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Dutta P, Mäkinen K. Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells. J Virol Methods 2025; 332:115066. [PMID: 39549925 DOI: 10.1016/j.jviromet.2024.115066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/18/2024]
Abstract
Potato virus A belongs to the genus Potyvirus, a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, viz., translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.
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Affiliation(s)
- Pinky Dutta
- Viikki Plants Science Centre and Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Kristiina Mäkinen
- Viikki Plants Science Centre and Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Finland.
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2
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Ezelarab HAA, Ali TFS, Abbas SH, Sayed AM, Beshr EAM, Hassan HA. New antiproliferative 3-substituted oxindoles inhibiting EGFR/VEGFR-2 and tubulin polymerization. Mol Divers 2024; 28:563-580. [PMID: 36790582 PMCID: PMC11070402 DOI: 10.1007/s11030-023-10603-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/06/2023] [Indexed: 02/16/2023]
Abstract
New 3-substituted oxindole derivatives were designed and synthesized as antiproliferative agents. The antiproliferative activity of compounds 6a-j was evaluated against 60 NCI cell lines. Among these tested compounds, compounds 6f and 6g showed remarkable antiproliferative activity, specifically against leukemia and breast cancer cell lines. Compound 6f was the most promising antiproliferative agent against MCF-7 (human breast cancer) with an IC50 value of 14.77 µM compared to 5-fluorouracil (5FU) (IC50 = 2.02 µM). Notably, compound 6f hampered receptor tyrosine EGFR fundamentally with an IC50 value of 1.38 µM, compared to the reference sunitinib with an IC50 value of 0.08 µM. Moreover, compound 6f afforded anti-tubulin polymerization activity with an IC50 value of 7.99 µM as an outstanding observable activity compared with the reference combretastatin A4 with an IC50 value of 2.64 µM. In silico molecular-docking results of compound 6f in the ATP-binding site of EGFR agreed with the in vitro results. Besides, the investigation of the physicochemical properties of compound 6f via the egg-boiled method clarified good lipophilicity, GIT absorption, and blood-brain barrier penetration properties.
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Affiliation(s)
- Hend A A Ezelarab
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519-Mini, Minia, Egypt
| | - Taha F S Ali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519-Mini, Minia, Egypt.
| | - Samar H Abbas
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519-Mini, Minia, Egypt.
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, 62513, Egypt
| | - Eman A M Beshr
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519-Mini, Minia, Egypt.
| | - Heba A Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519-Mini, Minia, Egypt
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3
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Roy A, Mandal M, Das S, Popek R, Rakwal R, Agrawal GK, Awasthi A, Sarkar A. The cellular consequences of particulate matter pollutants in plants: Safeguarding the harmonious integration of structure and function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169763. [PMID: 38181950 DOI: 10.1016/j.scitotenv.2023.169763] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
Particulate matter (PM) pollution is one of the pressing environmental concerns confronting human civilization in the face of the Anthropocene era. Plants are continuously exposed to an accelerating PM, threatening their growth and productivity. Although plants and plant-based infrastructures can potentially reduce ambient air pollutants, PM still affects them morphologically, anatomically, and physiologically. This review comprehensively summarizes an up-to-date review of plant-PM interaction among different functional plant groups, PM deposition and penetration through aboveground and belowground plant parts, and plants' cellular strategies. Upon exposure, PM represses lipid desaturases, eventually leading to modification of cell wall and membrane and altering cell fluidity; consequently, plants can sense the pollutants and, thus, adapt different cellular strategies. The PM also causes a reduction in the photosynthetically active radiation. The study demonstrated that plants reduce stomatal density to avoid PM uptake and increase stomatal index to compensate for decreased gaseous exchange efficiency and transpiration rates. Furthermore, genes and gene sets associated with photosynthesis, glycolysis, gluconeogenesis, and the TCA cycle were dramatically lowered by PM stress. Several transcription factors, including MYB, C2H2, C3H, G2-like, and WRKY were induced, and metabolites such as proline and soluble sugar were accumulated to increase resistance against stressors. In addition, enzymatic and non-enzymatic antioxidants were also accumulated to scavenge the PM-induced reactive oxygen species (ROS). Taken together, this review provides an insight into plants' underlying cellular mechanisms and gene regulatory networks in response to the PM to determine strategies to preserve their structural and functional blend in the face of particulate pollution. The study concludes by recommending that future research should precisely focus on plants' response to short- and long-term PM exposure.
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Affiliation(s)
- Anamika Roy
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Mamun Mandal
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Sujit Das
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India
| | - Robert Popek
- Section of Basic Research in Horticulture, Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences - SGGW (WULS-SGGW), Nowoursynowska 159, Warsaw, Poland
| | - Randeep Rakwal
- Institute of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8574, Japan; GRADE Academy (Pvt.) Ltd., Birgunj, Nepal
| | | | - Amit Awasthi
- Department of Applied Sciences, University of Petroleum and Energy Studies, Dehradun, India
| | - Abhijit Sarkar
- Laboratory of Applied Stress Biology, Department of Botany, University of Gour Banga, Malda 732 103, West Bengal, India.
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Spät P, Krauspe V, Hess WR, Maček B, Nalpas N. Deep Proteogenomics of a Photosynthetic Cyanobacterium. J Proteome Res 2023; 22:1969-1983. [PMID: 37146978 PMCID: PMC10243305 DOI: 10.1021/acs.jproteome.3c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 05/07/2023]
Abstract
Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth's biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial metabolism; however, proteome studies in cyanobacteria are limited and cover only a fraction of the theoretical proteome. Here, we performed a comprehensive proteogenomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover novel open reading frames (ORFs). By mapping extensive shotgun mass spectrometry proteomics data onto a six-frame translation of the Synechocystis genome, we refined the genomic annotation of 64 ORFs, including eight completely novel ORFs. Our study presents the largest reported (phospho)proteome dataset for a unicellular cyanobacterium, covering the expression of about 80% of the theoretical proteome under various cultivation conditions, such as nitrogen or carbon limitation. We report 568 phosphorylated S/T/Y sites that are present on numerous regulatory proteins, including the transcriptional regulators cyAbrB1 and cyAbrB2. We also catalogue the proteins that have never been detected under laboratory conditions and found that a large portion of them is plasmid-encoded. This dataset will serve as a resource, providing dedicated information on growth condition-dependent protein expression and phosphorylation.
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Affiliation(s)
- Philipp Spät
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Vanessa Krauspe
- Genetics
& Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Wolfgang R. Hess
- Genetics
& Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Boris Maček
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Nicolas Nalpas
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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5
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Wei L, Wang D, Gupta R, Kim ST, Wang Y. A Proteomics Insight into Advancements in the Rice-Microbe Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051079. [PMID: 36903938 PMCID: PMC10005616 DOI: 10.3390/plants12051079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 05/23/2023]
Abstract
Rice is one of the most-consumed foods worldwide. However, the productivity and quality of rice grains are severely constrained by pathogenic microbes. Over the last few decades, proteomics tools have been applied to investigate the protein level changes during rice-microbe interactions, leading to the identification of several proteins involved in disease resistance. Plants have developed a multi-layered immune system to suppress the invasion and infection of pathogens. Therefore, targeting the proteins and pathways associated with the host's innate immune response is an efficient strategy for developing stress-resistant crops. In this review, we discuss the progress made thus far with respect to rice-microbe interactions from side views of the proteome. Genetic evidence associated with pathogen-resistance-related proteins is also presented, and challenges and future perspectives are highlighted in order to understand the complexity of rice-microbe interactions and to develop disease-resistant crops in the future.
