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Mittelberger C, Moser M, Hause B, Janik K. 'Candidatus Phytoplasma mali' SAP11-Like protein modulates expression of genes involved in energy production, photosynthesis, and defense in Nicotiana occidentalis leaves. BMC PLANT BIOLOGY 2024; 24:393. [PMID: 38741080 PMCID: PMC11089699 DOI: 10.1186/s12870-024-05087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND 'Candidatus Phytoplasma mali', the causal agent of apple proliferation disease, exerts influence on its host plant through various effector proteins, including SAP11CaPm which interacts with different TEOSINTE BRANCHED1/ CYCLOIDEA/ PROLIFERATING CELL FACTOR 1 and 2 (TCP) transcription factors. This study examines the transcriptional response of the plant upon early expression of SAP11CaPm. For that purpose, leaves of Nicotiana occidentalis H.-M. Wheeler were Agrobacterium-infiltrated to induce transient expression of SAP11CaPm and changes in the transcriptome were recorded until 5 days post infiltration. RESULTS The RNA-seq analysis revealed that presence of SAP11CaPm in leaves leads to downregulation of genes involved in defense response and related to photosynthetic processes, while expression of genes involved in energy production was enhanced. CONCLUSIONS The results indicate that early SAP11CaPm expression might be important for the colonization of the host plant since phytoplasmas lack many metabolic genes and are thus dependent on metabolites from their host plant.
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Affiliation(s)
- Cecilia Mittelberger
- Molecular Biology and Microbiology, Group of Functional Genomics, Laimburg Research Centre, Pfatten (Vadena), South Tyrol, 39051, Italy
| | - Mirko Moser
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Trentino, 39098, Italy
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Saxony-Anhalt, Germany
| | - Katrin Janik
- Molecular Biology and Microbiology, Group of Functional Genomics, Laimburg Research Centre, Pfatten (Vadena), South Tyrol, 39051, Italy.
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2
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Barthel D, Cullinan C, Mejia-Aguilar A, Chuprikova E, McLeod BA, Kerschbamer C, Trenti M, Monsorno R, Prechsl UE, Janik K. Identification of spectral ranges that contribute to phytoplasma detection in apple trees - A step towards an on-site method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123246. [PMID: 37586278 DOI: 10.1016/j.saa.2023.123246] [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: 12/01/2022] [Revised: 07/07/2023] [Accepted: 08/06/2023] [Indexed: 08/18/2023]
Abstract
'Candidatus Phytoplasma mali' is the bacterial agent associated with Apple Proliferation, a disease that causes high economic losses in affected commercial apple growing regions. The identification of the disease is carried out by visual inspection performed by skilled professionals in the orchards. To confirm an infection, costly molecular laboratory methods must be applied. Furthermore, both methods are very time-consuming. Here, we analysed the potential of a non-destructive method using in-field measurements to differentiate infected from non-infected apple trees (Malus domestica) based on spectral signatures of fresh leaves. By using multivariate statistics, we were able to distinguish infected from non-infected trees and identified the wavelengths relevant for the differentiation. Factors affecting the differentiation performance were the sampling date and bacterial colonization behaviour.
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Affiliation(s)
- Dana Barthel
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy; Eurac Research, Drususallee 1/Viale Druso 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Cameron Cullinan
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy; Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Universitätsplatz 1/Piazza Università 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Abraham Mejia-Aguilar
- Eurac Research, Drususallee 1/Viale Druso 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Ekaterina Chuprikova
- Eurac Research, Drususallee 1/Viale Druso 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Ben Alexander McLeod
- Eurac Research, Drususallee 1/Viale Druso 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Christine Kerschbamer
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Massimiliano Trenti
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Roberto Monsorno
- Eurac Research, Drususallee 1/Viale Druso 1, IT-39100 Bozen (Bolzano), South Tyrol, Italy
| | - Ulrich E Prechsl
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Katrin Janik
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy.
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3
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Corretto E, Trenti M, Štarhová Serbina L, Howie JM, Dittmer J, Kerschbamer C, Candian V, Tedeschi R, Janik K, Schuler H. Multiple factors driving the acquisition efficiency of apple proliferation phytoplasma in Cacopsylla melanoneura. JOURNAL OF PEST SCIENCE 2023; 97:1299-1314. [PMID: 39188925 PMCID: PMC11344730 DOI: 10.1007/s10340-023-01699-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 08/28/2024]
Abstract
Phytoplasmas are bacterial pathogens located in the plant's phloem that are responsible for several plant diseases and are mainly transmitted by phloem-sucking insects. Apple proliferation (AP) is an economically important disease associated with the presence of 'Candidatus Phytoplasma mali' which is transmitted by two psyllid species. While Cacopsylla picta is a vector in different regions, the vector efficiency of C. melanoneura varies between different populations. This species is considered the main AP vector in Northwestern Italy but plays a minor role in Northeastern Italy and other European regions. To investigate whether the psyllid and/or the phytoplasma subtype drive the phytoplasma acquisition in C. melanoneura, a phytoplasma acquisition experiment was set up using single mating couples of overwintered individuals from different psyllid populations and phytoplasma subtypes. All analyzed insect populations acquired phytoplasma, but with different efficiencies and concentrations. The main factors driving the acquisition were the phytoplasma subtype and its concentration in the leaves of the infected trees together with the psyllid lineage. The phytoplasma concentration in the psyllids was again influenced by the phytoplasma subtype, the psyllid lineage and the region of origin, whereas the phytoplasma concentration in the leaves and the psyllid haplotype defined with the cytochrome oxidase I gene had only a minor impact on the phytoplasma concentration. This is the first study evaluating the roles of both the psyllid haplotype and the phytoplasma subtype on the acquisition process and highlights the importance of C. melanoneura as an additional AP vector. Supplementary Information The online version contains supplementary material available at 10.1007/s10340-023-01699-1.
