1
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Kang J, David L, Li Y, Cang J, Chen S. Three-in-One Simultaneous Extraction of Proteins, Metabolites and Lipids for Multi-Omics. Front Genet 2021; 12:635971. [PMID: 33936167 PMCID: PMC8082496 DOI: 10.3389/fgene.2021.635971] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022] Open
Abstract
Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics, and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical properties. Therefore, several sets/aliquots of samples are needed for extracting different molecules. Here we adapted a biphasic fractionation method to extract proteins, metabolites, and lipids from the same sample (3-in-1) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) multi-omics. To demonstrate utility of the improved method, we used bacteria-primed Arabidopsis leaves to generate multi-omics datasets from the same sample. In total, we were able to analyze 1849 proteins, 1967 metabolites, and 424 lipid species in single samples. The molecules cover a wide range of biological and molecular processes, and allow quantitative analyses of different molecules and pathways. Our results have shown the clear advantages of the multi-omics method, including sample conservation, high reproducibility, and tight correlation between different types of biomolecules.
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Affiliation(s)
- Jianing Kang
- College of Life Science, Northeast Agricultural University, Harbin, China.,Department of Biology, University of Florida, Gainesville, FL, United States.,University of Florida Genetics Institute, Gainesville, FL, United States
| | - Lisa David
- Department of Biology, University of Florida, Gainesville, FL, United States.,University of Florida Genetics Institute, Gainesville, FL, United States
| | - Yangyang Li
- Department of Biology, University of Florida, Gainesville, FL, United States.,College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jing Cang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL, United States.,University of Florida Genetics Institute, Gainesville, FL, United States.,Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
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2
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Iannetta AA, Rogers HT, Al-Mohanna T, O'Brien JN, Wommack AJ, Popescu SC, Hicks LM. Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:336-350. [PMID: 33481299 DOI: 10.1111/tpj.15165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Protein homeostasis (proteostasis) is crucial for proper cellular function, including the production of peptides with biological functions through controlled proteolysis. Proteostasis has roles in maintenance of cellular functions and plant interactions with the environment under physiological conditions. Plant stress continues to reduce agricultural yields causing substantial economic losses; thus, it is critical to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) TOP1 (also referred to as organellar oligopeptidase) and TOP2 (also referred to as cytosolic oligopeptidase) are essential components in plant response to pathogens, but further characterization of TOPs and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Herein, label-free peptidomics via liquid chromatography-tandem mass spectrometry was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays with recombinant TOPs and synthetic candidate peptides. These TOP substrates are derived from proteins involved in photosynthesis, glycolysis, protein folding, biogenesis, and antioxidant defense, implicating TOP involvement in processes aside from defense signaling. Sequence motif analysis revealed TOP cleavage preference for non-polar residues in the positions surrounding the cleavage site. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.
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Affiliation(s)
- Anthony A Iannetta
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holden T Rogers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | | | - Andrew J Wommack
- Department of Chemistry, High Point University, High Point, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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3
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Zhou J, Wang Z, Mao Y, Wang L, Xiao T, Hu Y, Zhang Y, Ma Y. Proteogenomic analysis of pitaya reveals cold stress-related molecular signature. PeerJ 2020; 8:e8540. [PMID: 32095361 PMCID: PMC7020823 DOI: 10.7717/peerj.8540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 01/09/2020] [Indexed: 11/20/2022] Open
Abstract
Pitayas (Hylocereus spp.) is an attractive, highly nutritious and commercially valuable tropical fruit. However, low-temperature damage limits crop production. Genome of pitaya has not been sequenced yet. In this study, we sequenced the transcriptome of pitaya as the reference and further investigated the proteome under low temperature. By RNAseq technique, approximately 25.3 million reads were obtained, and further trimmed and assembled into 81,252 unigene sequences. The unigenes were searched against UniProt, NR and COGs at NCBI, Pfam, InterPro and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and 57,905 unigenes were retrieved annotations. Among them, 44,337 coding sequences were predicted by Trandecoder (v2.0.1), which served as the reference database for label-free proteomic analysis study of pitaya. Here, we identified 116 Differentially Abundant Proteins (DAPs) associated with the cold stress in pitaya, of which 18 proteins were up-regulated and 98 proteins were down-regulated. KEGG analysis and other results showed that these DAPs mainly related to chloroplasts and mitochondria metabolism. In summary, chloroplasts and mitochondria metabolism-related proteins may play an important role in response to cold stress in pitayas.