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Affiliation(s)
- Lirong Wei
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dacheng Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Yiming Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Gao ZF, Yang X, Mei Y, Zhang J, Chao Q, Wang BC. A dynamic phosphoproteomic analysis provides insight into the C4 plant maize (Zea mays L.) response to natural diurnal changes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:291-307. [PMID: 36440987 DOI: 10.1111/tpj.16047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants need to respond to rapid changes in numerous environmental factors, mainly diurnal changes of light, temperature, and humidity. Maize is the world's most grown crop, and as a C4 plant it exhibits high photosynthesis capacity, reaching the highest rate of net photosynthesis at midday; that is, there is no "midday depression." Revealing the physiological responses to diurnal changes and underlying mechanisms will be of great significance for guiding maize improvement efforts. In this study, we collected maize leaf samples and analyzed the proteome and phosphoproteome at nine time points during a single day/night cycle, quantifying 7424 proteins and 5361 phosphosites. The new phosphosites identified in our study increased the total maize phosphoproteome coverage by 8.5%. Kinase-substrate network analysis indicated that 997 potential substrates were phosphorylated by 20 activated kinases. Through analysis of proteins with significant changes in abundance and phosphorylation, we found that the response to a heat stimulus involves a change in the abundance of numerous proteins. By contrast, the high light at noon and rapidly changing light conditions induced changes in the phosphorylation level of proteins involved in processes such as chloroplast movement, photosynthesis, and C4 pathways. Phosphorylation is involved in regulating the activity of large number of enzymes; for example, phosphorylation of S55 significantly enhanced the activity of maize phosphoenolpyruvate carboxykinase1 (ZmPEPCK1). Overall, the database of dynamic protein abundance and phosphorylation we have generated provides a resource for the improvement of C4 crop plants.
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Affiliation(s)
- Zhi-Fang Gao
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu Yang
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingchang Mei
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiao Zhang
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Chao
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
| | - Bai-Chen Wang
- Key Laboratory of Photobiology, CAS, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100093, China
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7
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Bawa G, Liu Z, Zhou Y, Fan S, Ma Q, Tissue DT, Sun X. Cotton proteomics: Dissecting the stress response mechanisms in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1035801. [PMID: 36466262 PMCID: PMC9714328 DOI: 10.3389/fpls.2022.1035801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton's response to stresses.
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Affiliation(s)
- George Bawa
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - David T. Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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Ojosnegros S, Alvarez JM, Grossmann J, Gagliardini V, Quintanilla LG, Grossniklaus U, Fernández H. The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades. Int J Mol Sci 2022; 23:ijms232214027. [PMID: 36430514 PMCID: PMC9693225 DOI: 10.3390/ijms232214027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Ferns are a diverse evolutionary lineage, sister to the seed plants, which is of great ecological importance and has a high biotechnological potential. Fern gametophytes represent one of the simplest autotrophic, multicellular plant forms and show several experimental advantages, including a simple and space-efficient in vitro culture system. However, the molecular basis of fern growth and development has hardly been studied. Here, we report on a proteomic study that identified 417 proteins shared by gametophytes of the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative Dryopteris oreades. Most proteins are predicted to localize to the cytoplasm, the chloroplast, or the nucleus, and are linked to enzymatic, binding, and structural activities. A subset of 145 proteins are involved in growth, reproduction, phytohormone signaling and biosynthesis, and gene expression, including homologs of SHEPHERD (SHD), HEAT SHOCK PROTEIN 90-5 (CR88), TRP4, BOBBER 1 (BOB1), FLAVONE 3'-O-METHYLTRANSFERASE 1 (OMT1), ZEAXANTHIN EPOXIDASE (ABA1), GLUTAMATE DESCARBOXYLASE 1 (GAD), and dsRNA-BINDING DOMAIN-LIKE SUPERFAMILY PROTEIN (HLY1). Nearly 25% of the annotated proteins are associated with responses to biotic and abiotic stimuli. As for biotic stress, the proteins PROTEIN SGT1 HOMOLOG B (SGT1B), SUPPRESSOR OF SA INSENSITIVE2 (SSI2), PHOSPHOLIPASE D ALPHA 1 (PLDALPHA1), SERINE/THREONINE-PROTEIN KINASE SRK2E (OST1), ACYL CARRIER PROTEIN 4 (ACP4), and NONHOST RESISTANCE TO P. S. PHASEOLICOLA1 (GLPK) are worth mentioning. Regarding abiotic stimuli, we found proteins associated with oxidative stress: SUPEROXIDE DISMUTASE[CU-ZN] 1 (CSD1), and GLUTATHIONE S-TRANSFERASE U19 (GSTU19), light intensity SERINE HYDROXYMETHYLTRANSFERASE 1 (SHM1) and UBIQUITIN-CONJUGATING ENZYME E2 35 (UBC35), salt and heavy metal stress included MITOCHONDRIAL PHOSPHATE CARRIER PROTEIN 3 (PHT3;1), as well as drought and thermotolerance: LEA7, DEAD-BOX ATP-DEPENDENT RNA HELICASE 38 (LOS4), and abundant heat-shock proteins and other chaperones. In addition, we identified interactomes using the STRING platform, revealing protein-protein associations obtained from co-expression, co-occurrence, text mining, homology, databases, and experimental datasets. By focusing on ferns, this proteomic study increases our knowledge on plant development and evolution, and may inspire future applications in crop species.
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Affiliation(s)
- Sara Ojosnegros
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - José Manuel Alvarez
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomic Center Zurich, University and ETH Zurich, 8092 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos, 28933 Móstoles, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, 8006 Zurich, Switzerland
| | - Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain
- Correspondence: ; Tel.: +34-985-104-811
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Usman K, Souchelnytskyi S, Al-Ghouti MA, Zouari N, Abu-Dieyeh MH. Proteomic analysis of T. qataranse exposed to lead (Pb) stress reveal new proteins with potential roles in Pb tolerance and detoxification mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:1009756. [PMID: 36340352 PMCID: PMC9630582 DOI: 10.3389/fpls.2022.1009756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Soil lead (Pb) contamination is one of the environmental problems facing the modern world. Sources of Pb in soil include industrial activities such as mining and smelting processes, agricultural activities such as application of insecticide and municipal sewage sludges, and urban activities such as use of lead in gasoline, paints, and other materials. Phytoremediation is the direct use of living green plants and is an effective, cheap, non-invasive, and environmentally friendly technique used to transfer or stabilize all the toxic metals and environmental pollutants in polluted soil or groundwater. Current work in this area is invested in elucidating mechanisms that underpin toxic-metal tolerance and detoxification mechanisms. The present study aims to gain insight into the mechanisms of Pb tolerance in T. qataranse by comparative proteomics. MALDI-TOF/MS and in silico proteome analysis showed differential protein expression between treated (50 mg kg⎯1 Pb) and untreated (0 mg kg⎯1 Pb) T. qataranse. A total of eighty-six (86) differentially expressed proteins, most of which function in ion and protein binding, antioxidant activity, transport, and abiotic response stress, were identified. In addition, essential stress-regulating metabolic pathways, including glutathione metabolism, cellular response to stress, and regulation of HSF1-mediated heat shock response, were also enriched. Also, at 52- and 49-kDa MW band areas, up to six hypothetical proteins with unknown functions were identified. Of these, protein AXX17_AT2G26660 is highly rich in glycine amino acid residues (up to 76%), suggesting that it is a probable glycine-rich protein (GRP) member. Although GRPs are known to be involved in plant defense against abiotic stress, including salinity and drought, there is no report on their role on Pb tolerance and or detoxification in plants. Further enrichment analysis in the current study reveals that the hypothetical proteins do not interact with known proteins and are not part of any enriched pathway. However, additional research is needed to functionally validate the role of the identified proteins in Pb detoxification mechanism.