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Affiliation(s)
- Erika Corretto
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
| | | | - Liliya Štarhová Serbina
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
| | - James Malcolm Howie
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences Vienna, BOKU, Vienna, Austria
| | - Jessica Dittmer
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
- UMR 1345, Institut Agro, INRAE, IRHS, SFR Quasav, Université d’Angers, Angers, France
| | | | - Valentina Candian
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Grugliasco, Italy
| | - Rosemarie Tedeschi
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Grugliasco, Italy
| | | | - Hannes Schuler
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
- Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bozen-Bolzano, Italy
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4
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Pamei I, Makandar R. Comparative proteome analysis reveals the role of negative floral regulators and defense-related genes in phytoplasma infected sesame. PROTOPLASMA 2022; 259:1441-1453. [PMID: 35190871 DOI: 10.1007/s00709-022-01737-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
"Candidatus Phytoplasma australiense" is associated with floral malformations in sesame but the interaction remains largely unexplored. A label-free quantitative shotgun proteomics approach through liquid chromatography-mass spectrometry quadruple time-of-flight was used to analyze changes in the proteome of asymptomatic (control) and symptomatic (phytoplasma-infected) sesame plants to identify proteins differentially expressed during phytoplasma infection at early stages of flower development. A total of 3457 and 1704 proteins were identified from asymptomatic and symptomatic samples respectively through proteome profiling with three runs per sample. Several differentially abundant proteins (DAPs) were identified which might be involved in sesame-phytoplasma interaction. The DAPs identified were related to transcription, cell division, chromosome partitioning, defense mechanisms, negative regulation of flower development, amino acid transport and metabolism, signal transduction and RNA processing, and its modifications. Of these proteins, 21 were downregulated while 212 were significantly upregulated in symptomatic sesame plants compared to the control plants. The floral development-related proteins like UBP16 and DCAF1 were found to be downregulated while negative regulators/repressors of floral development genes, HUA2, PIE1, and ICU2, were upregulated in symptomatic samples indicating phytoplasma's role in altering the expression of these genes. Validation of these genes through quantitative retro-transcripted PCR suggested that the DAPs observed in symptomatic sesame might be induced by phytoplasma presence to suppress flowering via negative regulation of flower development.
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Affiliation(s)
- Injangbuanang Pamei
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India.
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5
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Leetanasaksakul K, Roytrakul S, Phaonakrop N, Kittisenachai S, Thaisakun S, Srithuanok N, Sriroth K, Soulard L. Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach. PeerJ 2022; 10:e12740. [PMID: 35036104 PMCID: PMC8742537 DOI: 10.7717/peerj.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/13/2021] [Indexed: 01/07/2023] Open
Abstract
Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement.
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Affiliation(s)
- Kantinan Leetanasaksakul
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Suthathip Kittisenachai
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Nitiya Srithuanok
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
| | - Klanarong Sriroth
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
| | - Laurent Soulard
- Mitr Phol Innovation and Research Center, Khoksa-at, Phu Khiao, Chaiyaphum, Thailand
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6
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Barthel D, Dordevic N, Fischnaller S, Kerschbamer C, Messner M, Eisenstecken D, Robatscher P, Janik K. Detection of apple proliferation disease in Malus × domestica by near infrared reflectance analysis of leaves. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 263:120178. [PMID: 34280798 DOI: 10.1016/j.saa.2021.120178] [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: 05/12/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
In this study near infrared spectroscopical analysis of dried and ground leaves was performed and combined with a multivariate data analysis to distinguish 'Candidatus Phytoplasma mali' infected from non-infected apple trees (Malus × domestica). The bacterium is the causative agent of Apple Proliferation, one of the most threatening diseases in commercial apple growing regions. In a two-year study, leaves were sampled from three apple orchards, at different sampling events throughout the vegetation period. The spectral data were analyzed with a principal component analysis and classification models were developed. The model performance for the differentiation of Apple Proliferation diseased from non-infected trees increased throughout the vegetation period and gained best results in autumn. Even with asymptomatic leaves from infected trees a correct classification was possible indicating that the spectral-based method provides reliable results even if samples without visible symptoms are analyzed. The wavelength regions that contributed to the differentiation of infected and non-infected trees could be mainly assigned to a reduction of carbohydrates and N-containing organic compounds. Wet chemical analyses confirmed that N-containing compounds are reduced in leaves from infected trees. The results of our study provide a valuable indication that spectral analysis is a promising technique for Apple Proliferation detection in future smart farming approaches.