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Affiliation(s)
- Junliang Zhou
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Zhuang Wang
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yongya Mao
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Lijuan Wang
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Tujian Xiao
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Yang Hu
- Zhejiang Academy of Forestry, Hangzhou, Zhejiang, China.,Zhejiang Provincial Key Laboratory of Biological and Chemical Utilization of Forest Resources, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Fudan University, Institutes of Biomedical Sciences, Shanghai, Shanghai, China
| | - Yuhua Ma
- Guizhou Institute of Pomological Sciences, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
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4
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Li Y, Feng Y, Lü Q, Yan D, Liu Z, Zhang X. Comparative Proteomic Analysis of Plant-Pathogen Interactions in Resistant and Susceptible Poplar Ecotypes Infected with Botryosphaeria dothidea. PHYTOPATHOLOGY 2019; 109:2009-2021. [PMID: 31369364 DOI: 10.1094/phyto-12-18-0452-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Poplar are important forestry species in China, but the Botryosphaeria dothidea pathogen causes serious economic losses worldwide. To identify candidate B. dothidea resistance proteins and explore the molecular mechanisms involved in poplar-pathogen interactions, proteomic responses of stem samples from resistant and susceptible poplar ecotypes to B. dothidea were investigated using nanoflow liquid chromatography-tandem mass spectrometry with label-free quantitative analysis. We identified 588 proteins, divided into 21 biological process categories including 48 oxidoreductases, 72 hydrolytic enzymes, 80 metabolic enzymes, and 29 proteins of unknown function. Differential proteome analysis revealed large differences between resistant Populus tomentosa Carr and susceptible Populus beijingensis Hsu ecotypes before and after inoculation. Among 102 identified proteins, 22 were highly upregulated in the resistant genotype but downregulated in the susceptible genotype. Proteins induced in P. tomentosa Carr in response to B. dothidea are associated with plant defenses including oxidoreductase activity (catalase, isocitrate dehydrogenase, and superoxide dismutase), phenylpropanoid biosynthesis and phenylalanine metabolism (alcohol dehydrogenase), photosynthesis (ATP synthase subunit alpha, ATP synthase gamma chain, photosystem I P700 chlorophyll a apoprotein A2, photosystem II CP47 chlorophyll apoprotein), carbon fixation (pyruvate kinase, triosephosphate isomerase, malic enzyme, phosphoglycerate kinase, ribulose-1,5-bisphosphate carboxylase, and ribulose bisphosphate carboxylase small chain), and glycolysis/gluconeogenesis (fructose-bisphosphate aldolase). Kyoto Encyclopedia of Genes and Genomes pathway analysis identified 168 proteins related to metabolic pathways, 41 proteins related to the biosynthesis of phenylpropanoids, and 36 proteins related to the biosynthesis of plant hormones, the biosynthesis of alkaloids derived from ornithine, lysine, and nicotinic acid, and photosynthesis in response to B. dothidea. Our findings provide insight into plant-pathogen interactions in resistant and susceptible poplar ecotypes infected with B. dothidea and could assist the development of novel strategies for fighting poplar canker disease.
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Affiliation(s)
- Yongxia Li
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yuqian Feng
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Quan Lü
- Key Laboratory of Forest Protection, State Forestry Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Donghui Yan
- Key Laboratory of Forest Protection, State Forestry Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhenyu Liu
- College of Plant Protection, Shandong Agricultural University, Tai-an 271018, China
| | - Xingyao Zhang
- Laboratory of Forest Pathogen Integrated Biology, Research Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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5
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Souza PFN, Garcia-Ruiz H, Carvalho FEL. What proteomics can reveal about plant-virus interactions? Photosynthesis-related proteins on the spotlight. THEORETICAL AND EXPERIMENTAL PLANT PHYSIOLOGY 2019; 31:227-248. [PMID: 31355128 PMCID: PMC6660014 DOI: 10.1007/s40626-019-00142-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plant viruses are responsible for losses in worldwide production of numerous economically important food and fuel crops. As obligate cellular parasites with very small genomes, viruses rely on their hosts for replication, assembly, intra- and intercellular movement, and attraction of vectors for dispersal. Chloroplasts are photosynthesis and are the site of replication for several viruses. When viruses replicate in chloroplasts, photosynthesis, an essential process in plant physiology, is inhibited. The mechanisms underlying molecular and biochemical changes during compatible and incompatible plants-virus interactions, are only beginning to be elucidated, including changes in proteomic profiles induced by virus infections. In this review, we highlight the importance of proteomic studies to understand plant-virus interactions, especially emphasizing the changes in photosynthesis-related protein accumulation. We focus on: (a) chloroplast proteins that differentially accumulate during viral infection; (b) the significance with respect to chloroplast-virus interaction; and (c) alterations in plant's energetic metabolism and the subsequently the plant defense mechanisms to overcome viral infection.