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Affiliation(s)
- Kamal Usman
- Agricultural Research Station (ARS), Office of VP for Research & Graduate Studies, Doha, Qatar
| | | | - Mohammad A. Al-Ghouti
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar
| | - Nabil Zouari
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar
| | - Mohammed H. Abu-Dieyeh
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha, Qatar
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Liu X, Yang Z, Wang Y, Shen Y, Jia Q, Zhao C, Zhang M. Multiple caleosins have overlapping functions in oil accumulation and embryo development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3946-3962. [PMID: 35419601 DOI: 10.1093/jxb/erac153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Caleosins are lipid droplet- and endoplasmic reticulum-associated proteins. To investigate their functions in oil accumulation, expression levels of caleosins in developing seeds of Arabidopsis thaliana were examined and four seed-expressed caleosins (CLO1, CLO2, CLO4, and CLO6) were identified. The four single mutants showed similar minor changes of fatty acid composition in seeds. Two double mutants (clo1 clo2 and clo1×clo2) demonstrated distinct changes of fatty acid composition, a 16-23% decrease of oil content, and a 10-13% decrease of seed weight. Moreover, a 40% decrease of oil content, further fatty acid changes, and misshapen membranes of smaller lipid droplets were found in seeds of quadruple CLO RNAi lines. Notably, ~40% of quadruple CLO RNAi T1 seeds failed to germinate, and deformed embryos and seedlings were also observed. Complementation experiments showed that CLO1 rescued the phenotype of clo1 clo2. Overexpression of CLO1 in seedlings and BY2 cells increased triacylglycerol content up to 73.6%. Transcriptome analysis of clo1 clo2 developing seeds showed that expression levels of some genes related to lipid, embryo development, calcium signaling, and stress responses were affected. Together, these results suggest that the major seed-expressed caleosins have overlapping functions in oil accumulation and show pleiotropic effects on embryo development.
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Affiliation(s)
- Xiangling Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Yun Wang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Qingli Jia
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Abstract
Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.
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Affiliation(s)
- Julia Mergner
- Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany;
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany;
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
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12
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Tivendale ND, Millar AH. How is auxin linked with cellular energy pathways to promote growth? THE NEW PHYTOLOGIST 2022; 233:2397-2404. [PMID: 34984715 DOI: 10.1111/nph.17946] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/02/2021] [Indexed: 05/12/2023]
Abstract
Auxin is the 'growth hormone' and modulation of its concentration correlates with changes in photosynthesis and respiration, influencing the cellular energy budget for biosynthesis and proliferation. However, the relative importance of mechanisms by which auxin directly influences photosynthesis and respiration, or vice versa, are unclear. Here we bring together recent evidence linking auxin with photosynthesis, plastid biogenesis, mitochondrial metabolism and retrograde signalling and through it we propose three hypotheses to test to unify current findings. These require delving into the control of auxin conjugation to primary metabolic intermediates, translational control under auxin regulation and post-translational influences of auxin on primary metabolic processes.
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Affiliation(s)
- Nathan D Tivendale
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
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13
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Schröder L, Hohnjec N, Senkler M, Senkler J, Küster H, Braun HP. The gene space of European mistletoe (Viscum album). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:278-294. [PMID: 34713513 DOI: 10.1111/tpj.15558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
European mistletoe (Viscum album) is a hemiparasitic flowering plant that is known for its very special life cycle and extraordinary biochemical properties. Particularly, V. album has an unusual mode of cellular respiration that takes place in the absence of mitochondrial complex I. However, insights into the molecular biology of V. album so far are very limited. Since the genome of V. album is extremely large (estimated 600 times larger than the genome of the model plant Arabidopsis thaliana) it has not been sequenced up to now. We here report sequencing of the V. album gene space (defined as the space including and surrounding genic regions, encompassing coding as well as 5' and 3' non-coding regions). mRNA fractions were isolated from different V. album organs harvested in summer or winter and were analyzed via single-molecule real-time sequencing. We determined sequences of 39 092 distinct open reading frames encoding 32 064 V. album proteins (designated V. album protein space). Our data give new insights into the metabolism and molecular biology of V. album, including the biosynthesis of lectins and viscotoxins. The benefits of the V. album gene space information are demonstrated by re-evaluating mass spectrometry-based data of the V. album mitochondrial proteome, which previously had been evaluated using the A. thaliana genome sequence. Our re-examination allowed the additional identification of nearly 200 mitochondrial proteins, including four proteins related to complex I, which all have a secondary function not related to respiratory electron transport. The V. album gene space sequences are available at the NCBI.
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Affiliation(s)
- Lucie Schröder
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Natalija Hohnjec
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Michael Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Helge Küster
- Plant Genomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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14
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Kumari M, Pradhan UK, Joshi R, Punia A, Shankar R, Kumar R. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC PLANT BIOLOGY 2021; 21:604. [PMID: 34937558 PMCID: PMC8693493 DOI: 10.1186/s12870-021-03394-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. RESULTS We were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. CONCLUSIONS This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.
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Affiliation(s)
- Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upendra Kumar Pradhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
- Present address: ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, 110012, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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15
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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16
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Fernández H, Grossmann J, Gagliardini V, Feito I, Rivera A, Rodríguez L, Quintanilla LG, Quesada V, Cañal MJ, Grossniklaus U. Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles. FRONTIERS IN PLANT SCIENCE 2021; 12:718932. [PMID: 34868105 PMCID: PMC8633544 DOI: 10.3389/fpls.2021.718932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
The gametophyte of ferns reproduces either by sexual or asexual means. In the latter, apogamy represents a peculiar case of apomixis, in which an embryo is formed from somatic cells. A proteomic and physiological approach was applied to the apogamous fern Dryopteris affinis ssp. affinis and its sexual relative D. oreades. The proteomic analysis compared apogamous vs. female gametophytes, whereas the phytohormone study included, in addition to females, three apogamous stages (filamentous, spatulate, and cordate). The proteomic profiles revealed a total of 879 proteins and, after annotation, different regulation was found in 206 proteins of D. affinis and 166 of its sexual counterpart. The proteins upregulated in D. affinis are mostly associated to protein metabolism (including folding, transport, and proteolysis), ribosome biogenesis, gene expression and translation, while in the sexual counterpart, they account largely for starch and sucrose metabolism, generation of energy and photosynthesis. Likewise, ultra-performance liquid chromatography-tandem spectrometry (UHPLC-MS/MS) was used to assess the levels of indol-3-acetic acid (IAA); the cytokinins: 6-benzylaminopurine (BA), trans-Zeatine (Z), trans-Zeatin riboside (ZR), dyhidrozeatine (DHZ), dyhidrozeatin riboside (DHZR), isopentenyl adenine (iP), isopentenyl adenosine (iPR), abscisic acid (ABA), the gibberellins GA3 and GA4, salicylic acid (SA), and the brassinosteroids: brassinolide (BL) and castasterone (CS). IAA, the cytokinins Z, ZR, iPR, the gibberellin GA4, the brassinosteoids castasterone, and ABA accumulated more in the sexual gametophyte than in the apogamous one. When comparing the three apogamous stages, BA and SA peaked in filamentous, GA3 and BL in spatulate and DHRZ in cordate gametophytes. The results point to the existence of large metabolic differences between apogamous and sexual gametophytes, and invite to consider the fern gametophyte as a good experimental system to deepen our understanding of plant reproduction.
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Affiliation(s)
- Helena Fernández
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Jonas Grossmann
- Functional Genomics Center, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Valeria Gagliardini
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Alejandro Rivera
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Finca Experimental La Mata, Grado, Spain
| | - Luis G. Quintanilla
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Móstoles, Spain
| | - Víctor Quesada
- Department of Biochemistry and Molecular Biology, Institute of Oncology of the Principality of Asturias, Oviedo University, Móstoles, Spain
| | - Mª Jesús Cañal
- Area of Plant Physiology, Department of Organisms and Systems Biology, Oviedo University, Oviedo, Spain
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich and Basel Plant Science Center, University of Zurich, Zurich, Switzerland
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17
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Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. Microbiol Spectr 2021; 9:e0049021. [PMID: 34523988 PMCID: PMC8557916 DOI: 10.1128/spectrum.00490-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cyanobacteria, capable of oxygenic photosynthesis, play a vital role in nitrogen and carbon cycles. Nostoc sp. PCC 7120 (Nostoc 7120) is a model cyanobacterium commonly used to study cell differentiation and nitrogen metabolism. Although its genome was released in 2002, a high-quality genome annotation remains unavailable for this model cyanobacterium. Therefore, in this study, we performed an in-depth proteogenomic analysis based on high-resolution mass spectrometry (MS) data to refine the genome annotation of Nostoc 7120. We unambiguously identified 5,519 predicted protein-coding genes and revealed 26 novel genes, 75 revised genes, and 27 different kinds of posttranslational modifications in Nostoc 7120. A subset of these novel proteins were further validated at both the mRNA and peptide levels. Functional analysis suggested that many newly annotated proteins may participate in nitrogen or cadmium/mercury metabolism in Nostoc 7120. Moreover, we constructed an updated Nostoc 7120 database based on our proteogenomic results and presented examples of how the updated database could be used to improve the annotation of proteomic data. Our study provides the most comprehensive annotation of the Nostoc 7120 genome thus far and will serve as a valuable resource for the study of nitrogen metabolism in Nostoc 7120. IMPORTANCE Cyanobacteria are a large group of prokaryotes capable of oxygenic photosynthesis and play a vital role in nitrogen and carbon cycles on Earth. Nostoc 7120 is a commonly used model cyanobacterium for studying cell differentiation and nitrogen metabolism. In this study, we presented the first comprehensive draft map of the Nostoc 7120 proteome and a wide range of posttranslational modifications. In addition, we constructed an updated database of Nostoc 7120 based on our proteogenomic results and presented examples of how the updated database could be used for system-level studies of Nostoc 7120. Our study provides the most comprehensive annotation of Nostoc 7120 genome and a valuable resource for the study of nitrogen metabolism in this model cyanobacterium.