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Affiliation(s)
- Dana Barthel
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy.
| | - Nikola Dordevic
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Stefanie Fischnaller
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Christine Kerschbamer
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Manuel Messner
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Daniela Eisenstecken
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Peter Robatscher
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy
| | - Katrin Janik
- Laimburg Research Centre, Laimburg 6, Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol, Italy.
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7
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Rodriguez-Saona C, Polashock JJ, Kyryczenko-Roth V, Holdcraft R, Jimenez-Gonzalez G, De Moraes CM, Mescher MC. Application of Plant Defense Elicitors Fails to Enhance Herbivore Resistance or Mitigate Phytoplasma Infection in Cranberries. FRONTIERS IN PLANT SCIENCE 2021; 12:700242. [PMID: 34456943 PMCID: PMC8387625 DOI: 10.3389/fpls.2021.700242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Synthetic elicitors of the salicylic acid (SA) and jasmonic acid (JA) plant defense pathways can be used to increase crop protection against herbivores and pathogens. In this study, we tested the hypothesis that elicitors of plant defenses interact with pathogen infection to influence crop resistance against vector and nonvector herbivores. To do so, we employed a trophic system comprising of cranberries (Vaccinium macrocarpon), the phytoplasma that causes false blossom disease, and two herbivores-the blunt-nosed leafhopper (Limotettix vaccinii), the vector of false blossom disease, and the nonvector gypsy moth (Lymantria dispar). We tested four commercial elicitors, including three that activate mainly SA-related plant defenses (Actigard, LifeGard, and Regalia) and one activator of JA-related defenses (Blush). A greenhouse experiment in which phytoplasma-infected and uninfected plants received repeated exposure to elicitors revealed that both phytoplasma infection and elicitor treatment individually improved L. vaccinii and L. dispar mass compared to uninfected, untreated controls; however, SA-based elicitor treatments reduced L. vaccinii mass on infected plants. Regalia also improved L. vaccinii survival. Phytoplasma infection reduced plant size and mass, increased levels of nitrogen (N) and SA, and lowered carbon/nitrogen (C/N) ratios compared to uninfected plants, irrespective of elicitor treatment. Although none of our elicitor treatments influenced transcript levels of a phytoplasma-specific marker gene, all of them increased N and reduced C/N levels; the three SA activators also reduced JA levels. Taken together, our findings reveal positive effects of both phytoplasma infection and elicitor treatment on the performance of L. vaccinii and L. dispar in cranberries, likely via enhancement of plant nutrition and changes in phytohormone profiles, specifically increases in SA levels and corresponding decreases in levels of JA. Thus, we found no evidence that the tested elicitors of plant defenses increase resistance to insect herbivores or reduce disease incidence in cranberries.
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Affiliation(s)
| | - James J Polashock
- Genetic Improvement of Fruits and Vegetables Lab, United States Department of Agriculture-Agricultural Research Service, Chatsworth, NJ, United States
| | - Vera Kyryczenko-Roth
- P.E. Marucci Center, Rutgers University, Lake Oswego, Chatsworth, NJ, United States
| | - Robert Holdcraft
- P.E. Marucci Center, Rutgers University, Lake Oswego, Chatsworth, NJ, United States
| | - Giovanna Jimenez-Gonzalez
- Escuela de Ciencias Agrícolas, Pecuarias y del Medio Ambiente (ECAPMA), Universidad Nacional Abierta y a Distancia (UNAD), Bogotá, Colombia
| | | | - Mark C Mescher
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Differential Response of Grapevine to Infection with ' Candidatus Phytoplasma solani' in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes. Int J Mol Sci 2021; 22:ijms22073531. [PMID: 33805429 PMCID: PMC8037961 DOI: 10.3390/ijms22073531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.
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9
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Tan Y, Li Q, Zhao Y, Wei H, Wang J, Baker CJ, Liu Q, Wei W. Integration of metabolomics and existing omics data reveals new insights into phytoplasma-induced metabolic reprogramming in host plants. PLoS One 2021; 16:e0246203. [PMID: 33539421 PMCID: PMC7861385 DOI: 10.1371/journal.pone.0246203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/14/2021] [Indexed: 12/03/2022] Open
Abstract
Phytoplasmas are cell wall-less bacteria that induce abnormal plant growth and various diseases, causing severe economic loss. Phytoplasmas are highly dependent on nutrients imported from host cells because they have lost many genes involved in essential metabolic pathways during reductive evolution. However, metabolic crosstalk between phytoplasmas and host plants and the mechanisms of phytoplasma nutrient acquisition remain poorly understood. In this study, using metabolomics approach, sweet cherry virescence (SCV) phytoplasma-induced metabolite alterations in sweet cherry trees were investigated. A total of 676 metabolites were identified in SCV phytoplasma-infected and mock inoculated leaves, of which 187 metabolites were differentially expressed, with an overwhelming majority belonging to carbohydrates, fatty acids/lipids, amino acids, and flavonoids. Available omics data of interactions between plant and phytoplasma were also deciphered and integrated into the present study. The results demonstrated that phytoplasma infection promoted glycolysis and pentose phosphate pathway activities, which provide energy and nutrients, and facilitate biosynthesis of necessary low-molecular metabolites. Our findings indicated that phytoplasma can induce reprograming of plant metabolism to obtain nutrients for its own replication and infection. The findings from this study provide new insight into interactions of host plants and phytoplasmas from a nutrient acquisition perspective.
