohu Chen and Chenggang Wang

Int. J. Mol. Sci. 2019, 20(15), 3760; https://doi.org/10.3390/ijms20153760 - 1 Aug 2019

Cited by 22 | Viewed by 3976

Abstract

The genotype WS-1, previously identified from novel wucai germplasm, is tolerant to both low-temperature (LT) and high-temperature (HT) stress. However, it is unclear which signal transduction pathway or acclimation mechanisms are involved in the temperature-stress response. In this study, we used the proteomic [...] Read more.

The genotype WS-1, previously identified from novel wucai germplasm, is tolerant to both low-temperature (LT) and high-temperature (HT) stress. However, it is unclear which signal transduction pathway or acclimation mechanisms are involved in the temperature-stress response. In this study, we used the proteomic method of tandem mass tag (TMT) coupled with liquid chromatography-mass spectrometry (LC-MS/MS) to identify 1022 differentially expressed proteins (DEPs) common to WS-1, treated with either LT or HT. Among these 1022 DEPs, 172 were upregulated in response to both LT and HT, 324 were downregulated in response to both LT and HT, and 526 were upregulated in response to one temperature stress and downregulated in response to the other. To illustrate the common regulatory pathway in WS-1, 172 upregulated DEPs were further analyzed. The redox homeostasis, photosynthesis, carbohydrate metabolism, heat-shockprotein, and chaperones and signal transduction pathways were identified to be associated with temperature stress tolerance in wucai. In addition, 35S:BcccrGLU1 overexpressed in Arabidopsis, exhibited higher reduced glutathione (GSH) content and reduced glutathione/oxidized glutathione (GSH/GSSG) ratio and less oxidative damage under temperature stress. This result is consistent with the dynamic regulation of the relevant proteins involved in redox homeostasis. These data demonstrate that maintaining redox homeostasis is an important common regulatory pathway for tolerance to temperature stress in novel wucai germplasm. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

26 pages, 2940 KiB

Open AccessArticle

Comparative Proteomics and Physiological Analyses Reveal Important Maize Filling-Kernel Drought-Responsive Genes and Metabolic Pathways

by Xuan Wang, Tinashe Zenda, Songtao Liu, Guo Liu, Hongyu Jin, Liang Dai, Anyi Dong, Yatong Yang and Huijun Duan

Int. J. Mol. Sci. 2019, 20(15), 3743; https://doi.org/10.3390/ijms20153743 - 31 Jul 2019

Cited by 40 | Viewed by 5637

Abstract

Despite recent scientific headway in deciphering maize (Zea mays L.) drought stress responses, the overall picture of key proteins and genes, pathways, and protein–protein interactions regulating maize filling-kernel drought tolerance is still fragmented. Yet, maize filling-kernel drought stress remains devastating and its [...] Read more.

Despite recent scientific headway in deciphering maize (Zea mays L.) drought stress responses, the overall picture of key proteins and genes, pathways, and protein–protein interactions regulating maize filling-kernel drought tolerance is still fragmented. Yet, maize filling-kernel drought stress remains devastating and its study is critical for tolerance breeding. Here, through a comprehensive comparative proteomics analysis of filling-kernel proteomes of two contrasting (drought-tolerant YE8112 and drought-sensitive MO17) inbred lines, we report diverse but key molecular actors mediating drought tolerance in maize. Using isobaric tags for relative quantification approach, a total of 5175 differentially abundant proteins (DAPs) were identified from four experimental comparisons. By way of Venn diagram analysis, four critical sets of drought-responsive proteins were mined out and further analyzed by bioinformatics techniques. The YE8112-exclusive DAPs chiefly participated in pathways related to “protein processing in the endoplasmic reticulum” and “tryptophan metabolism”, whereas MO17-exclusive DAPs were involved in “starch and sucrose metabolism” and “oxidative phosphorylation” pathways. Most notably, we report that YE8112 kernels were comparatively drought tolerant to MO17 kernels attributable to their redox post translational modifications and epigenetic regulation mechanisms, elevated expression of heat shock proteins, enriched energy metabolism and secondary metabolites biosynthesis, and up-regulated expression of seed storage proteins. Further, comparative physiological analysis and quantitative real time polymerase chain reaction results substantiated the proteomics findings. Our study presents an elaborate understanding of drought-responsive proteins and metabolic pathways mediating maize filling-kernel drought tolerance, and provides important candidate genes for subsequent functional validation. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

20 pages, 2472 KiB

Open AccessArticle

Nitrogen Fertilizer Induced Alterations in The Root Proteome of Two Rice Cultivars

by Jichao Tang, Zhigui Sun, Qinghua Chen, Rebecca Njeri Damaris, Bilin Lu and Zhengrong Hu

Int. J. Mol. Sci. 2019, 20(15), 3674; https://doi.org/10.3390/ijms20153674 - 26 Jul 2019

Cited by 14 | Viewed by 3615

Abstract

Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and [...] Read more.

Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and critical for the reductions of N fertilizer pollution and production cost. In the present study, we investigated the effects of N nutrition on the growth and yield of the two rice (Oryza sativa L.) cultivars, conventional rice Huanghuazhan and indica hybrid rice Quanliangyou 681, which were grown at three levels of N fertilizer (including 135, 180 and 225 kg/hm², labeled as N9, N12, N15, respectively). Then, a proteomic approach was employed in the roots of the two rice cultivars treated with N fertilizer at the level of N15. A total of 6728 proteins were identified, among which 6093 proteins were quantified, and 511 differentially expressed proteins were found in the two rice cultivars after N fertilizer treatment. These differentially expressed proteins were mainly involved in ammonium assimilation, amino acid metabolism, carbohydrate metabolism, lipid metabolism, signal transduction, energy production/regulation, material transport, and stress/defense response. Together, this study provides new insights into the regulatory mechanism of nitrogen fertilization in cereal crops. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

17 pages, 2025 KiB

Open AccessArticle

Unravelling the MicroRNA-Mediated Gene Regulation in Developing Pongamia Seeds by High-Throughput Small RNA Profiling

by Ye Jin, Lin Liu, Xuehong Hao, David E. Harry, Yizhi Zheng, Tengbo Huang and Jianzi Huang

Int. J. Mol. Sci. 2019, 20(14), 3509; https://doi.org/10.3390/ijms20143509 - 17 Jul 2019

Cited by 7 | Viewed by 2833

Abstract

Pongamia (Millettia pinnata syn. Pongamia pinnata) is a multipurpose biofuel tree which can withstand a variety of abiotic stresses. Commercial applications of Pongamia trees may substantially benefit from improvements in their oil-seed productivity, which is governed by complex regulatory mechanisms underlying [...] Read more.