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18
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Antil N, Kumar M, Behera SK, Arefian M, Kotimoole CN, Rex DAB, Prasad TSK. Unraveling Toxoplasma gondii GT1 Strain Virulence and New Protein-Coding Genes with Proteogenomic Analyses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:591-604. [PMID: 34468217 DOI: 10.1089/omi.2021.0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Toxoplasma gondii is one of the most widespread parasites of great relevance to planetary health. It infects approximately one-third of the world population. T. gondii establishes itself in warm-blooded animals and causes adverse health outcomes, particularly in immunocompromised patients. T. gondii is also widely used as a model organism to study other related apicomplexan parasites, which requires a deeper understanding of its molecular biology. Type I strains (GT1 and RH) of T. gondii are considered the most virulent forms. The whole-genome sequencing of T. gondii annotated 8460 predicted gene models in the parasite. To this end, the proteogenomics technology allows harnessing of mass spectrometry (MS)-derived proteomic data to unravel new protein-coding genes, not to mention validation and correction of the existing gene models. In this study using the proteogenomic approach, we report the identification of 31 novel protein-coding genes while reannotating 88 existing gene models. Notably, the genome annotations were corrected for genes, such as SAG5C, GRA6, ROP4, ROP5, and ROP26. The associated proteins are known to play important roles in host-parasite interactions, particularly in relation to parasite virulence, suppression of host immune response, and distinctively pertinent for the survival of the parasite inside the host system. These new findings offer new insights, informing planetary health broadly and the knowledge base on T. gondii virulence specifically. The proteogenomics approach also provides a concrete example to study related apicomplexan organisms of relevance to planetary health, and so as to develop new diagnostics and therapeutics against toxoplasmosis and related diseases.
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Affiliation(s)
- Neelam Antil
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Centre for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Santosh Kumar Behera
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Arefian
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Devasahayam Arokia Balaya Rex
- Centre for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
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19
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Poidevin L, Forment J, Unal D, Ferrando A. Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth. PLANT, CELL & ENVIRONMENT 2021. [PMID: 33289138 DOI: 10.1101/2020.05.29.122937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant reproduction is one key biological process that is very sensitive to heat stress and, as a result, enhanced global warming becomes a serious threat to agriculture. In this work, we have studied the effects of heat on germinated pollen of Arabidopsis thaliana both at the transcriptional and translational level. We have used a high-resolution ribosome profiling technology to provide a comprehensive study of the transcriptome and the translatome of germinated pollen at permissive and restrictive temperatures. We have found significant down-regulation of key membrane transporters required for pollen tube growth by heat, thus uncovering heat-sensitive targets. A subset of the heat-repressed transporters showed coordinated up-regulation with canonical heat-shock genes at permissive conditions. We also found specific regulations at the translational level and we have uncovered the presence of ribosomes on sequences annotated as non-coding. Our results demonstrate that heat impacts mostly on membrane transporters thus explaining the deleterious effects of heat stress on pollen growth. The specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlights novel regulatory aspects on plant fertilization.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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20
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Chen Y, Wang Y, Yang J, Zhou W, Dai S. Exploring the diversity of plant proteome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1197-1210. [PMID: 33650765 DOI: 10.1111/jipb.13087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/10/2023]
Abstract
The tremendous functional, spatial, and temporal diversity of the plant proteome is regulated by multiple factors that continuously modify protein abundance, modifications, interactions, localization, and activity to meet the dynamic needs of plants. Dissecting the proteome complexity and its underlying genetic variation is attracting increasing research attention. Mass spectrometry (MS)-based proteomics has become a powerful approach in the global study of protein functions and their relationships on a systems level. Here, we review recent breakthroughs and strategies adopted to unravel the diversity of the proteome, with a specific focus on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. We also consider PTM crosstalk and multiple PTMs temporally regulating the life cycle of proteins. Finally, we discuss recent quantitative studies using MS to measure protein turnover rates and examine future directions in the study of the plant proteome.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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21
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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22
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Poidevin L, Forment J, Unal D, Ferrando A. Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth. PLANT, CELL & ENVIRONMENT 2021; 44:2167-2184. [PMID: 33289138 DOI: 10.1111/pce.13972] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 05/12/2023]
Abstract
Plant reproduction is one key biological process that is very sensitive to heat stress and, as a result, enhanced global warming becomes a serious threat to agriculture. In this work, we have studied the effects of heat on germinated pollen of Arabidopsis thaliana both at the transcriptional and translational level. We have used a high-resolution ribosome profiling technology to provide a comprehensive study of the transcriptome and the translatome of germinated pollen at permissive and restrictive temperatures. We have found significant down-regulation of key membrane transporters required for pollen tube growth by heat, thus uncovering heat-sensitive targets. A subset of the heat-repressed transporters showed coordinated up-regulation with canonical heat-shock genes at permissive conditions. We also found specific regulations at the translational level and we have uncovered the presence of ribosomes on sequences annotated as non-coding. Our results demonstrate that heat impacts mostly on membrane transporters thus explaining the deleterious effects of heat stress on pollen growth. The specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlights novel regulatory aspects on plant fertilization.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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23
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Darbani B. Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44. Int J Mol Sci 2021; 22:ijms22115669. [PMID: 34073512 PMCID: PMC8199184 DOI: 10.3390/ijms22115669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 12/14/2022] Open
Abstract
Gene clusters are becoming promising tools for gene identification. The study reveals the purposive genomic distribution of genes toward higher inheritance rates of intact metabolic pathways/phenotypes and, thereby, higher fitness. The co-localization of co-expressed, co-interacting, and functionally related genes was found as genome-wide trends in humans, mouse, golden eagle, rice fish, Drosophila, peanut, and Arabidopsis. As anticipated, the analyses verified the co-segregation of co-localized events. A negative correlation was notable between the likelihood of co-localization events and the inter-loci distances. The evolution of genomic blocks was also found convergent and uniform along the chromosomal arms. Calling a genomic block responsible for adjacent metabolic reactions is therefore recommended for identification of candidate genes and interpretation of cellular functions. As a case story, a function in the metabolism of energy and secondary metabolites was proposed for Slc25A44, based on its genomic local information. Slc25A44 was further characterized as an essential housekeeping gene which has been under evolutionary purifying pressure and belongs to the phylogenetic ETC-clade of SLC25s. Pathway enrichment mapped the Slc25A44s to the energy metabolism. The expression of peanut and human Slc25A44s in oocytes and Saccharomyces cerevisiae strains confirmed the transport of common precursors for secondary metabolites and ubiquinone. These results suggest that SLC25A44 is a mitochondrion-ER-nucleus zone transporter with biotechnological applications. Finally, a conserved three-amino acid signature on the cytosolic face of transport cavity was found important for rational engineering of SLC25s.