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Affiliation(s)
- Yue Tan
- Shandong Institute of Pomology, Taian, China
| | - Qingliang Li
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Yan Zhao
- United States Department of Agriculture, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, United States of America
| | - Hairong Wei
- Shandong Institute of Pomology, Taian, China
| | - Jiawei Wang
- Shandong Institute of Pomology, Taian, China
| | - Con Jacyn Baker
- United States Department of Agriculture, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, United States of America
| | | | - Wei Wei
- United States Department of Agriculture, Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, Beltsville, MD, United States of America
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10
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Mullins Y, Keogh K, Blackshields G, Kenny DA, Kelly AK, Waters SM. Transcriptome assisted label free proteomics of hepatic tissue in response to both dietary restriction and compensatory growth in cattle. J Proteomics 2020; 232:104048. [PMID: 33217582 DOI: 10.1016/j.jprot.2020.104048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 11/28/2022]
Abstract
Compensatory growth (CG) is a naturally occurring phenomenon where, following a period of under nutrition, an animal exhibits accelerated growth upon re-alimentation. The objective was to identify and quantify hepatic proteins involved in the regulation of CG in cattle. Forty Holstein Friesian bulls were equally assigned to one of four groups. Groups; A1 and A2 had ad libitum access to feed for 125 days, groups R1 and R2 were feed restricted. Following this, R1 and A1 animals were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum feeding for a successive 55 days. At slaughter hepatic tissue samples were collected and label-free quantitative proteomics undertaken with spectra searched against a custom built transcriptome database specific to the animals in this study. 24 differentially abundant proteins were identified during CG (R2 vs. R1) including; PSPH, ASNS and GSTM1, which are involved in nutrient metabolism, immune response and cellular growth. Proteins involved in biochemical pathways related to nutrient metabolism were down-regulated during CG, indicating a possible adaptive response by the liver to a period of fluctuating nutrient availability. The livers ability to regulate its metabolic activity may have profound effects on the efficiency of whole body energy utilization during CG. SIGNIFICANCE: This study is the first to unravel the effect of compensatory growth on the hepatic proteome of cattle using transcriptome-assisted shot gun proteomics. Proteins identified as being affected by dietary restriction and subsequent expression of compensatory growth in this study may, following appropriate validation, contribute to the identification of functional genetic variants. Such information could be harnessed within the context of genomic selection in cattle breeding programs to identify animals with a greater genetic potential to undergo compensatory growth, thus increasing the profitability of the beef sector and accelerating genetic gain.
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Affiliation(s)
- Yvonne Mullins
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Kate Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Gordon Blackshields
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Alan K Kelly
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
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11
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Mittelberger C, Stellmach H, Hause B, Kerschbamer C, Schlink K, Letschka T, Janik K. A Novel Effector Protein of Apple Proliferation Phytoplasma Disrupts Cell Integrity of Nicotiana spp. Protoplasts. Int J Mol Sci 2019; 20:E4613. [PMID: 31540359 PMCID: PMC6770106 DOI: 10.3390/ijms20184613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 01/19/2023] Open
Abstract
Effector proteins play an important role in the virulence of plant pathogens such as phytoplasma, which are the causative agents of hundreds of different plant diseases. The plant hosts comprise economically relevant crops such as apples (Malus × domestica), which can be infected by 'Candidatus Phytoplasma mali' (P. mali), a highly genetically dynamic plant pathogen. As the result of the genetic and functional analyses in this study, a new putative P. mali effector protein was revealed. The so-called "Protein in Malus Expressed 2" (PME2), which is expressed in apples during P. mali infection but not in the insect vector, shows regional genetic differences. In a heterologous expression assay using Nicotiana benthamiana and Nicotiana occidentalis mesophyll protoplasts, translocation of both PME2 variants in the cell nucleus was observed. Overexpression of the effector protein affected cell integrity in Nicotiana spp. protoplasts, indicating a potential role of this protein in pathogenic virulence. Interestingly, the two genetic variants of PME2 differ regarding their potential to manipulate cell integrity. However, the exact function of PME2 during disease manifestation and symptom development remains to be further elucidated. Aside from the first description of the function of a novel effector of P. mali, the results of this study underline the necessity for a more comprehensive description and understanding of the genetic diversity of P. mali as an indispensable basis for a functional understanding of apple proliferation disease.
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Affiliation(s)
- Cecilia Mittelberger
- Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer/Ora (BZ), Italy.
| | - Hagen Stellmach
- Jasmonate Function & Mycorrhiza, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Bettina Hause
- Jasmonate Function & Mycorrhiza, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Christine Kerschbamer
- Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer/Ora (BZ), Italy.
| | - Katja Schlink
- Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer/Ora (BZ), Italy.
| | - Thomas Letschka
- Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer/Ora (BZ), Italy.
| | - Katrin Janik
- Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer/Ora (BZ), Italy.