Pongamia (Millettia pinnata syn. Pongamia pinnata) is a multipurpose biofuel tree which can withstand a variety of abiotic stresses. Commercial applications of Pongamia trees may substantially benefit from improvements in their oil-seed productivity, which is governed by complex regulatory mechanisms underlying seed development. MicroRNAs (miRNAs) are important molecular regulators of plant development, while relatively little is known about their roles in seed development, especially for woody plants. In this study, we identified 236 conserved miRNAs within 49 families and 143 novel miRNAs via deep sequencing of Pongamia seeds sampled at three developmental phases. For these miRNAs, 1327 target genes were computationally predicted. Furthermore, 115 differentially expressed miRNAs (DEmiRs) between successive developmental phases were sorted out. The DEmiR-targeted genes were preferentially enriched in the functional categories associated with DNA damage repair and photosynthesis. The combined analyses of expression profiles for DEmiRs and functional annotations for their target genes revealed the involvements of both conserved and novel miRNA-target modules in Pongamia seed development. Quantitative Real-Time PCR validated the expression changes of 15 DEmiRs as well as the opposite expression changes of six targets. These results provide valuable miRNA candidates for further functional characterization and breeding practice in Pongamia and other oilseed plants. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

22 pages, 7279 KiB

Open AccessArticle

Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis

by Zhuang Yang, Wen Li, Xiao Su, Pingfei Ge, Yan Zhou, Yuanyuan Hao, Huangying Shu, Chonglun Gao, Shanhan Cheng, Guopeng Zhu and Zhiwei Wang

Int. J. Mol. Sci. 2019, 20(13), 3321; https://doi.org/10.3390/ijms20133321 - 6 Jul 2019

Cited by 33 | Viewed by 4704

Abstract

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the [...] Read more.

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis—antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA–miRNA–mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

14 pages, 1993 KiB

Open AccessArticle

Identification and Analysis of Micro-Exon Genes in the Rice Genome

by Qi Song, Fang Lv, Muhammad Tahir ul Qamar, Feng Xing, Run Zhou, Huan Li and Ling-Ling Chen

Int. J. Mol. Sci. 2019, 20(11), 2685; https://doi.org/10.3390/ijms20112685 - 31 May 2019

Cited by 5 | Viewed by 4253

Abstract

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been [...] Read more.

Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

19 pages, 3742 KiB

Open AccessArticle

iTRAQ-Based Quantitative Analysis of Responsive Proteins Under PEG-Induced Drought Stress in Wheat Leaves

by Yajing Wang, Xinying Zhang, Guirong Huang, Fu Feng, Xiaoying Liu, Rui Guo, Fengxue Gu, Xiuli Zhong and Xurong Mei

Int. J. Mol. Sci. 2019, 20(11), 2621; https://doi.org/10.3390/ijms20112621 - 28 May 2019

Cited by 16 | Viewed by 4346

Abstract

Drought is an important abiotic stress that seriously restricts crop productivity. An understanding of drought tolerance mechanisms offers guidance for cultivar improvement. In order to understand how a well-known wheat genotype Jinmai 47 responds to drought, we adopted the iTRAQ and LC/MS approaches [...] Read more.

Drought is an important abiotic stress that seriously restricts crop productivity. An understanding of drought tolerance mechanisms offers guidance for cultivar improvement. In order to understand how a well-known wheat genotype Jinmai 47 responds to drought, we adopted the iTRAQ and LC/MS approaches and conducted proteomics analysis of leaves after exposure to 20% of polyethylene glycol-6000 (PEG)-induced stress for 4 days. The study identified 176 differentially expressed proteins (DEPs), with 65 (36.5%) of them being up-regulated, and 111 (63.5%) down-regulated. DEPs, located in cellular membranes and cytosol mainly, were involved in stress and redox regulation (51), carbohydrate and energy metabolism (36), amino acid metabolism (24), and biosynthesis of other secondary metabolites (20) primarily. Under drought stress, TCA cycle related proteins were up-regulated. Antioxidant system, signaling system, and nucleic acid metabolism etc. were relatively weakened. In comparison, the metabolism pathways that function in plasma dehydration protection and protein structure protection were strongly enhanced, as indicated by the improved biosynthesis of 2 osmolytes, sucrose and Proline, and strongly up-regulated protective proteins, LEA proteins and chaperones. SUS4, P5CSs, OAT, Rab protein, and Lea14-A were considered to be important candidate proteins, which deserve to be further investigated. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

19 pages, 3626 KiB

Open AccessArticle

Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass Taraxacum Kok-saghyz

by Quanliang Xie, Guohua Ding, Liping Zhu, Li Yu, Boxuan Yuan, Xuan Gao, Dan Wang, Yong Sun, Yang Liu, Hongbin Li and Xuchu Wang

Int. J. Mol. Sci. 2019, 20(10), 2596; https://doi.org/10.3390/ijms20102596 - 27 May 2019

Cited by 18 | Viewed by 5841

Abstract

The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process [...] Read more.

The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process involving many genes, proteins and their cofactors. The TKS genome has just been annotated and many NRB-related genes have been determined. However, there is limited knowledge about the protein regulation mechanism for NRB in TKS roots. We identified 371 protein species from the mature roots of TKS by combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Meanwhile, a large-scale shotgun analysis of proteins in TKS roots at the enlargement stage was performed, and 3545 individual proteins were determined. Subsequently, all identified proteins from 2-DE gel and shotgun MS in TKS roots were subject to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and most proteins were involved in carbon metabolic process with catalytic activity in membrane-bounded organelles, followed by proteins with binding ability, transportation and phenylpropanoid biosynthesis activities. Fifty-eight NRB-related proteins, including eight small rubber particle protein (SRPP) and two rubber elongation factor(REF) members, were identified from the TKS roots, and these proteins were involved in both mevalonate acid (MVA) and methylerythritol phosphate (MEP) pathways. To our best knowledge, it is the first high-resolution draft proteome map of the mature TKS roots. Our proteomics of TKS roots revealed both MVA and MEP pathways are important for NRB, and SRPP might be more important than REF for NRB in TKS roots. These findings would not only deepen our understanding of the TKS root proteome, but also provide new evidence on the roles of these NRB-related proteins in the mature TKS roots. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

20 pages, 2697 KiB

Open AccessArticle

Quantitative Proteomic Analysis Reveals Novel Insights into Intracellular Silicate Stress-Responsive Mechanisms in the Diatom Skeletonema dohrnii

by Satheeswaran Thangaraj, Xiaomei Shang, Jun Sun and Haijiao Liu

Int. J. Mol. Sci. 2019, 20(10), 2540; https://doi.org/10.3390/ijms20102540 - 23 May 2019

Cited by 15 | Viewed by 4150

Abstract

Diatoms are a successful group of marine phytoplankton that often thrives under adverse environmental stress conditions. Members of the Skeletonema genus are ecologically important which may subsist during silicate stress and form a dense bloom following higher silicate concentration. However, our understanding of [...] Read more.