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Affiliation(s)
- Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; or ; Tel.: +45-(53)-578055
- Research Center Flakkebjerg, Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
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Yadav A, Sanyal I, Rai SP, Lata C. An overview on miRNA-encoded peptides in plant biology research. Genomics 2021; 113:2385-2391. [PMID: 34022345 DOI: 10.1016/j.ygeno.2021.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/20/2021] [Accepted: 05/17/2021] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are short (21-23 nt) regulatory RNA molecules present in plants and animals which are known for regulating the mRNA target gene expression either by cleavage or translational repression. With the advancements in miRNAs research in plants towards their biogenesis and applications has directed the recent discovery of pri-miRNAs encoding functional peptides or microRNA peptides (miPEPs). These miPEPs are encoded by 5' of pri-miRs containing short ORFs (miORFs). miPEPs are known to enhance the activity of their associated miRNAs by increasing their accumulation and hence downregulating the target genes. Since miPEPs are very specific for each miRNA, they are considered as novel and effective tools for improving traits of interest for plant growth promotion and plant-microbe interaction. Entire peptidome research is the need of the hour. This review thus summarizes recent advancements in miPEP research and its applications as a technology with important agronomical implications with miRNAs augmentation.
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Affiliation(s)
- Ankita Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Faculty of Science, Banaras Hindu University, Varanasi 221005, India
| | - Indraneel Sanyal
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Shashi Pandey Rai
- Faculty of Science, Banaras Hindu University, Varanasi 221005, India
| | - Charu Lata
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi 110067, India.
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Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics 2021; 18:221-232. [PMID: 33877947 DOI: 10.1080/14789450.2021.1914594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cancer cell lines (CCLs) have been a major resource for cancer research. Over the past couple of decades, they have been instrumental in omic profiling method development and as model systems to generate new knowledge in cell and cancer biology. More recently, with the increasing amount of genomic, transcriptomic and proteomic data being generated in hundreds of CCLs, there is growing potential for integrative proteogenomic data analyses to be performed.Areas covered: In this review, we first describe the most commonly used proteome profiling methods in CCLs. We then discuss how these proteomics data can be integrated with genomics data for proteogenomics analyses. Finally, we highlight some of the recent biological discoveries that have arisen from proteogenomics analyses of CCLs.Expert opinion: Protegeonomics analyses of CCLs have so far enabled the discovery of novel proteins and proteoforms. It has also improved our understanding of biological processes including post-transcriptional regulation of protein abundance and the presentation of antigens by major histocompatibility complex alleles. With proteomics data to be generated in hundreds to thousands of CCLs in coming years, there will be further potential for large-scale proteogenomics analyses and data integration with the phenotypically well-characterized CCLs.
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Affiliation(s)
- Olson Tsang
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Jason W H Wong
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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Klein A, Husselmann LHH, Williams A, Bell L, Cooper B, Ragar B, Tabb DL. Proteomic Identification and Meta-Analysis in Salvia hispanica RNA-Seq de novo Assemblies. PLANTS (BASEL, SWITZERLAND) 2021; 10:765. [PMID: 33919777 PMCID: PMC8070742 DOI: 10.3390/plants10040765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/24/2022]
Abstract
While proteomics has demonstrated its value for model organisms and for organisms with mature genome sequence annotations, proteomics has been of less value in nonmodel organisms that are unaccompanied by genome sequence annotations. This project sought to determine the value of RNA-Seq experiments as a basis for establishing a set of protein sequences to represent a nonmodel organism, in this case, the pseudocereal chia. Assembling four publicly available chia RNA-Seq datasets produced transcript sequence sets with a high BUSCO completeness, though the number of transcript sequences and Trinity "genes" varied considerably among them. After six-frame translation, ProteinOrtho detected substantial numbers of orthologs among other species within the taxonomic order Lamiales. These protein sequence databases demonstrated a good identification efficiency for three different LC-MS/MS proteomics experiments, though a seed proteome showed considerable variability in the identification of peptides based on seed protein sequence inclusion. If a proteomics experiment emphasizes a particular tissue, an RNA-Seq experiment incorporating that same tissue is more likely to support a database search identification of that proteome.
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Affiliation(s)
- Ashwil Klein
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Lizex H. H. Husselmann
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Achmat Williams
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
| | - Liam Bell
- Centre for Proteomic and Genomic Research, Cape Town 7925, South Africa;
| | - Bret Cooper
- USDA Agricultural Research Service, Beltsville, MD 20705, USA;
| | - Brent Ragar
- Departments of Internal Medicine and Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02150, USA;
| | - David L. Tabb
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (A.K.); (L.H.H.H.); (A.W.)
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch 7602, South Africa
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Wu B, Qiao J, Wang X, Liu M, Xu S, Sun D. Factors affecting the rapid changes of protein under short-term heat stress. BMC Genomics 2021; 22:263. [PMID: 33849452 PMCID: PMC8042900 DOI: 10.1186/s12864-021-07560-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Protein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. RESULTS We quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively. CONCLUSION In this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.
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Affiliation(s)
- Bingjin Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jianwen Qiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Jorrin Novo JV. Proteomics and plant biology: contributions to date and a look towards the next decade. Expert Rev Proteomics 2021; 18:93-103. [PMID: 33770454 DOI: 10.1080/14789450.2021.1910028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION This review presents the view of the author, that is opinionable and even speculative, on the field of proteomics, its application to plant biology knowledge, and translation to biotechnology. Written in a more academic than scientific style, it is based on past original and review articles by the author´s group, and those published by leading scientists in the last two years. AREAS COVERED Starting with a general definition and references to historical milestones, it covers sections devoted to the different platforms employed, the plant biology discourse in the protein language, challenges and future prospects, ending with the author opinion. EXPERT OPINION In 25 years, five proteomics platform generations have appeared. We are now moving from proteomics to Systems Biology. While feasible with model organisms, proteomics of orphan species remains challenging. Proteomics, even in its simplest approach, sheds light on plant biological processes, central dogma, and molecular bases of phenotypes of interest, and it can be translated to areas such as food traceability and allergen detection. Proteomics should be validated and optimized to each experimental system, objectives, and hypothesis. It has limitations, artifacts, and biases. We should not blindly accept proteomics data and just create a list of proteins, networks, and avoid speculative biological interpretations. From the hundred to thousand proteins identified and quantified, it is important to obtain a focus and validate some of them, otherwise it is merely. We are starting to have the protein pieces, so let, from now, build the proteomics and biological puzzle.
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Affiliation(s)
- J V Jorrin Novo
- Dpt. Biochemistry and Molecular Biology, Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, ETSIAM, University of Cordoba, Cordoba , Spain
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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Thiedig K, Weisshaar B, Stracke R. Functional and evolutionary analysis of the Arabidopsis 4R-MYB protein SNAPc4 as part of the SNAP complex. PLANT PHYSIOLOGY 2021; 185:1002-1020. [PMID: 33693812 PMCID: PMC8133616 DOI: 10.1093/plphys/kiaa067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Transcription initiation of the genes coding for small nuclear RNA (snRNA) has been extensively analyzed in humans and fruit fly, but only a single ortholog of a snRNA-activating protein complex (SNAPc) subunit has so far been characterized in plants. The genome of the model plant Arabidopsis thaliana encodes orthologs of all three core SNAPc subunits, including A. thaliana SNAP complex 4 (AtSNAPc4)-a 4R-MYB-type protein with four-and-a-half adjacent MYB repeat units. We report the conserved role of AtSNAPc4 as subunit of a protein complex involved in snRNA gene transcription and present genetic evidence that AtSNAPc4 is an essential gene in gametophyte and zygote development. We present experimental evidence that the three A. thaliana SNAPc subunits assemble into a SNAP complex and demonstrate the binding of AtSNAPc4 to snRNA promoters. In addition, co-localization studies show a link between AtSNAPc4 accumulation and Cajal bodies, known to aggregate at snRNA gene loci in humans. Moreover, we show the strong evolutionary conservation of single-copy 4R-MYB/SNAPc4 genes in a broad range of eukaryotes and present additional shared protein features besides the MYB domain, suggesting a conservation of the snRNA transcription initiation machinery along the course of the eukaryotic evolution.