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12
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Dermastia M. Plant Hormones in Phytoplasma Infected Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:477. [PMID: 31057582 PMCID: PMC6478762 DOI: 10.3389/fpls.2019.00477] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/28/2019] [Indexed: 05/21/2023]
Abstract
Phytoplasmas are bacterial plant pathogens that need a plant host and an insect vector for their spread and survival. In plants, the physiological responses that phytoplasmas trigger result in symptom development through effects on hormonal, nutritional, and stress signaling pathways, and the interactions between these. In this review, recent advances on the involvement of plant hormones together with their known and deduced roles in plants infected with phytoplasmas are discussed. Several studies have directly, or in many cases indirectly, addressed plant hormone systems in phytoplasma-infected plants. These have provided accumulating evidence that phytoplasmas extensively affect plant hormone pathways. Phytoplasmas thus, with disturbing complex plant hormone networks, suppress plant immunity and modify plant structure, while optimizing their nutrient acquisition and facilitating their colonization of the plants, and their dissemination among plants by their insect vectors.
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Affiliation(s)
- Marina Dermastia
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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13
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Aizat WM, Ibrahim S, Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM. Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation. PeerJ 2018; 6:e5525. [PMID: 30186693 PMCID: PMC6118203 DOI: 10.7717/peerj.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown. METHOD In this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression. RESULTS From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147). DISCUSSION MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.
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Affiliation(s)
- Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Sarah Ibrahim
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | - Kok-Keong Loke
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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14
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Poleti MD, Regitano LC, Souza GH, Cesar AS, Simas RC, Silva-Vignato B, Oliveira GB, Andrade SC, Cameron LC, Coutinho LL. Longissimus dorsi muscle label-free quantitative proteomic reveals biological mechanisms associated with intramuscular fat deposition. J Proteomics 2018; 179:30-41. [DOI: 10.1016/j.jprot.2018.02.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/14/2018] [Accepted: 02/26/2018] [Indexed: 02/06/2023]
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15
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Gai YP, Zhao HN, Zhao YN, Zhu BS, Yuan SS, Li S, Guo FY, Ji XL. MiRNA-seq-based profiles of miRNAs in mulberry phloem sap provide insight into the pathogenic mechanisms of mulberry yellow dwarf disease. Sci Rep 2018; 8:812. [PMID: 29339758 PMCID: PMC5770470 DOI: 10.1038/s41598-018-19210-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022] Open
Abstract
A wide range of miRNAs have been identified as phloem-mobile molecules that play important roles in coordinating plant development and physiology. Phytoplasmas are associated with hundreds of plant diseases, and the pathogenesis involved in the interactions between phytoplasmas and plants is still poorly understood. To analyse the molecular mechanisms of phytoplasma pathogenicity, the miRNAs profiles in mulberry phloem saps were examined in response to phytoplasma infection. A total of 86 conserved miRNAs and 19 novel miRNAs were identified, and 30 conserved miRNAs and 13 novel miRNAs were differentially expressed upon infection with phytoplasmas. The target genes of the differentially expressed miRNAs are involved in diverse signalling pathways showing the complex interactions between mulberry and phytoplasma. Interestingly, we found that mul-miR482a-5p was up-regulated in the infected phloem saps, and grafting experiments showed that it can be transported from scions to rootstock. Based on the results, the complexity and roles of the miRNAs in phloem sap and the potential molecular mechanisms of their changes were discussed. It is likely that the phytoplasma-responsive miRNAs in the phloem sap modulate multiple pathways and work cooperatively in response to phytoplasma infection, and their expression changes may be responsible for some symptoms in the infected plants.
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Affiliation(s)
- Ying-Ping Gai
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Huai-Ning Zhao
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Ya-Nan Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Bing-Sen Zhu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo-Shuo Yuan
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Shuo Li
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Fang-Yue Guo
- College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
| | - Xian-Ling Ji
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China. .,College of Forestry, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China.
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16
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17
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Jassbi AR, Zare S, Asadollahi M, Schuman MC. Ecological Roles and Biological Activities of Specialized Metabolites from the Genus Nicotiana. Chem Rev 2017; 117:12227-12280. [PMID: 28960061 DOI: 10.1021/acs.chemrev.7b00001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Species of Nicotiana grow naturally in different parts of the world and have long been used both medicinally and recreationally by human societies. More recently in our history, Nicotiana tabacum has attracted interest as one of the most economically important industrial crops. Nicotiana species are frequently investigated for their bioactive natural products, and the ecological role of their specialized metabolites in responses to abiotic stress or biotic stress factors like pathogens and herbivores. The interest of tobacco companies in genetic information as well as the success of a few wild tobacco species as experimental model organisms have resulted in growing knowledge about the molecular biology and ecology of these plants and functional studies of the plant's natural products. Although a large number of reviews and books on biologically active natural products already exists, mostly from N. tabacum, we focus our attention on the ecological roles and biological activity of natural products, versus products from cured and processed material, in this Review. The studied compounds include alkaloids, aromatic compounds, flavonoids, volatiles, sesquiterpenoids, diterpenes alcohols, and sugar esters from trichomes of the plants, and recently characterized acyclic hydroxygeranyllinalool diterpene glycosides (HGL-DTGs). In this Review (1800s-2017), we describe the above-mentioned classes of natural products, emphasizing their biological activities and functions as they have been determined either in bioassay-guided purification approaches or in bioassays with plants in which the expression of specific biosynthetic genes has been genetically manipulated. Additionally, a review on the history, taxonomy, ecology, and medicinal application of different Nicotiana species growing around the globe presented in this Review may be of interest for pharmacognosists, natural products, and ecological chemists.