Diatoms are a successful group of marine phytoplankton that often thrives under adverse environmental stress conditions. Members of the Skeletonema genus are ecologically important which may subsist during silicate stress and form a dense bloom following higher silicate concentration. However, our understanding of diatoms’ underlying molecular mechanism involved in these intracellular silicate stress-responses are limited. Here an iTRAQ-based proteomic method was coupled with multiple physiological techniques to explore distinct cellular responses associated with oxidative stress in the diatom Skeletonema dohrnii to the silicate limitation. In total, 1768 proteins were detected; 594 proteins were identified as differentially expressed (greater than a two-fold change; p < 0.05). In Si-limited cells, downregulated proteins were mainly related to photosynthesis metabolism, light-harvesting complex, and oxidative phosphorylation, corresponding to inducing oxidative stress, and ROS accumulation. None of these responses were identified in Si-limited cells; in comparing with other literature, Si-stress cells showed that ATP-limited diatoms are unable to rely on photosynthesis, which will break down and reshuffle carbon metabolism to compensate for photosynthetic carbon fixation losses. Our findings have a good correlation with earlier reports and provides a new molecular level insight into the systematic intracellular responses employed by diatoms in response to silicate stress in the marine environment. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

13 pages, 2870 KiB

Open AccessArticle

Transcriptomic Analysis of Leaf Sheath Maturation in Maize

by Lei Dong, Lei Qin, Xiuru Dai, Zehong Ding, Ran Bi, Peng Liu, Yanhui Chen, Thomas P. Brutnell, Xianglan Wang and Pinghua Li

Int. J. Mol. Sci. 2019, 20(10), 2472; https://doi.org/10.3390/ijms20102472 - 19 May 2019

Cited by 16 | Viewed by 5597

Abstract

The morphological development of the leaf greatly influences plant architecture and crop yields. The maize leaf is composed of a leaf blade, ligule and sheath. Although extensive transcriptional profiling of the tissues along the longitudinal axis of the developing maize leaf blade has [...] Read more.

The morphological development of the leaf greatly influences plant architecture and crop yields. The maize leaf is composed of a leaf blade, ligule and sheath. Although extensive transcriptional profiling of the tissues along the longitudinal axis of the developing maize leaf blade has been conducted, little is known about the transcriptional dynamics in sheath tissues, which play important roles in supporting the leaf blade. Using a comprehensive transcriptome dataset, we demonstrated that the leaf sheath transcriptome dynamically changes during maturation, with the construction of basic cellular structures at the earliest stages of sheath maturation with a transition to cell wall biosynthesis and modifications. The transcriptome again changes with photosynthesis and lignin biosynthesis at the last stage of sheath tissue maturation. The different tissues of the maize leaf are highly specialized in their biological functions and we identified 15 genes expressed at significantly higher levels in the leaf sheath compared with their expression in the leaf blade, including the BOP2 homologs GRMZM2G026556 and GRMZM2G022606, DOGT1 (GRMZM2G403740) and transcription factors from the B3 domain, C2H2 zinc finger and homeobox gene families, implicating these genes in sheath maturation and organ specialization. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

23 pages, 10121 KiB

Open AccessArticle

Metabolome and Transcriptome Association Analysis Reveals Dynamic Regulation of Purine Metabolism and Flavonoid Synthesis in Transdifferentiation during Somatic Embryogenesis in Cotton

by Huihui Guo, Haixia Guo, Li Zhang, Zhengmin Tang, Xiaoman Yu, Jianfei Wu and Fanchang Zeng

Int. J. Mol. Sci. 2019, 20(9), 2070; https://doi.org/10.3390/ijms20092070 - 26 Apr 2019

Cited by 74 | Viewed by 6409

Abstract

Plant regeneration via somatic embryogenesis (SE) is a key step during genetic engineering. In the current study, integrated widely targeted metabolomics and RNA sequencing were performed to investigate the dynamic metabolic and transcriptional profiling of cotton SE. Our data revealed that a total [...] Read more.

Plant regeneration via somatic embryogenesis (SE) is a key step during genetic engineering. In the current study, integrated widely targeted metabolomics and RNA sequencing were performed to investigate the dynamic metabolic and transcriptional profiling of cotton SE. Our data revealed that a total of 581 metabolites were present in nonembryogenic staged calli (NEC), primary embryogenic calli (PEC), and initiation staged globular embryos (GE). Of the differentially accumulated metabolites (DAMs), nucleotides, and lipids were specifically accumulated during embryogenic differentiation, whereas flavones and hydroxycinnamoyl derivatives were accumulated during somatic embryo development. Additionally, metabolites related to purine metabolism were significantly enriched in PEC vs. NEC, whereas in GE vs. PEC, DAMs were remarkably associated with flavonoid biosynthesis. An association analysis of the metabolome and transcriptome data indicated that purine metabolism and flavonoid biosynthesis were co-mapped based on the Kyoto encyclopedia of genes and genomes (KEGG) database. Moreover, purine metabolism-related genes associated with signal recognition, transcription, stress, and lipid binding were significantly upregulated. Moreover, several classic somatic embryogenesis (SE) genes were highly correlated with their corresponding metabolites that were involved in purine metabolism and flavonoid biosynthesis. The current study identified a series of potential metabolites and corresponding genes responsible for SE transdifferentiation, which provides a valuable foundation for a deeper understanding of the regulatory mechanisms underlying cell totipotency at the molecular and biochemical levels. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

14 pages, 3088 KiB

Open AccessArticle

Overexpression of a S-Adenosylmethionine Decarboxylase from Sugar Beet M14 Increased Araidopsis Salt Tolerance

by Meichao Ji, Kun Wang, Lin Wang, Sixue Chen, Haiying Li, Chunquan Ma and Yuguang Wang

Int. J. Mol. Sci. 2019, 20(8), 1990; https://doi.org/10.3390/ijms20081990 - 23 Apr 2019

Cited by 26 | Viewed by 4356

Abstract

Polyamines play an important role in plant growth and development, and response to abiotic stresses. Previously, differentially expressed proteins in sugar beet M14 (BvM14) under salt stress were identified by iTRAQ-based quantitative proteomics. One of the proteins was an S-adenosylmethionine decarboxylase [...] Read more.