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Affiliation(s)
- Pedro F N Souza
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Fabricio E L Carvalho
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
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6
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Kallamadi PR, Dandu K, Kirti PB, Rao CM, Thakur SS, Mulpuri S. An Insight into Powdery Mildew-Infected, Susceptible, Resistant, and Immune Sunflower Genotypes. Proteomics 2018; 18:e1700418. [DOI: 10.1002/pmic.201700418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/26/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Prathap Reddy Kallamadi
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
- University of Hyderabad; Prof. C.R. Rao Road 500 046 Hyderabad India
| | - Kamakshi Dandu
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | | | - Chintalagiri Mohan Rao
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Suman S Thakur
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Sujatha Mulpuri
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
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7
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Pang M, Bai XY, Li Y, Bai JZ, Yuan LR, Ren SA, Hu XY, Zhang XR, Yu BF, Guo R, Wang HL. Label-free LC-MS/MS shotgun proteomics to investigate the anti-inflammatory effect of rCC16. Mol Med Rep 2016; 14:4496-4504. [PMID: 27748820 PMCID: PMC5101986 DOI: 10.3892/mmr.2016.5841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 08/18/2016] [Indexed: 12/30/2022] Open
Abstract
Clara cell protein (CC16) is an anti-inflammatory protein, which is expressed in the airway epithelium. It is involved in the development of airway inflammatory diseases, including chronic obstructive pulmonary disease and asthma. However, the exact molecular mechanism underlying its anti‑inflammatory action remains to be fully elucidated. The aim of the present study was to define the protein profiles of the anti‑inflammatory effect of CC16 in lipopolysaccharide (LPS)‑treated rat tracheal epithelial (RTE) cells using shotgun proteomics. Protein extracts were obtained from control RTE cells, RTE cells treated with LPS and RTE cells treated with LPS and recombinant CC16 (rCC16). Subsequent label‑free quantification and bioinformatics analyses identified 12 proteins that were differentially expressed in the three treatment groups as a cluster of five distinct groups according to their molecular functions. Five of the twelve proteins were revealed to be associated with the cytoskeleton: Matrix metalloproteinase‑9, myosin heavy chain 10, actin‑related protein‑3 homolog, elongation factor 1‑α‑1 (EF‑1‑α‑1), and acidic ribosomal phosphoprotein P0. Five of the twelve proteins were associated with cellular proliferation: DNA‑dependent protein kinase catalytic subunit, EF‑1‑α‑1, tyrosine 3‑monooxygenase, caspase recruitment domain (CARD) protein 12 and adenosylhomocysteinase (SAHH) 3. Three proteins were associated with gene regulation: EF‑1‑α‑1, SAHH 3 and acidic ribosomal phosphoprotein P0. Three proteins were associated with inflammation: Tyrosine 3‑monooxygenase, CARD protein 12 and statin‑related protein. ATPase (H+‑transporting, V1 subunit A, isoform 1) was revealed to be associated with energy metabolism, and uridine diphosphate glycosyltransferase 1 family polypeptide A8 with drug metabolism and detoxification. The identified proteins were further validated using reverse transcription‑quantitative polymerase chain reaction. These protein profiles, and their interacting protein network, may facilitate the elucidation of the molecular mechanisms underlying the anti‑inflammatory effects of CC16.