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Affiliation(s)
- Katharina Thiedig
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, Sequenz 1, Bielefeld 33615, Germany
| | - Bernd Weisshaar
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, Sequenz 1, Bielefeld 33615, Germany
| | - Ralf Stracke
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, Sequenz 1, Bielefeld 33615, Germany
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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Heinemann B, Künzler P, Eubel H, Braun HP, Hildebrandt TM. Estimating the number of protein molecules in a plant cell: protein and amino acid homeostasis during drought. PLANT PHYSIOLOGY 2021; 185:385-404. [PMID: 33721903 PMCID: PMC8133651 DOI: 10.1093/plphys/kiaa050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/17/2020] [Indexed: 05/21/2023]
Abstract
During drought stress, cellular proteostasis on the one hand and amino acid homeostasis on the other hand are severely challenged, because the decrease in photosynthesis induces massive proteolysis, leading to drastic changes in both the proteome and the free amino acid pool. Thus, we selected progressive drought stress in Arabidopsis (Arabidopsis thaliana) as a model to investigate on a quantitative level the balance between protein and free amino acid homeostasis. We analyzed the mass composition of the leaf proteome based on proteomics datasets, and estimated how many protein molecules are present in a plant cell and its subcellular compartments. In addition, we calculated stress-induced changes in the distribution of individual amino acids between the free and protein-bound pools. Under control conditions, an average Arabidopsis mesophyll cell contains about 25 billion protein molecules, of which 80% are localized in chloroplasts. Severe water deficiency leads to degradation of more than 40% of the leaf protein mass, and thus causes a drastic shift in distribution toward the free amino acid pool. Stress-induced proteolysis of just half of the 340 million RubisCO hexadecamers present in the chloroplasts of a single mesophyll cell doubles the cellular content of free amino acids. A major fraction of the amino acids released from proteins is channeled into synthesis of proline, which is a compatible osmolyte. Complete oxidation of the remaining fraction as an alternative respiratory substrate can fully compensate for the lack of photosynthesis-derived carbohydrates for several hours.
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Affiliation(s)
- Björn Heinemann
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Patrick Künzler
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Holger Eubel
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Hans-Peter Braun
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Tatjana M Hildebrandt
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
- Address for communication:
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Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
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Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
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Kimberlin A, Holtsclaw RE, Koo AJ. Differential Regulation of the Ribosomal Association of mRNA Transcripts in an Arabidopsis Mutant Defective in Jasmonate-Dependent Wound Response. FRONTIERS IN PLANT SCIENCE 2021; 12:637959. [PMID: 33777072 PMCID: PMC7990880 DOI: 10.3389/fpls.2021.637959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/01/2021] [Indexed: 06/02/2023]
Abstract
Jasmonoyl-L-isoleucine (JA-Ile) is a powerful oxylipin responsible for the genome-wide transcriptional reprogramming in plants that results in major physiological shifts from growth to defense. The double T-DNA insertion Arabidopsis mutant, cyp94b1cyp94b3 (b1b3), defective in cytochrome p450s, CYP94B1 and CYP94B3, which are responsible for oxidizing JA-Ile, accumulates several fold higher levels of JA-Ile yet displays dampened JA-Ile-dependent wound responses-the opposite of what is expected. Transcriptomic and proteomic analyses showed that while the transcriptional response to wounding was largely unchanged in b1b3 compared to wild type (WT), many proteins were found to be significantly reduced in the mutant, which was verified by immunoblot analyses of marker proteins. To understand this protein phenotype and their hypothesized contribution to the b1b3 phenotypes, wounded rosette leaf samples from both WT and b1b3 were subject to a translating ribosome affinity purification RNA sequencing analysis. More than 1,600 genes whose transcripts do not change in abundance by wounding changed their association with the ribosomes after wounding in WT leaves. Consistent with previous observations, the total pool of mRNA transcripts was similar between WT and b1b3; however, the ribosome-associated pool of transcripts was changed significantly. Most notably, fewer transcripts were associated with the ribosome pool in b1b3 than in WT, potentially explaining the reduction of many proteins in the mutant. Among those genes with fewer ribosome-associated transcripts in b1b3 were genes relating to stress response, specialized metabolism, protein metabolism, ribosomal subunits, and transcription factors, consistent with the biochemical phenotypes of the mutant. These results show previously unrecognized regulations at the translational level that are affected by misregulation of JA homeostasis during the wound response in plants.
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Affiliation(s)
- Athen Kimberlin
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Rebekah E. Holtsclaw
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Abraham J. Koo
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
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The composition and turnover of the Arabidopsis thaliana 80S cytosolic ribosome. Biochem J 2021; 477:3019-3032. [PMID: 32744327 PMCID: PMC7452503 DOI: 10.1042/bcj20200385] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/26/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Cytosolic 80S ribosomes contain proteins of the mature cytosolic ribosome (r-proteins) as well as proteins with roles in ribosome biogenesis, protein folding or modification. Here, we refined the core r-protein composition in Arabidopsis thaliana by determining the abundance of different proteins during enrichment of ribosomes from cell cultures using peptide mass spectrometry. The turnover rates of 26 40S subunit r-proteins and 29 60S subunit r-proteins were also determined, showing that half of the ribosome population is replaced every 3–4 days. Three enriched proteins showed significantly shorter half-lives; a protein annotated as a ribosomal protein uL10 (RPP0D, At1g25260) with a half-life of 0.5 days and RACK1b and c with half-lives of 1–1.4 days. The At1g25260 protein is a homologue of the human Mrt4 protein, a trans-acting factor in the assembly of the pre-60S particle, while RACK1 has known regulatory roles in cell function beyond its role in the 40S subunit. Our experiments also identified 58 proteins that are not from r-protein families but co-purify with ribosomes and co-express with r-proteins; 26 were enriched more than 10-fold during ribosome enrichment. Some of these enriched proteins have known roles in translation, while others are newly proposed ribosome-associated factors in plants. This analysis provides an improved understanding of A. thaliana ribosome protein content, shows that most r-proteins turnover in unison in vivo, identifies a novel set of potential plant translatome components, and how protein turnover can help identify r-proteins involved in ribosome biogenesis or regulation in plants.
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Al-Mohanna T, Nejat N, Iannetta AA, Hicks LM, Popescu GV, Popescu SC. Arabidopsis thimet oligopeptidases are redox-sensitive enzymes active in the local and systemic plant immune response. J Biol Chem 2021; 296:100695. [PMID: 33894200 PMCID: PMC8215294 DOI: 10.1016/j.jbc.2021.100695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
Upon pathogen infection, receptors in plants will activate a localized immune response, the effector-triggered immunity (ETI), and a systemic immune response, the systemic acquired response (SAR). Infection also induces oscillations in the redox environment of plant cells, triggering response mechanisms involving sensitive cysteine residues that subsequently alter protein function. Arabidopsis thaliana thimet oligopeptidases TOP1 and TOP2 are required for plant defense against pathogens and the oxidative stress response. Herein, we evaluated the biochemical attributes of TOP isoforms to determine their redox sensitivity using ex vivo Escherichia coli cultures and recombinant proteins. Moreover, we explored the link between their redox regulation and plant immunity in wild-type and mutant Arabidopsis lines. These analyses revealed that redox regulation of TOPs occurs through two mechanisms: (1) oxidative dimerization of full-length TOP1 via intermolecular disulfides engaging cysteines in the N-terminal signal peptide, and (2) oxidative activation of all TOPs via cysteines that are unique and conserved. Further, we detected increased TOP activity in wild-type plants undergoing ETI or SAR following inoculation with Pseudomonas syringae strains. Mutants unable to express the chloroplast NADPH-dependent thioredoxin reductase C (NTRC) showed elevated TOP activity under unstressed conditions and were SAR-incompetent. A top1top2 knockout mutant challenged with P. syringae exhibited misregulation of ROS-induced gene expression in pathogen-inoculated and distal tissues. Furthermore, TOP1 and TOP2 could cleave a peptide derived from the immune component ROC1 with distinct efficiencies at common and specific sites. We propose that Arabidopsis TOPs are thiol-regulated peptidases active in redox-mediated signaling of local and systemic immunity.