Polyamines play an important role in plant growth and development, and response to abiotic stresses. Previously, differentially expressed proteins in sugar beet M14 (BvM14) under salt stress were identified by iTRAQ-based quantitative proteomics. One of the proteins was an S-adenosylmethionine decarboxylase (SAMDC), a key rate-limiting enzyme involved in the biosynthesis of polyamines. In this study, the BvM14-SAMDC gene was cloned from the sugar beet M14. The full-length BvM14-SAMDC was 1960 bp, and its ORF contained 1119 bp encoding the SAMDC of 372 amino acids. In addition, we expressed the coding sequence of BvM14-SAMDC in Escherichia coli and purified the ~40 kD BvM14-SAMDC with high enzymatic activity. Quantitative real-time PCR analysis revealed that the BvM14-SAMDC was up-regulated in the BvM14 roots and leaves under salt stress. To investigate the functions of the BvM14-SAMDC, it was constitutively expressed in Arabidopsis thaliana. The transgenic plants exhibited greater salt stress tolerance, as evidenced by longer root length and higher fresh weight and chlorophyll content than wild type (WT) under salt treatment. The levels of spermidine (Spd) and spermin (Spm) concentrations were increased in the transgenic plants as compared with the WT. Furthermore, the overexpression plants showed higher activities of antioxidant enzymes and decreased cell membrane damage. Compared with WT, they also had low expression levels of RbohD and RbohF, which are involved in reactive oxygen species (ROS) production. Together, these results suggest that the BvM14-SAMDC mediated biosynthesis of Spm and Spd contributes to plant salt stress tolerance through enhancing antioxidant enzymes and decreasing ROS generation. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

23 pages, 5873 KiB

Open AccessArticle

Phosphoproteomic Analysis of Two Contrasting Maize Inbred Lines Provides Insights into the Mechanism of Salt-Stress Tolerance

by Xiaoyun Zhao, Xue Bai, Caifu Jiang and Zhen Li

Int. J. Mol. Sci. 2019, 20(8), 1886; https://doi.org/10.3390/ijms20081886 - 16 Apr 2019

Cited by 37 | Viewed by 4469

Abstract

Salinity is a major abiotic stress that limits maize yield and quality throughout the world. We investigated phosphoproteomics differences between a salt-tolerant inbred line (Zheng58) and a salt-sensitive inbred line (Chang7-2) in response to short-term salt stress using label-free quantitation. A total of [...] Read more.

Salinity is a major abiotic stress that limits maize yield and quality throughout the world. We investigated phosphoproteomics differences between a salt-tolerant inbred line (Zheng58) and a salt-sensitive inbred line (Chang7-2) in response to short-term salt stress using label-free quantitation. A total of 9448 unique phosphorylation sites from 4116 phosphoproteins in roots and shoots of Zheng58 and Chang7-2 were identified. A total of 209 and 243 differentially regulated phosphoproteins (DRPPs) in response to NaCl treatment were detected in roots and shoots, respectively. Functional analysis of these DRPPs showed that they were involved in carbon metabolism, glutathione metabolism, transport, and signal transduction. Among these phosphoproteins, the expression of 6-phosphogluconate dehydrogenase 2, pyruvate dehydrogenase, phosphoenolpyruvate carboxykinase, glutamate decarboxylase, glutamate synthase, l-gulonolactone oxidase-like, potassium channel AKT1, high-affinity potassium transporter, sodium/hydrogen exchanger, and calcium/proton exchanger CAX1-like protein were significantly regulated in roots, while phosphoenolpyruvate carboxylase 1, phosphoenolpyruvate carboxykinase, sodium/hydrogen exchanger, plasma membrane intrinsic protein 2, glutathione transferases, and abscisic acid-insensitive 5-like protein were significantly regulated in shoots. Zheng58 may activate carbon metabolism, glutathione and ascorbic acid metabolism, potassium and sodium transportation, and the accumulation of glutamate to enhance its salt tolerance. Our results help to elucidate the mechanisms of salt response in maize seedlings. They also provide a basis for further study of the mechanism underlying salt response and tolerance in maize and other crops. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

34 pages, 5950 KiB

Open AccessArticle

Dynamic TMT-Based Quantitative Proteomics Analysis of Critical Initiation Process of Totipotency during Cotton Somatic Embryogenesis Transdifferentiation

by Haixia Guo, Huihui Guo, Li Zhang, Yijie Fan, Yupeng Fan, Zhengmin Tang and Fanchang Zeng

Int. J. Mol. Sci. 2019, 20(7), 1691; https://doi.org/10.3390/ijms20071691 - 4 Apr 2019

Cited by 18 | Viewed by 4217

Abstract

The somatic embryogenesis (SE) process of plants, as one of the typical responses to abiotic stresses with hormone, occurs through the dynamic expression of different proteins that constitute a complex regulatory network in biological activities and promotes plant totipotency. Plant SE includes two [...] Read more.

The somatic embryogenesis (SE) process of plants, as one of the typical responses to abiotic stresses with hormone, occurs through the dynamic expression of different proteins that constitute a complex regulatory network in biological activities and promotes plant totipotency. Plant SE includes two critical stages: primary embryogenic calli redifferentiation and somatic embryos development initiation, which leads to totipotency. The isobaric labels tandem mass tags (TMT) large-scale and quantitative proteomics technique was used to identify the dynamic protein expression changes in nonembryogenic calli (NEC), primary embryogenic calli (PEC) and globular embryos (GEs) of cotton. A total of 9369 proteins (6730 quantified) were identified; 805, 295 and 1242 differentially accumulated proteins (DAPs) were identified in PEC versus NEC, GEs versus PEC and GEs versus NEC, respectively. Eight hundred and five differentially abundant proteins were identified, 309 of which were upregulated and 496 down regulated in PEC compared with NEC. Of the 295 DAPs identified between GEs and PEC, 174 and 121 proteins were up- and down regulated, respectively. Of 1242 differentially abundant proteins, 584 and 658 proteins were up- and down regulated, respectively, in GEs versus NEC. We have also complemented the authenticity and accuracy of the proteomic analysis. Systematic analysis indicated that peroxidase, photosynthesis, environment stresses response processes, nitrogen metabolism, phytohormone response/signal transduction, transcription/posttranscription and modification were involved in somatic embryogenesis. The results generated in this study demonstrate a proteomic molecular basis and provide a valuable foundation for further investigation of the roles of DAPs in the process of SE transdifferentiation during cotton totipotency. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