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Affiliation(s)
| | | | | | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology , Jena 07745, Germany
- German Centre for Integrative Biodiversity Research (iDiv) , Deutscher Platz 5e, Leipzig 04103, Germany
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18
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Comparative Proteomic Analysis of Paulownia fortunei Response to Phytoplasma Infection with Dimethyl Sulfate Treatment. Int J Genomics 2017; 2017:6542075. [PMID: 29038787 PMCID: PMC5605944 DOI: 10.1155/2017/6542075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/01/2017] [Accepted: 08/09/2017] [Indexed: 12/02/2022] Open
Abstract
Paulownia fortunei is a widely cultivated economic forest tree species that is susceptible to infection with phytoplasma, resulting in Paulownia witches' broom (PaWB) disease. Diseased P. fortunei is characterized by stunted growth, witches' broom, shortened internodes, and etiolated and smaller leaves. To understand the molecular mechanism of its pathogenesis, we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography coupled with tandem mass spectrometry approaches to study changes in the proteomes of healthy P. fortunei, PaWB-infected P. fortunei, and PaWB-infected P. fortunei treated with 15 mg·L−1 or 75 mg·L−1 dimethyl sulfate. We identified 2969 proteins and 104 and 32 differentially abundant proteins that were phytoplasma infection responsive and dimethyl sulfate responsive, respectively. Based on our analysis of the different proteomes, 27 PaWB-related proteins were identified. The protein-protein interactions of these 27 proteins were analyzed and classified into four groups (photosynthesis-related, energy-related, ribosome-related, and individual proteins). These PaWB-related proteins may help in developing a deeper understanding of how PaWB affects the morphological characteristics of P. fortunei and further establish the mechanisms involved in the response of P. fortunei to phytoplasma.
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19
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Menschaert G, David F. Proteogenomics from a bioinformatics angle: A growing field. MASS SPECTROMETRY REVIEWS 2017; 36:584-599. [PMID: 26670565 PMCID: PMC6101030 DOI: 10.1002/mas.21483] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/01/2015] [Indexed: 05/16/2023]
Abstract
Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:584-599, 2017.
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Affiliation(s)
- Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of
Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience
Engineering, Ghent University, Ghent, Belgium
- To whom correspondence should be addressed. Tel:
+32 9 264 99 22; Fax: +32 9 264 6220;
| | - Fenyö David
- Center for Health Informatics and Bioinformatics and Department of
Biochemistry and Molecular Pharmacology, New York University School of Medicine, New
York, New York, USA
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20
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Wang Z, Liu W, Fan G, Zhai X, Zhao Z, Dong Y, Deng M, Cao Y. Quantitative proteome-level analysis of paulownia witches' broom disease with methyl methane sulfonate assistance reveals diverse metabolic changes during the infection and recovery processes. PeerJ 2017; 5:e3495. [PMID: 28690927 PMCID: PMC5497676 DOI: 10.7717/peerj.3495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/02/2017] [Indexed: 12/17/2022] Open
Abstract
Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P. fortunei (PF), PaWB-infected P. fortunei (PFI), and PaWB-infected P. fortunei treated with 20 mg L-1 or 60 mg L-1 methyl methane sulfonate (MMS) (PFI-20 and PFI-60, respectively). A total of 2,358 proteins were identified. We investigated the proteins profiles in PF vs. PFI (infected process) and PFI-20 vs. PFI-60 (recovered process), and further found that many of the MMS-response proteins mapped to "photosynthesis" and "ribosome" pathways. Based on our comparison scheme, 36 PaWB-related proteins were revealed. Among them, 32 proteins were classified into three functional groups: (1) carbohydrate and energy metabolism, (2) protein synthesis and degradation, and (3) stress resistance. We then investigated the PaWB-related proteins involved in the infected and recovered processes, and discovered that carbohydrate and energy metabolism was inhibited, and protein synthesis and degradation decreased, as the plant responded to PaWB. Our observations may be useful for characterizing the proteome-level changes that occur at different stages of PaWB disease. The data generated in this study may serve as a valuable resource for elucidating the pathogenesis of PaWB disease during phytoplasma infection and recovery stages.