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Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Najmeh Nejat
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Anthony A Iannetta
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
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Jorge GL, Balbuena TS. Identification of novel protein-coding sequences in Eucalyptus grandis plants by high-resolution mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140594. [PMID: 33385527 DOI: 10.1016/j.bbapap.2020.140594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding. This study aimed to confidently identify and confirm the existence of previously unknown protein-coding sequences in the Eucalyptus grandis genome. To this end, we used a modified spectral correlation strategy and a dedicated de novo peptide sequencing pipeline. Upon the strategy used here, we confidently identified 41 novel peptide forms and six peptides containing at least one single amino acid substitution. The most representative genomic class of novel peptides was identified as originating from alternative reading frames. In contrast, no clear single amino acid substitution pattern was identified. Validation of the identifications was carried out using a parallel reaction monitoring approach that provided further mass spectrometry support for the existence of the novel peptide sequences. Data are available via ProteomeXchange with identifier PXD022110.
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Affiliation(s)
- Gabriel Lemes Jorge
- Sao Paulo State University, Department of Technology, Jaboticabal, Sao Paulo, Brazil.
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Yang M, Zhu Z, Zhuang Z, Bai Y, Wang S, Ge F. Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production. Mol Cell Proteomics 2020; 20:100013. [PMID: 33568340 PMCID: PMC7950108 DOI: 10.1074/mcp.ra120.002144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Aspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.
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Affiliation(s)
- Mingkun Yang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhuo Zhu
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youhuang Bai
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- School of Life Sciences, and Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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Bassal M, Abukhalaf M, Majovsky P, Thieme D, Herr T, Ayash M, Tabassum N, Al Shweiki MR, Proksch C, Hmedat A, Ziegler J, Lee J, Neumann S, Hoehenwarter W. Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity. MOLECULAR PLANT 2020; 13:1709-1732. [PMID: 33007468 DOI: 10.1016/j.molp.2020.09.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/21/2020] [Accepted: 09/25/2020] [Indexed: 05/21/2023]
Abstract
Proteome remodeling is a fundamental adaptive response, and proteins in complexes and functionally related proteins are often co-expressed. Using a deep sampling strategy we define core proteomes of Arabidopsis thaliana tissues with around 10 000 proteins per tissue, and absolutely quantify (copy numbers per cell) nearly 16 000 proteins throughout the plant lifecycle. A proteome-wide survey of global post-translational modification revealed amino acid exchanges pointing to potential conservation of translational infidelity in eukaryotes. Correlation analysis of protein abundance uncovered potentially new tissue- and age-specific roles of entire signaling modules regulating transcription in photosynthesis, seed development, and senescence and abscission. Among others, the data suggest a potential function of RD26 and other NAC transcription factors in seed development related to desiccation tolerance as well as a possible function of cysteine-rich receptor-like kinases (CRKs) as ROS sensors in senescence. All of the components of ribosome biogenesis factor (RBF) complexes were found to be co-expressed in a tissue- and age-specific manner, indicating functional promiscuity in the assembly of these less-studied protein complexes in Arabidopsis.Furthermore, we characterized detailed proteome remodeling in basal immunity by treating Arabidopsis seeldings with flg22. Through simultaneously monitoring phytohormone and transcript changes upon flg22 treatment, we obtained strong evidence of suppression of jasmonate (JA) and JA-isoleucine (JA-Ile) levels by deconjugation and hydroxylation by IAA-ALA RESISTANT3 (IAR3) and JASMONATE-INDUCED OXYGENASE 2 (JOX2), respectively, under the control of JASMONATE INSENSITIVE 1 (MYC2), suggesting an unrecognized role of a new JA regulatory switch in pattern-triggered immunity. Taken together, the datasets generated in this study present extensive coverage of the Arabidopsis proteome in various biological scenarios, providing a rich resource available to the whole plant science community.
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Affiliation(s)
- Mona Bassal
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mohammad Abukhalaf
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Petra Majovsky
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Domenika Thieme
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Tobias Herr
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mohamed Ayash
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Naheed Tabassum
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Mhd Rami Al Shweiki
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Carsten Proksch
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Ali Hmedat
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Jörg Ziegler
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany
| | - Wolfgang Hoehenwarter
- Leibniz Institute of Plant Biochemistry, Biochemistry of Plant Interactions Department, Proteome Biology of Plant Interactions Research Group, Weinberg 3, Halle/Saale D-06120, Germany.
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40
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Schmitz J, Hüdig M, Meier D, Linka N, Maurino VG. The genome of Ricinus communis encodes a single glycolate oxidase with different functions in photosynthetic and heterotrophic organs. PLANTA 2020; 252:100. [PMID: 33170407 PMCID: PMC7655567 DOI: 10.1007/s00425-020-03504-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The biochemical characterization of glycolate oxidase in Ricinus communis hints to different physiological functions of the enzyme depending on the organ in which it is active. Enzymatic activities of the photorespiratory pathway are not restricted to green tissues but are present also in heterotrophic organs. High glycolate oxidase (GOX) activity was detected in the endosperm of Ricinus communis. Phylogenetic analysis of the Ricinus L-2-hydroxy acid oxidase (Rc(L)-2-HAOX) family indicated that Rc(L)-2-HAOX1 to Rc(L)-2-HAOX3 cluster with the group containing streptophyte long-chain 2-hydroxy acid oxidases, whereas Rc(L)-2-HAOX4 clusters with the group containing streptophyte GOX. Rc(L)-2-HAOX4 is the closest relative to the photorespiratory GOX genes of Arabidopsis. We obtained Rc(L)-2-HAOX4 as a recombinant protein and analyze its kinetic properties in comparison to the Arabidopsis photorespiratory GOX. We also analyzed the expression of all Rc(L)-2-HAOXs and conducted metabolite profiling of different Ricinus organs. Phylogenetic analysis indicates that Rc(L)-2-HAOX4 is the only GOX encoded in the Ricinus genome (RcGOX). RcGOX has properties resembling those of the photorespiratory GOX of Arabidopsis. We found that glycolate, the substrate of GOX, is highly abundant in non-green tissues, such as roots, embryo of germinating seeds and dry seeds. We propose that RcGOX fulfills different physiological functions depending on the organ in which it is active. In autotrophic organs it oxidizes glycolate into glyoxylate as part of the photorespiratory pathway. In fast growing heterotrophic organs, it is most probably involved in the production of serine to feed the folate pathway for special demands of those tissues.
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Affiliation(s)
- Jessica Schmitz
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Meike Hüdig
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Dieter Meier
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nicole Linka
- Institute for Plant Biochemistry, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Division, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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Yang S, Zhang F, Wang Y, Xue H, Jiang Q, Shi J, Dai H, Zhang Z, Li L, He P, Li Y, Ma Y. MdHAL3, a 4'-phosphopantothenoylcysteine decarboxylase, is involved in the salt tolerance of autotetraploid apple. PLANT CELL REPORTS 2020; 39:1479-1491. [PMID: 32761275 DOI: 10.1007/s00299-020-02576-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
MdHAL3 has PPCDC activity and is involved in the salt tolerance of autotetraploid apple. Apple (Malus × domestica) is the most widely planted fruit tree species worldwide. However, the growth and development of apple have been increasingly affected by abiotic stress, such as high salinity. In our previous study, RNA sequencing (RNA-seq) analysis revealed that the expression level of the MdHAL3 gene was significantly upregulated in the autotetraploid apple cultivar Hanfu. In the present study, we first isolated HAL3, whose product was shown to exert 4'-phosphopantothenoylcysteine decarboxylase (PPCDC) activity, from apple. MdHAL3 was expressed in all organs of apple, and its expression was rapidly induced by salt stress. The MdHAL3 protein was localized to the cytomembrane and cytoplasm. Five MdHAL3 overexpression (OE) lines and five MdHAL3-RNAi apple lines were obtained. We found that MdHAL3 enhanced the salt stress tolerance of apple and that the OE plants rooted more easily than the wild-type (WT) plants. The coenzyme A (CoA) content in the leaves of the OE plants was greater than that in the leaves of the WT plants, and the CoA content in the MdHAL3-RNAi plants was lower than that in the WT plants. Taken together, our findings indicate that MdHAL3 plays an essential role in the response to salt stress in apple.