18 pages, 4666 KiB

Open AccessArticle

Cytological and Proteomic Analysis of Wheat Pollen Abortion Induced by Chemical Hybridization Agent

by Shuping Wang, Yingxin Zhang, Zhengwu Fang, Yamin Zhang, Qilu Song, Zehao Hou, Kunkun Sun, Yulong Song, Ying Li, Dongfang Ma, Yike Liu, Zhanwang Zhu, Na Niu, Junwei Wang, Shoucai Ma and Gaisheng Zhang

Int. J. Mol. Sci. 2019, 20(7), 1615; https://doi.org/10.3390/ijms20071615 - 1 Apr 2019

Cited by 9 | Viewed by 4057

Abstract

In plants, pollen grain transfers the haploid male genetic material from anther to stigma, both between flowers (cross-pollination) and within the same flower (self-pollination). In order to better understand chemical hybridizing agent (CHA) SQ-1-induced pollen abortion in wheat, comparative cytological and proteomic analyses [...] Read more.

In plants, pollen grain transfers the haploid male genetic material from anther to stigma, both between flowers (cross-pollination) and within the same flower (self-pollination). In order to better understand chemical hybridizing agent (CHA) SQ-1-induced pollen abortion in wheat, comparative cytological and proteomic analyses were conducted. Results indicated that pollen grains underwent serious structural injury, including cell division abnormality, nutritional deficiencies, pollen wall defect and pollen grain malformations in the CHA-SQ-1-treated plants, resulting in pollen abortion and male sterility. A total of 61 proteins showed statistically significant differences in abundance, among which 18 proteins were highly abundant and 43 proteins were less abundant in CHA-SQ-1 treated plants. 60 proteins were successfully identified using MALDI-TOF/TOF mass spectrometry. These proteins were found to be involved in pollen maturation and showed a change in the abundance of a battery of proteins involved in multiple biological processes, including pollen development, carbohydrate and energy metabolism, stress response, protein metabolism. Interactions between these proteins were predicted using bioinformatics analysis. Gene ontology and pathway analyses revealed that the majority of the identified proteins were involved in carbohydrate and energy metabolism. Accordingly, a protein-protein interaction network involving in pollen abortion was proposed. These results provide information for the molecular events underlying CHA-SQ-1-induced pollen abortion and may serve as an additional guide for practical hybrid breeding. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

17 pages, 7867 KiB

Open AccessArticle

A Cotton (Gossypium hirsutum) Myo-Inositol-1-Phosphate Synthase (GhMIPS1D) Gene Promotes Root Cell Elongation in Arabidopsis

by Rendi Ma, Wangyang Song, Fei Wang, Aiping Cao, Shuangquan Xie, Xifeng Chen, Xiang Jin and Hongbin Li

Int. J. Mol. Sci. 2019, 20(5), 1224; https://doi.org/10.3390/ijms20051224 - 11 Mar 2019

Cited by 13 | Viewed by 4107

Abstract

Myo-inositol-1-phosphate synthase (MIPS, EC 5.5.1.4) plays important roles in plant growth and development, stress responses, and cellular signal transduction. MIPS genes were found preferably expressed during fiber cell initiation and early fast elongation in upland cotton (Gossypium hirsutum), however, current [...] Read more.

Myo-inositol-1-phosphate synthase (MIPS, EC 5.5.1.4) plays important roles in plant growth and development, stress responses, and cellular signal transduction. MIPS genes were found preferably expressed during fiber cell initiation and early fast elongation in upland cotton (Gossypium hirsutum), however, current understanding of the function and regulatory mechanism of MIPS genes to involve in cotton fiber cell growth is limited. Here, by genome-wide analysis, we identified four GhMIPS genes anchoring onto four chromosomes in G. hirsutum and analyzed their phylogenetic relationship, evolutionary dynamics, gene structure and motif distribution, which indicates that MIPS genes are highly conserved from prokaryotes to green plants, with further exon-intron structure analysis showing more diverse in Brassicales plants. Of the four GhMIPS members, based on the significant accumulated expression of GhMIPS1D at the early stage of fiber fast elongating development, thereby, the GhMIPS1D was selected to investigate the function of participating in plant development and cell growth, with ectopic expression in the loss-of-function Arabidopsis mips1 mutants. The results showed that GhMIPS1D is a functional gene to fully compensate the abnormal phenotypes of the deformed cotyledon, dwarfed plants, increased inflorescence branches, and reduced primary root lengths in Arabidopsis mips1 mutants. Furthermore, shortened root cells were recovered and normal root cells were significantly promoted by ectopic expression of GhMIPS1D in Arabidopsis mips1 mutant and wild-type plants respectively. These results serve as a foundation for understanding the MIPS family genes in cotton, and suggest that GhMIPS1D may function as a positive regulator for plant cell elongation. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

17 pages, 3425 KiB

Open AccessArticle

The Proteomic Analysis of Maize Endosperm Protein Enriched by Phos-tag^tm Reveals the Phosphorylation of Brittle-2 Subunit of ADP-Glc Pyrophosphorylase in Starch Biosynthesis Process

by Guowu Yu, Yanan Lv, Leiyang Shen, Yongbin Wang, Yun Qing, Nan Wu, Yangping Li, Huanhuan Huang, Na Zhang, Yinghong Liu, Yufeng Hu, Hanmei Liu, Junjie Zhang and Yubi Huang

Int. J. Mol. Sci. 2019, 20(4), 986; https://doi.org/10.3390/ijms20040986 - 24 Feb 2019

Cited by 19 | Viewed by 4487

Abstract

AGPase catalyzes a key rate-limiting step that converts ATP and Glc-1-p into ADP-glucose and diphosphate in maize starch biosynthesis. Previous studies suggest that AGPase is modulated by redox, thermal and allosteric regulation. However, the phosphorylation of AGPase is unclear in the kernel starch [...] Read more.