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Affiliation(s)
- Zhe Wang
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China
| | - Wenshan Liu
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | | | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China.,College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yabing Cao
- Institute of Paulownia, Henan Agricultural University, Zhengzhou, China
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21
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Cao X, Fan G, Dong Y, Zhao Z, Deng M, Wang Z, Liu W. Proteome Profiling of Paulownia Seedlings Infected with Phytoplasma. FRONTIERS IN PLANT SCIENCE 2017; 8:342. [PMID: 28344590 PMCID: PMC5344924 DOI: 10.3389/fpls.2017.00342] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/27/2017] [Indexed: 05/29/2023]
Abstract
Phytoplasma is an insect-transmitted pathogen that causes witches' broom disease in many plants. Paulownia witches' broom is one of the most destructive diseases threatening Paulownia production. The molecular mechanisms associated with this disease have been investigated by transcriptome sequencing, but changes in protein abundance have not been investigated with isobaric tags for relative and absolute quantitation. Previous results have shown that methyl methane sulfonate (MMS) can help Paulownia seedlings recover from the symptoms of witches' broom and reinstate a healthy morphology. In this study, a transcriptomic-assisted proteomic technique was used to analyze the protein changes in phytoplasma-infected Paulownia tomentosa seedlings, phytoplasma-infected seedlings treated with 20 and 60 mg·L-1 MMS, and healthy seedlings. A total of 2,051 proteins were obtained, 879 of which were found to be differentially abundant in pairwise comparisons between the sample groups. Among the differentially abundant proteins, 43 were related to Paulownia witches' broom disease and many of them were annotated to be involved in photosynthesis, expression of dwarf symptom, energy production, and cell signal pathways.
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Affiliation(s)
- Xibing Cao
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Guoqiang Fan
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Yanpeng Dong
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Zhenli Zhao
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Minjie Deng
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
| | - Zhe Wang
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
| | - Wenshan Liu
- Institute of Paulownia, Henan Agricultural UniversityZhengzhou, China
- College of Forestry, Henan Agricultural UniversityZhengzhou, China
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22
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Zhang J, Yang MK, Zeng H, Ge F. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics 2016; 15:3529-3539. [PMID: 27630248 DOI: 10.1074/mcp.m116.060046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.
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Affiliation(s)
- Jia Zhang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ming-Kun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Honghui Zeng
- §Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; .,§Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
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23
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Luge T, Fischer C, Sauer S. Efficient Application of De Novo RNA Assemblers for Proteomics Informed by Transcriptomics. J Proteome Res 2016; 15:3938-3943. [DOI: 10.1021/acs.jproteome.6b00301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Toni Luge
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Cornelius Fischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- BIMSB
and BIH Genomics Platforms, Laboratory of Functional Genomics, Nutrigenomics
and Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße
10, 13125 Berlin, Germany
| | - Sascha Sauer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- BIMSB
and BIH Genomics Platforms, Laboratory of Functional Genomics, Nutrigenomics
and Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Straße
10, 13125 Berlin, Germany
- CU Systems
Medicine, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
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24
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Mahadevan C, Krishnan A, Saraswathy GG, Surendran A, Jaleel A, Sakuntala M. Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem. FRONTIERS IN PLANT SCIENCE 2016; 7:785. [PMID: 27379110 PMCID: PMC4913111 DOI: 10.3389/fpls.2016.00785] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/22/2016] [Indexed: 05/22/2023]
Abstract
Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887.
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Affiliation(s)
| | - Anu Krishnan
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Gayathri G. Saraswathy
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Arun Surendran
- Proteomics Core Facility, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Abdul Jaleel
- Proteomics Core Facility, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
| | - Manjula Sakuntala
- Division of Plant Molecular Biology, Rajiv Gandhi Center for BiotechnologyThiruvananthapuram, India
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25
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Reis RS, Vale EDM, Heringer AS, Santa-Catarina C, Silveira V. Putrescine induces somatic embryo development and proteomic changes in embryogenic callus of sugarcane. J Proteomics 2016; 130:170-9. [DOI: 10.1016/j.jprot.2015.09.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/27/2015] [Accepted: 09/21/2015] [Indexed: 01/29/2023]
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27
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Luge T, Sauer S. Generating Sample-Specific Databases for Mass Spectrometry-Based Proteomic Analysis by Using RNA Sequencing. Methods Mol Biol 2016; 1394:219-232. [PMID: 26700052 DOI: 10.1007/978-1-4939-3341-9_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mass spectrometry-based methods allow for the direct, comprehensive analysis of expressed proteins and their quantification among different conditions. However, in general identification of proteins by assigning experimental mass spectra to peptide sequences of proteins relies on matching mass spectra to theoretical spectra derived from genomic databases of organisms. This conventional approach limits the applicability of proteomic methodologies to species for which a genome reference sequence is available. Recently, RNA-sequencing (RNA-Seq) became a valuable tool to overcome this limitation by de novo construction of databases for organisms for which no DNA sequence is available, or by refining existing genomic databases with transcriptomic data. Here we present a generic pipeline to make use of transcriptomic data for proteomics experiments. We show in particular how to efficiently fuel proteomic analysis workflows with sample-specific RNA-sequencing databases. This approach is useful for the proteomic analysis of so far unsequenced organisms, complex microbial metatranscriptomes/metaproteomes (for example in the human body), and for refining current proteomics data analysis that solely relies on the genomic sequence and predicted gene expression but not on validated gene products. Finally, the approach used in the here presented protocol can help to improve the data quality of conventional proteomics experiments that can be influenced by genetic variation or splicing events.
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Affiliation(s)
- Toni Luge
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Sascha Sauer
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany.
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28
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Heringer AS, Barroso T, Macedo AF, Santa-Catarina C, Souza GHMF, Floh EIS, de Souza-Filho GA, Silveira V. Label-Free Quantitative Proteomics of Embryogenic and Non-Embryogenic Callus during Sugarcane Somatic Embryogenesis. PLoS One 2015; 10:e0127803. [PMID: 26035435 PMCID: PMC4452777 DOI: 10.1371/journal.pone.0127803] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/18/2015] [Indexed: 02/05/2023] Open
Abstract
The development of somatic cells in to embryogenic cells occurs in several stages and ends in somatic embryo formation, though most of these biochemical and molecular changes have yet to be elucidated. Somatic embryogenesis coupled with genetic transformation could be a biotechnological tool to improve potential crop yields potential in sugarcane cultivars. The objective of this study was to observe somatic embryo development and to identify differentially expressed proteins in embryogenic (E) and non-embryogenic (NE) callus during maturation treatment. E and NE callus were cultured on maturation culture medium supplemented with different concentrations (0.0, 0.75, 1.5 and 2.0 g L(-1)) of activated charcoal (AC). Somatic embryo formation and differential protein expression were evaluated at days 0 and 21 using shotgun proteomic analyses. Treatment with 1.5 g L(-1) AC resulted in higher somatic embryo maturation rates (158 somatic embryos in 14 days) in E callus but has no effect in NE callus. A total of 752 co-expressed proteins were identified through the SUCEST (The Sugarcane EST Project), including many housekeeping proteins. E callus showed 65 exclusive proteins on day 0, including dehydrogenase, desiccation-related protein, callose synthase 1 and nitric oxide synthase. After 21 days on maturation treatment, 14 exclusive proteins were identified in E callus, including catalase and secreted protein. NE callus showed 23 exclusive proteins on day 0 and 10 exclusive proteins after 21 days on maturation treatment, including many proteins related to protein degradation. The induction of maturation leads to somatic embryo development, which likely depends on the expression of specific proteins throughout the process, as seen in E callus under maturation treatment. On the other hand, some exclusive proteins can also specifically prevent of somatic embryos development, as seen in the NE callus.
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Affiliation(s)
- Angelo Schuabb Heringer
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Tatiana Barroso
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Amanda Ferreira Macedo
- Laboratório de Biologia Celular de Plantas, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | | | | | - Eny Iochevet Segal Floh
- Laboratório de Biologia Celular de Plantas, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Gonçalo Apolinário de Souza-Filho
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF). Campos dos Goytacazes, RJ, Brazil
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29
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Sauer S, Luge T. Nutriproteomics: Facts, concepts, and perspectives. Proteomics 2015; 15:997-1013. [DOI: 10.1002/pmic.201400383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Sascha Sauer
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Toni Luge
- Otto Warburg Laboratory; Max Planck Institute for Molecular Genetics; Berlin Germany
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30
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Abbà S, Galetto L, Carle P, Carrère S, Delledonne M, Foissac X, Palmano S, Veratti F, Marzachì C. RNA-Seq profile of flavescence dorée phytoplasma in grapevine. BMC Genomics 2014; 15:1088. [PMID: 25495145 PMCID: PMC4299374 DOI: 10.1186/1471-2164-15-1088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 12/04/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insecticides. Further studies of the pathogen, the vector and the mechanisms of phytoplasma-host interactions could improve our understanding of the disease. In this work, RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting field-grown Vitis vinifera leaves. RESULTS With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 215 annotated genes, and identified 10 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 draft genome. Furthermore, we improved the annotation of 44 genes with the addition of 5'/3' untranslated regions. Functional classification revealed that the most expressed genes were either related to translation and protein biosynthesis or hypothetical proteins with unknown function. Some of these hypothetical proteins were predicted to be secreted, so they could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies. CONCLUSIONS The RNA-Seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine infection. Our results provided new insights into the transcriptional organization and gene structure of FD. This may represent the starting point for the application of high-throughput sequencing technologies to study differential expression in FD and in other phytoplasmas with an unprecedented resolution.
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Affiliation(s)
- Simona Abbà
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Luciana Galetto
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Patricia Carle
- />INRA, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
- />Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
| | - Sébastien Carrère
- />INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326 France
- />CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326 France
| | - Massimo Delledonne
- />Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, I-37134 Verona, Italy
| | - Xavier Foissac
- />INRA, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
- />Université de Bordeaux, UMR1332 Biologie du Fruit et Pathologie, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d’Ornon, Cedex, France
| | - Sabrina Palmano
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Flavio Veratti
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
| | - Cristina Marzachì
- />Istituto per la Protezione Sostenibile delle Piante, IPSP-CNR, Strada delle Cacce 73, I-10135 Torino, Italy
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Yan H, Yoo MJ, Koh J, Liu L, Chen Y, Acikgoz D, Wang Q, Chen S. Molecular Reprogramming of Arabidopsis in Response to Perturbation of Jasmonate Signaling. J Proteome Res 2014; 13:5751-66. [DOI: 10.1021/pr500739v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huizhuan Yan
- Department
of Horticulture, Zhejiang University, Hangzhou 310058, China
| | | | | | - Lihong Liu
- Department
of Horticulture, Zhejiang University, Hangzhou 310058, China
| | | | | | - Qiaomei Wang
- Department
of Horticulture, Zhejiang University, Hangzhou 310058, China
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