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Affiliation(s)
- Min Pang
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xin-Yan Bai
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Yan Li
- Fan‑Xing Biological Technology Co., Ltd., Beijing 010000, P.R. China
| | - Ji-Zhong Bai
- Department of Physiology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Li-Rong Yuan
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Shou-An Ren
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xiao-Yun Hu
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xin-Ri Zhang
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Bao-Feng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Rui Guo
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Hai-Long Wang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
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8
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Mahadevan C, Krishnan A, Saraswathy GG, Surendran A, Jaleel A, Sakuntala M. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem. FRONTIERS IN PLANT SCIENCE 2016; 7:785. [PMID: 27379110 PMCID: PMC4913111 DOI: 10.3389/fpls.2016.00785] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/22/2016] [Indexed: 05/22/2023]
Abstract
Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887.
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Affiliation(s)
| | - Anu Krishnan
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Gayathri G. Saraswathy
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Arun Surendran
- Proteomics Core Facility, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Abdul Jaleel
- Proteomics Core Facility, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Manjula Sakuntala
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
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9
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Mahadevan C, Jaleel A, Deb L, Thomas G, Sakuntala M. Development of an Efficient Virus Induced Gene Silencing Strategy in the Non-Model Wild Ginger-Zingiber zerumbet and Investigation of Associated Proteome Changes. PLoS One 2015; 10:e0124518. [PMID: 25918840 PMCID: PMC4412686 DOI: 10.1371/journal.pone.0124518] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/15/2015] [Indexed: 12/25/2022] Open
Abstract
Zingiber zerumbet (Zingiberaceae) is a wild, tropical medicinal herb that shows a high degree of resistance to diseases affecting cultivated ginger. Barley stripe mosaic virus (BSMV) silencing vectors containing an endogenous phytoene desaturase (PDS) gene fragment were agroinfiltrated into young leaves of Z. zerumbet under controlled growth conditions to effect virus-induced gene silencing (VIGS). Infiltrated leaves as well as newly emerged leaves and tillers showed visual signs of PDS silencing after 30 days. Replication and systemic movement of the viral vectors in silenced plants were confirmed by RT-PCR. Real-time quantitative PCR analysis verified significant down-regulation of PDS transcripts in the silenced tissues. Label-free proteomic analysis was conducted in leaves with established PDS transcript down regulation and buffer-infiltrated (mock) leaves. A total of 474 proteins were obtained, which were up-regulated, down-regulated or modulated de novo during VIGS. Most of these proteins were localized to the chloroplast, as revealed by UniprotKB analysis, and among the up-regulated proteins there were abiotic stress responsive, photosynthetic, metabolic and membrane proteins. Moreover, the demonstration of viral proteins together with host proteins proved successful viral infection. We report for the first time the establishment of a high-throughput gene functional analysis platform using BSMV-mediated VIGS in Z. zerumbet, as well as proteomic changes associated with VIGS.
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Affiliation(s)
- Chidambareswaren Mahadevan
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala State, India-695014
| | - Abdul Jaleel
- Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala State, India-695014
| | - Lokesh Deb
- Institute of Bioresources and Sustainable Development, Imphal, Manipur, India-795001
| | - George Thomas
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala State, India-695014
| | - Manjula Sakuntala
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala State, India-695014
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10
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Fang X, Chen J, Dai L, Ma H, Zhang H, Yang J, Wang F, Yan C. Proteomic dissection of plant responses to various pathogens. Proteomics 2015; 15:1525-43. [DOI: 10.1002/pmic.201400384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/28/2014] [Accepted: 01/12/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Xianping Fang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jianping Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Liangying Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
| | - Huasheng Ma
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Fang Wang
- Laboratory of Biotechnology; Institute of Biotechnology; Ningbo Academy of Agricultural Sciences; Ningbo P. R. China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
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11
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Engineer CB, Ghassemian M, Anderson JC, Peck SC, Hu H, Schroeder JI. Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development. Nature 2014; 513:246-50. [PMID: 25043023 PMCID: PMC4274335 DOI: 10.1038/nature13452] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 05/06/2014] [Indexed: 12/31/2022]
Abstract
Environmental stimuli, including elevated carbon dioxide levels, regulate stomatal development; however, the key mechanisms mediating the perception and relay of the CO2 signal to the stomatal development machinery remain elusive. To adapt CO2 intake to water loss, plants regulate the development of stomatal gas exchange pores in the aerial epidermis. A diverse range of plant species show a decrease in stomatal density in response to the continuing rise in atmospheric CO2 (ref. 4). To date, one mutant that exhibits deregulation of this CO2-controlled stomatal development response, hic (which is defective in cell-wall wax biosynthesis, ref. 5), has been identified. Here we show that recently isolated Arabidopsis thaliana β-carbonic anhydrase double mutants (ca1 ca4) exhibit an inversion in their response to elevated CO2, showing increased stomatal development at elevated CO2 levels. We characterized the mechanisms mediating this response and identified an extracellular signalling pathway involved in the regulation of CO2-controlled stomatal development by carbonic anhydrases. RNA-seq analyses of transcripts show that the extracellular pro-peptide-encoding gene EPIDERMAL PATTERNING FACTOR 2 (EPF2), but not EPF1 (ref. 9), is induced in wild-type leaves but not in ca1 ca4 mutant leaves at elevated CO2 levels. Moreover, EPF2 is essential for CO2 control of stomatal development. Using cell-wall proteomic analyses and CO2-dependent transcriptomic analyses, we identified a novel CO2-induced extracellular protease, CRSP (CO2 RESPONSE SECRETED PROTEASE), as a mediator of CO2-controlled stomatal development. Our results identify mechanisms and genes that function in the repression of stomatal development in leaves during atmospheric CO2 elevation, including the carbonic-anhydrase-encoding genes CA1 and CA4 and the secreted protease CRSP, which cleaves the pro-peptide EPF2, in turn repressing stomatal development. Elucidation of these mechanisms advances the understanding of how plants perceive and relay the elevated CO2 signal and provides a framework to guide future research into how environmental challenges can modulate gas exchange in plants.
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Affiliation(s)
- Cawas B Engineer
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Jeffrey C Anderson
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Scott C Peck
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Honghong Hu
- 1] Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA [2] College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Julian I Schroeder
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
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Wang H, Li Y, Yang L, Yu B, Yan P, Pang M, Li X, Yang H, Zheng G, Xie J, Guo R. Mass spectrometry-based, label-free quantitative proteomics of round spermatids in mice. Mol Med Rep 2014; 10:2009-24. [PMID: 25109358 PMCID: PMC4148364 DOI: 10.3892/mmr.2014.2460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 01/17/2023] Open
Abstract
Round haploid spermatids are formed at the completion of meiosis. These spermatids then undergo morphological and cytological changes during spermiogenesis. Although sperm proteomes have been extensively studied, relatively few studies have specifically investigated the proteome of round spermatids. We developed a label-free quantitative method in combination with 2D-nano-LC-ESI-MS/MS to investigate the proteome of round spermatids in mice. Analysis of the proteomic data identified 2,331 proteins in the round spermatids. Functional classification of the proteins based on Gene Ontology terms and enrichment analysis further revealed the following: 504 of the identified proteins are predicted to be involved in the generation of precursor metabolites and energy; 343 proteins in translation and protein targeting; 298 proteins in nucleotide and nucleic acid metabolism; 275 and 289 proteins in transport and cellular component organization, respectively. A number of the identified proteins were associated with cytoskeleton organization (183), protein degradation (116) and response to stimulus (115). KEGG pathway analysis identified 68 proteins that are annotated as components of the ribosomal pathway and 17 proteins were related to aminoacyl-tRNA biosynthesis. The round spermatids also contained 28 proteins involved in the proteasome pathway and 40 proteins in the lysosome pathway. A total of 60 proteins were annotated as parts of the spliceosome pathway, in which heterogeneous nuclear RNA is converted to mRNA. Approximately 94 proteins were identified as actin-binding proteins, involved in the regulation of the actin cytoskeleton. In conclusion, using a label-free shotgun proteomic approach, we identified numerous proteins associated with spermiogenesis in round spermatids.
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Affiliation(s)
- Hailong Wang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Yan Li
- Fan-Xing Biological Technology Co., Ltd., Beijing 010000, P.R. China
| | - Lijuan Yang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Baofeng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Ping Yan
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Min Pang
- Respiratory Department, The First Affiliated Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xiaobing Li
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Hong Yang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Guoping Zheng
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Rui Guo
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
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