AGPase catalyzes a key rate-limiting step that converts ATP and Glc-1-p into ADP-glucose and diphosphate in maize starch biosynthesis. Previous studies suggest that AGPase is modulated by redox, thermal and allosteric regulation. However, the phosphorylation of AGPase is unclear in the kernel starch biosynthesis process. Phos-tag^TM technology is a novel method using phos-tag^TM agarose beads for separation, purification, and detection of phosphorylated proteins. Here we identified phos-tag^TM agarose binding proteins from maize endosperm. Results showed a total of 1733 proteins identified from 10,678 distinct peptides. Interestingly, a total of 21 unique peptides for AGPase sub-unit Brittle-2 (Bt2) were identified. Bt2 was demonstrated by immunoblot when enriched maize endosperm protein with phos-tag^TM agarose was in different pollination stages. In contrast, Bt2 would lose binding to phos-tag^TM when samples were treated with alkaline phosphatase (ALP). Furthermore, Bt2 could be detected by Pro-Q diamond staining specifically for phosphorylated protein. We further identified the phosphorylation sites of Bt2 at Ser¹⁰, Thr⁴⁵¹, and Thr⁴⁶² by iTRAQ. In addition, dephosphorylation of Bt2 decreased the activity of AGPase in the native gel assay through ALP treatment. Taking together, these results strongly suggest that the phosphorylation of AGPase may be a new model to regulate AGPase activity in the starch biosynthesis process. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

23 pages, 6749 KiB

Open AccessArticle

Root Proteomics Reveals the Effects of Wood Vinegar on Wheat Growth and Subsequent Tolerance to Drought Stress

by Yuying Wang, Ling Qiu, Qilu Song, Shuping Wang, Yajun Wang and Yihong Ge

Int. J. Mol. Sci. 2019, 20(4), 943; https://doi.org/10.3390/ijms20040943 - 21 Feb 2019

Cited by 48 | Viewed by 7375

Abstract

Wood vinegar (WV) or pyroligneous acid (PA) is a reddish-brown liquid created during the dry distillation of biomass, a process called pyrolysis. WV contains important biologically active components, which can enhance plant growth and tolerance to drought stress. However, its mechanism of action [...] Read more.

Wood vinegar (WV) or pyroligneous acid (PA) is a reddish-brown liquid created during the dry distillation of biomass, a process called pyrolysis. WV contains important biologically active components, which can enhance plant growth and tolerance to drought stress. However, its mechanism of action remains unknown. Our results after presoaking wheat seeds with various concentrations of WV indicate that a 1:900 WV concentration can significantly enhance growth. To investigate the response of wheat roots to drought stress, we compared quantitative proteomic profiles in the roots of wheat plants grown from seeds either presoaked (treatment) or non-presoaked (control) with WV. Our results indicated that the abscisic acid (ABA) content of wheat roots in the WV treatment was significantly increased. Reactive oxygen species (ROS) and malonaldehyde (MDA) levels roots were significantly lower than in the control treatment under drought stress, while the activity of major antioxidant enzymes was significantly increased. Two-dimensional electrophoresis (2D-PAGE) identified 138 differentially accumulated protein (DAP) spots representing 103 unique protein species responding to drought stress in wheat roots of the control and WV-treated groups. These DAPs are mostly involved in the stress response, carbohydrate metabolism, protein metabolism, and secondary metabolism. Proteome profiles showed the DAPs involved in carbohydrate metabolism, stress response, and secondary metabolism had increased accumulation in roots of the WV-treated groups. These findings suggest that the roots from wheat seeds presoaked with WV can initiate an early defense mechanism to mitigate drought stress. These results provide an explanation of how WV enhances the tolerance of wheat plants to drought stress. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

24 pages, 3703 KiB

Open AccessArticle

Proteomics Analysis of E. angustifolia Seedlings Inoculated with Arbuscular Mycorrhizal Fungi under Salt Stress

by Tingting Jia, Jian Wang, Wei Chang, Xiaoxu Fan, Xin Sui and Fuqiang Song

Int. J. Mol. Sci. 2019, 20(3), 788; https://doi.org/10.3390/ijms20030788 - 12 Feb 2019

Cited by 44 | Viewed by 6312

Abstract

To reveal the mechanism of salinity stress alleviation by arbuscular mycorrhizal fungi (AMF), we investigated the growth parameter, soluble sugar, soluble protein, and protein abundance pattern of E. angustifolia seedlings that were cultured under salinity stress (300 mmol/L NaCl) and inoculated by Rhizophagus [...] Read more.

To reveal the mechanism of salinity stress alleviation by arbuscular mycorrhizal fungi (AMF), we investigated the growth parameter, soluble sugar, soluble protein, and protein abundance pattern of E. angustifolia seedlings that were cultured under salinity stress (300 mmol/L NaCl) and inoculated by Rhizophagus irregularis (RI). Furthermore, a label-free quantitative proteomics approach was used to reveal the stress-responsive proteins in the leaves of E. angustifolia. The result indicates that the abundance of 75 proteins in the leaves was significantly influenced when E. angustifolia was inoculated with AMF, which were mainly involved in the metabolism, signal transduction, and reactive oxygen species (ROS) scavenging. Furthermore, we identified chorismate mutase, elongation factor mitochondrial, peptidyl-prolyl cis-trans isomerase, calcium-dependent kinase, glutathione S-transferase, glutathione peroxidase, NADH dehydrogenase, alkaline neutral invertase, peroxidase, and other proteins closely related to the salt tolerance process. The proteomic results indicated that E. angustifolia seedlings inoculated with AMF increased the secondary metabolism level of phenylpropane metabolism, enhanced the signal transduction of Ca²⁺ and ROS scavenging ability, promoted the biosynthesis of protein, accelerated the protein folding, and inhibited the degradation of protein under salt stress. Moreover, AMF enhanced the synthesis of ATP and provided sufficient energy for plant cell activity. This study implied that symbiosis of halophytes and AMF has potential as an application for the improvement of saline-alkali soils. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

14 pages, 1993 KiB

Open AccessArticle

Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis

by Yuan Wang, Yuting Cong, Yonghua Wang, Zihu Guo, Jinrong Yue, Zhenyu Xing, Xiangnan Gao and Xiaojie Chai

Int. J. Mol. Sci. 2019, 20(3), 599; https://doi.org/10.3390/ijms20030599 - 30 Jan 2019

Cited by 26 | Viewed by 4246

Abstract

Salt stress is one of the most serious abiotic factors that inhibit plant growth. Dunaliella salina has been recognized as a model organism for stress response research due to its high capacity to tolerate extreme salt stress. A proteomic approach based on isobaric [...] Read more.