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Affiliation(s)
- Shuang Yang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Feng Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yangshu Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hao Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Qiu Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Jiajun Shi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hongyan Dai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Linguang Li
- Shandong Institute of Pomology, Tai'an, Shandong, 271000, People's Republic of China
| | - Ping He
- Shandong Institute of Pomology, Tai'an, Shandong, 271000, People's Republic of China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong, 271018, People's Republic of China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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Eseverri Á, Baysal C, Medina V, Capell T, Christou P, Rubio LM, Caro E. Transit Peptides From Photosynthesis-Related Proteins Mediate Import of a Marker Protein Into Different Plastid Types and Within Different Species. FRONTIERS IN PLANT SCIENCE 2020; 11:560701. [PMID: 33101328 PMCID: PMC7545105 DOI: 10.3389/fpls.2020.560701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/07/2020] [Indexed: 06/01/2023]
Abstract
Nucleus-encoded plastid proteins are synthesized as precursors with N-terminal targeting signals called transit peptides (TPs), which mediate interactions with the translocon complexes at the outer (TOC) and inner (TIC) plastid membranes. These complexes exist in multiple isoforms in higher plants and show differential specificity and tissue abundance. While some show specificity for photosynthesis-related precursor proteins, others distinctly recognize nonphotosynthetic and housekeeping precursor proteins. Here we used TPs from four Arabidopsis thaliana proteins, three related to photosynthesis (chlorophyll a/b binding protein, Rubisco activase) and photo-protection (tocopherol cyclase) and one involved in the assimilation of ammonium into amino-acids, and whose expression is most abundant in the root (ferredoxin dependent glutamate synthase 2), to determine whether they were able to mediate import of a nuclear-encoded marker protein into plastids of different tissues of a dicot and a monocot species. In A. thaliana, import and processing efficiency was high in all cases, while TP from the rice Rubisco small chain 1, drove very low import in Arabidopsis tissues. Noteworthy, our results show that Arabidopsis photosynthesis TPs also mediate plastid import in rice callus, and in leaf and root tissues with almost a 100% efficiency, providing new biotechnological tools for crop improvement strategies based on recombinant protein accumulation in plastids by the expression of nuclear-encoded transgenes.
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Affiliation(s)
- Álvaro Eseverri
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Vicente Medina
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Teresa Capell
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Luis M. Rubio
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Elena Caro
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
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Ye C, Luo Q, Guo L, Gao C, Xu N, Zhang L, Liu L, Chen X. Improving lysine production through construction of an Escherichia coli enzyme-constrained model. Biotechnol Bioeng 2020; 117:3533-3544. [PMID: 32648933 DOI: 10.1002/bit.27485] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/28/2020] [Accepted: 07/09/2020] [Indexed: 12/28/2022]
Abstract
Microbial cell factories are widely used for the production of high-value chemicals. However, maximizing production titers is made difficult by the complicated regulatory mechanisms of these cell platforms. Here, kcat values were incorporated to construct an Escherichia coli enzyme-constrained model. The resulting ec_iML1515 model showed that the protein demand and protein synthesis rate were the key factors affecting lysine production. By optimizing the expression of the 20 top-demanded proteins, lysine titers reached 95.7 ± 0.7 g/L, with a 0.45 g/g glucose yield. Moreover, adjusting NH4 + and dissolved oxygen levels to regulate the synthesis rate of energy metabolism-related proteins caused lysine titers and glucose yields to increase to 193.6 ± 1.8 g/L and 0.74 g/g, respectively. The ec_iML1515 model provides insight into how enzymes required for the biosynthesis of certain products are distributed between and within metabolic pathways. This information can be used to accurately predict and rationally design lysine production.
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Affiliation(s)
- Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Li Zhang
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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44
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Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 2020; 579:409-414. [PMID: 32188942 DOI: 10.1038/s41586-020-2094-2] [Citation(s) in RCA: 308] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/17/2020] [Indexed: 01/05/2023]
Abstract
Plants are essential for life and are extremely diverse organisms with unique molecular capabilities1. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interactions.
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Ye C, Xu N, Gao C, Liu G, Xu J, Zhang W, Chen X, Nielsen J, Liu L. Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole-cell model WM_S288C. Biotechnol Bioeng 2020; 117:1562-1574. [PMID: 32022245 DOI: 10.1002/bit.27298] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/28/2020] [Accepted: 02/03/2020] [Indexed: 02/01/2023]
Abstract
Biological network construction for Saccharomyces cerevisiae is a widely used approach for simulating phenotypes and designing cell factories. However, due to a complicated regulatory mechanism governing the translation of genotype to phenotype, precise prediction of phenotypes remains challenging. Here, we present WM_S288C, a computational whole-cell model that includes 15 cellular states and 26 cellular processes and which enables integrated analyses of physiological functions of Saccharomyces cerevisiae. Using WM_S288C to predict phenotypes of S. cerevisiae, the functions of 1140 essential genes were characterized and linked to phenotypes at five levels. During the cell cycle, the dynamic allocation of intracellular molecules could be tracked in real-time to simulate cell activities. Additionally, one-third of non-essential genes were identified to affect cell growth via regulating nucleotide concentrations. These results demonstrated the value of WM_S288C as a tool for understanding and investigating the phenotypes of S. cerevisiae.
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Affiliation(s)
- Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Nan Xu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Gaoqiang Liu
- Hunan Provincial Key Laboratory for Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jianzhong Xu
- Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China
| | - Weiguo Zhang
- Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Jiangnan University, Ministry of Education, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019; 6:278. [PMID: 31757973 DOI: 10.6084/m9.figshare.c.4647293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 05/26/2023] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019. [PMID: 31757973 DOI: 10.1038/s41597-019-0294-0)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L. Arabidopsis proteome and the mass spectral assay library. Sci Data 2019; 6:278. [PMID: 31757973 PMCID: PMC6874543 DOI: 10.1038/s41597-019-0294-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
Arabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses. Measurement(s) | Proteome | Technology Type(s) | mass spectrometry assay • computational modeling technique | Sample Characteristic - Organism | Arabidopsis thaliana |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9959036
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Affiliation(s)
- Huoming Zhang
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia.
| | - Pei Liu
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Huayan Zhao
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- King Abdallah University of Science and Technology, Core Labs, Thuwal, Kingdom of Saudi Arabia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculry of Science, University of Zurich, Zurich, Switzerland
| | - Liming Xiong
- Division of Biological and Environmental Science and Engineering, King Abdallah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Department of Biology, Hong Kong Baptist University, Kowlong Tong, Hong Kong, SAR, China
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species. PLANTS 2019; 8:plants8110488. [PMID: 31717908 PMCID: PMC6918222 DOI: 10.3390/plants8110488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 01/25/2023]
Abstract
Soluble sugars and organic acids are the main determinants of fruit organoleptic quality. To investigate the genes responsible for the soluble sugar and organic acid contents of apple fruits, a label-free proteomic analysis involving liquid chromatography (LC)-mass spectrometry (MS)/MS was conducted with the fruits of two Malus species, M. sargentii and M. niedzwetzkyana, which exhibit significant differences in soluble sugar and organic acid contents. A total of 13,036 unique peptides and 1,079 differentially-expressed proteins were identified. To verify the LC-MS/MS results, five candidate proteins were further analyzed by parallel reaction monitoring. The results were consistent with the LC-MS/MS data, which confirmed the reliability of the LC-MS/MS analysis. The functional annotation of the differentially-expressed proteins, based on the gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, revealed that they were mainly related to biological processes and cellular components. Additionally, the main enriched KEGG pathways were related to metabolic processes. Moreover, 31 proteins involved in soluble sugar metabolism, organic acid metabolism, and H+-transport were identified. The results of this study may be useful for the comprehensive characterization of the complex mechanism regulating apple fruit-soluble sugar and organic acid contents.
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