Salt stress is one of the most serious abiotic factors that inhibit plant growth. Dunaliella salina has been recognized as a model organism for stress response research due to its high capacity to tolerate extreme salt stress. A proteomic approach based on isobaric tags for relative and absolute quantitation (iTRAQ) was used to analyze the proteome of D. salina during early response to salt stress and identify the differentially abundant proteins (DAPs). A total of 141 DAPs were identified in salt-treated samples, including 75 upregulated and 66 downregulated DAPs after 3 and 24 h of salt stress. DAPs were annotated and classified into gene ontology functional groups. The Kyoto Encyclopedia of Genes and Genomes pathway analysis linked DAPs to tricarboxylic acid cycle, photosynthesis and oxidative phosphorylation. Using search tool for the retrieval of interacting genes (STRING) software, regulatory protein–protein interaction (PPI) networks of the DAPs containing 33 and 52 nodes were built at each time point, which showed that photosynthesis and ATP synthesis were crucial for the modulation of early salinity-responsive pathways. The corresponding transcript levels of five DAPs were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). These results presented an overview of the systematic molecular response to salt stress. This study revealed a complex regulatory mechanism of early salt tolerance in D. salina and potentially contributes to developing strategies to improve stress resilience. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

18 pages, 2393 KiB

Open AccessArticle

Physiological Analysis and Proteome Quantification of Alligator Weed Stems in Response to Potassium Deficiency Stress

by Li-Qin Li, Cheng-Cheng Lyu, Jia-Hao Li, Zhu Tong, Yi-Fei Lu, Xi-Yao Wang, Su Ni, Shi-Min Yang, Fu-Chun Zeng and Li-Ming Lu

Int. J. Mol. Sci. 2019, 20(1), 221; https://doi.org/10.3390/ijms20010221 - 8 Jan 2019

Cited by 15 | Viewed by 5046

Abstract

The macronutrient potassium is essential to plant growth, development and stress response. Alligator weed (Alternanthera philoxeroides) has a high tolerance to potassium deficiency (LK) stress. The stem is the primary organ responsible for transporting molecules from the underground root system to [...] Read more.

The macronutrient potassium is essential to plant growth, development and stress response. Alligator weed (Alternanthera philoxeroides) has a high tolerance to potassium deficiency (LK) stress. The stem is the primary organ responsible for transporting molecules from the underground root system to the aboveground parts of the plant. However, proteomic changes in response to LK stress are largely unknown in alligator weed stems. In this study, we investigated the physiological and proteomic changes in alligator weed stems under LK stress. First, the chlorophyll and soluble protein content and SOD and POD activity were significantly altered after 15 days of LK treatment. The quantitative proteomic analysis suggested that a total of 296 proteins were differentially abundant proteins (DAPs). The functional annotation analysis revealed that LK stress elicited complex proteomic alterations that were involved in oxidative phosphorylation, plant-pathogen interactions, glycolysis/gluconeogenesis, sugar metabolism, and transport in stems. The subcellular locations analysis suggested 104 proteins showed chloroplastic localization, 81 proteins showed cytoplasmic localization and 40 showed nuclear localization. The protein–protein interaction analysis revealed that 56 proteins were involved in the interaction network, including 9 proteins involved in the ribosome network and 9 in the oxidative phosphorylation network. Additionally, the expressed changes of 5 DAPs were similar between the proteomic quantification analysis and the PRM-MS analysis, and the expression levels of eight genes that encode DAPs were further verified using an RT-qPCR analysis. These results provide valuable information on the adaptive mechanisms in alligator weed stems under LK stress and facilitate the development of efficient strategies for genetically engineering potassium-tolerant crops. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

27 pages, 26798 KiB

Open AccessArticle

Global Phosphoproteomic Analysis Reveals the Defense and Response Mechanisms of Jatropha Curcas Seedling under Chilling Stress

by Hui Liu, Fen-Fen Wang, Xian-Jun Peng, Jian-Hui Huang and Shi-Hua Shen

Int. J. Mol. Sci. 2019, 20(1), 208; https://doi.org/10.3390/ijms20010208 - 8 Jan 2019

Cited by 11 | Viewed by 5112

Abstract

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub and its growth is affected by one of major abiotic stress, chilling. Therefore, we adopt the phosphoproteomic analysis, physiological measurement and ultrastructure observation to illustrate the responsive mechanism [...] Read more.

As a promising energy plant for biodiesel, Jatropha curcas is a tropical and subtropical shrub and its growth is affected by one of major abiotic stress, chilling. Therefore, we adopt the phosphoproteomic analysis, physiological measurement and ultrastructure observation to illustrate the responsive mechanism of J. curcas seedling under chilling (4 °C) stress. After chilling for 6 h, 308 significantly changed phosphoproteins were detected. Prolonged the chilling treatment for 24 h, obvious physiological injury can be observed and a total of 332 phosphoproteins were examined to be significantly changed. After recovery (28 °C) for 24 h, 291 phosphoproteins were varied at the phosphorylation level. GO analysis showed that significantly changed phosphoproteins were mainly responsible for cellular protein modification process, transport, cellular component organization and signal transduction at the chilling and recovery periods. On the basis of protein-protein interaction network analysis, phosphorylation of several protein kinases, such as SnRK2, MEKK1, EDR1, CDPK, EIN2, EIN4, PI4K and 14-3-3 were possibly responsible for cross-talk between ABA, Ca²⁺, ethylene and phosphoinositide mediated signaling pathways. We also highlighted the phosphorylation of HOS1, APX and PIP2 might be associated with response to chilling stress in J. curcas seedling. These results will be valuable for further study from the molecular breeding perspective. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

16 pages, 2239 KiB

Open AccessArticle

Identification of Two Novel Wheat Drought Tolerance-Related Proteins by Comparative Proteomic Analysis Combined with Virus-Induced Gene Silencing

by Xinbo Wang, Yanhua Xu, Jingjing Li, Yongzhe Ren, Zhiqiang Wang, Zeyu Xin and Tongbao Lin

Int. J. Mol. Sci. 2018, 19(12), 4020; https://doi.org/10.3390/ijms19124020 - 12 Dec 2018

Cited by 15 | Viewed by 4256

Abstract

Drought is a major adversity that limits crop yields. Further exploration of wheat drought tolerance-related genes is critical for the genetic improvement of drought tolerance in this crop. Here, comparative proteomic analysis of two wheat varieties, XN979 and LA379, with contrasting drought tolerance [...] Read more.

Drought is a major adversity that limits crop yields. Further exploration of wheat drought tolerance-related genes is critical for the genetic improvement of drought tolerance in this crop. Here, comparative proteomic analysis of two wheat varieties, XN979 and LA379, with contrasting drought tolerance was conducted to screen for drought tolerance-related proteins/genes. Virus-induced gene silencing (VIGS) technology was used to verify the functions of candidate proteins. A total of 335 differentially abundant proteins (DAPs) were exclusively identified in the drought-tolerant variety XN979. Most DAPs were mainly involved in photosynthesis, carbon fixation, glyoxylate and dicarboxylate metabolism, and several other pathways. Two DAPs (W5DYH0 and W5ERN8), dubbed TaDrSR1 and TaDrSR2, respectively, were selected for further functional analysis using VIGS. The relative electrolyte leakage rate and malonaldehyde content increased significantly, while the relative water content and proline content significantly decreased in the TaDrSR1- and TaDrSR2-knock-down plants compared to that in non-knocked-down plants under drought stress conditions. TaDrSR1- and TaDrSR2-knock-down plants exhibited more severe drooping and wilting phenotypes than non-knocked-down plants under drought stress conditions, suggesting that the former were more sensitive to drought stress. These results indicate that TaDrSR1 and TaDrSR2 potentially play vital roles in conferring drought tolerance in common wheat. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

19 pages, 5632 KiB

Open AccessArticle

Comparative Proteomic Analysis during the Involvement of Nitric Oxide in Hydrogen Gas-Improved Postharvest Freshness in Cut Lilies

by Jianqiang Huo, Dengjing Huang, Jing Zhang, Hua Fang, Bo Wang, Chunlei Wang, Zhanjun Ma and Weibiao Liao

Int. J. Mol. Sci. 2018, 19(12), 3955; https://doi.org/10.3390/ijms19123955 - 9 Dec 2018

Cited by 25 | Viewed by 3802

Abstract

Our previous studies suggested that both hydrogen gas (H₂) and nitric oxide (NO) could enhance the postharvest freshness of cut flowers. However, the crosstalk of H₂ and NO during that process is unknown. Here, cut lilies (Lilium “Manissa”) were [...] Read more.

Our previous studies suggested that both hydrogen gas (H₂) and nitric oxide (NO) could enhance the postharvest freshness of cut flowers. However, the crosstalk of H₂ and NO during that process is unknown. Here, cut lilies (Lilium “Manissa”) were used to investigate the relationship between H₂ and NO and to identify differentially accumulated proteins during postharvest freshness. The results revealed that 1% hydrogen-rich water (HRW) and 150 μM sodium nitroprusside (SNP) significantly extended the vase life and quality, while NO inhibitors suppressed the positive effects of HRW. Proteomics analysis found 50 differentially accumulated proteins in lilies leaves which were classified into seven functional categories. Among them, ATP synthase CF1 alpha subunit (chloroplast) (AtpA) was up-regulated by HRW and down-regulated by NO inhibitor. The expression level of LlatpA gene was consistent with the result of proteomics analysis. The positive effect of HRW and SNP on ATP synthase activity was inhibited by NO inhibitor. Meanwhile, the physiological-level analysis of chlorophyll fluorescence and photosynthetic parameters also agreed with the expression of AtpA regulated by HRW and SNP. Altogether, our results suggested that NO might be involved in H₂-improved freshness of cut lilies, and AtpA protein may play important roles during that process. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research

15 pages, 1046 KiB

Open AccessReview

The Function of Inositol Phosphatases in Plant Tolerance to Abiotic Stress

by Qi Jia, Defeng Kong, Qinghua Li, Song Sun, Junliang Song, Yebao Zhu, Kangjing Liang, Qingming Ke, Wenxiong Lin and Jinwen Huang

Int. J. Mol. Sci. 2019, 20(16), 3999; https://doi.org/10.3390/ijms20163999 - 16 Aug 2019

Cited by 71 | Viewed by 9390

Abstract

Inositol signaling is believed to play a crucial role in various aspects of plant growth and adaptation. As an important component in biosynthesis and degradation of myo-inositol and its derivatives, inositol phosphatases could hydrolyze the phosphate of the inositol ring, thus affecting [...] Read more.

Inositol signaling is believed to play a crucial role in various aspects of plant growth and adaptation. As an important component in biosynthesis and degradation of myo-inositol and its derivatives, inositol phosphatases could hydrolyze the phosphate of the inositol ring, thus affecting inositol signaling. Until now, more than 30 members of inositol phosphatases have been identified in plants, which are classified intofive families, including inositol polyphosphate 5-phosphatases (5PTases), suppressor of actin (SAC) phosphatases, SAL1 phosphatases, inositol monophosphatase (IMP), and phosphatase and tensin homologue deleted on chromosome 10 (PTEN)-related phosphatases. The current knowledge was revised here in relation to their substrates and function in response to abiotic stress. The potential mechanisms were also concluded with the focus on their activities of inositol phosphatases. The general working model might be that inositol phosphatases would degrade the Ins(1,4,5)P₃ or phosphoinositides, subsequently resulting in altering Ca²⁺ release, abscisic acid (ABA) signaling, vesicle trafficking or other cellular processes. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Figure 1

13 pages, 1448 KiB

Open AccessReview

The Latest Studies on Lotus (Nelumbo nucifera)-an Emerging Horticultural Model Plant

by Zhongyuan Lin, Cheng Zhang, Dingding Cao, Rebecca Njeri Damaris and Pingfang Yang

Int. J. Mol. Sci. 2019, 20(15), 3680; https://doi.org/10.3390/ijms20153680 - 27 Jul 2019

Cited by 74 | Viewed by 12281

Abstract

Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and [...] Read more.

Lotus (Nelumbo nucifera) is a perennial aquatic basal eudicot belonging to a small family Nelumbonaceace, which contains only one genus with two species. It is an important horticultural plant, with its uses ranging from ornamental, nutritional to medicinal values, and has been widely used, especially in Southeast Asia. Recently, the lotus obtained a lot of attention from the scientific community. An increasing number of research papers focusing on it have been published, which have shed light on the mysteries of this species. Here, we comprehensively reviewed the latest advancement of studies on the lotus, including phylogeny, genomics and the molecular mechanisms underlying its unique properties, its economic important traits, and so on. Meanwhile, current limitations in the research of the lotus were addressed, and the potential prospective were proposed as well. We believe that the lotus will be an important model plant in horticulture with the generation of germplasm suitable for laboratory operation and the establishment of a regeneration and transformation system. Full article

(This article belongs to the Special Issue Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses)

► Show Figures

Graphical abstract

Journal Menu

Journal Browser

Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (28 papers)

Editorial

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI