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Zhang X, Chen L, Ye L, Zhang B, Zhang X, Li X. Label-free based comparative proteomics approach revealed the changes in proteomic profiles driven by different maturities in two Chinese white truffles, Tuber panzhihuanense and Tuber latisporum. Food Chem 2024; 443:138535. [PMID: 38295568 DOI: 10.1016/j.foodchem.2024.138535] [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: 08/03/2023] [Revised: 12/15/2023] [Accepted: 01/20/2024] [Indexed: 02/02/2024]
Abstract
T. panzhihuanense and T. latisporum are white truffle species native to China, of which T. panzhihuanense has significant commercial potential, with high nutritional value and unique flavor. Maturity is an important factor affecting the nutrition and aroma of truffles, which determines their economic status. Here, a label-free-based comparative proteomics method was used to determine the proteomic profiles of T. panzhihuanense and T. latisporum at two different stages of maturity. The results showed that both maturity and species significantly affected the protein expression patterns. T. panzhihuanense responded stronger to maturity than T. latisporum, accompanied by a more complex interaction network between proteins. Some critical proteins were regulated by maturity and variety, including those involved in aroma formation, e.g., S-adenosyl-methionine synthetase. The enrichment of oxidation-reduction processes, glycolysis, and SNARE interactions in vesicular transport were driven by species and maturity. This study provides the first insights into the proteomic profiles of T. panzhihuanense and T. latisporum, revealing the roles of key proteins and biological processes in their maturation.
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Affiliation(s)
- Xiaoping Zhang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Li Chen
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
| | - Lei Ye
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
| | - Bo Zhang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaolin Li
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
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2
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Phong WN, Gibberd MR, Payne AD, Dykes GA, Coorey R. Methods used for extraction of plant volatiles have potential to preserve truffle aroma: A review. Compr Rev Food Sci Food Saf 2022; 21:1677-1701. [PMID: 35179824 DOI: 10.1111/1541-4337.12927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 11/30/2022]
Abstract
Truffles are considered one of the world's most highly prized foods mainly due to their desirable organoleptic properties and rarity. However, truffles are seasonal (harvested mostly in winter from June to August in the Southern Hemisphere and from December to February in the Northern Hemisphere) and extremely perishable. Truffles deteriorate rapidly showing undesirable changes within 10 days from harvest in aroma and visual appearance after harvest. The very short postharvest shelf life (about 7-10 days) limits the potential for export and domestic consumption all year round. Several preservation methods have been studied to prolong their shelf life without the loss of aroma. However, all traditional preservation techniques have their own shortcomings and remain challenging. The extraction of natural truffle aroma volatiles for food applications could be a potential alternative to replace the existing synthetic flavoring used for processed truffle products. Four commonly used extraction methods for recovering volatile compounds from plants, namely, supercritical carbon dioxide extraction, Soxhlet extraction, distillation, and cold pressing, are critically analyzed. Up to date, existing research about the extraction of aroma volatiles from truffles is limited in the literature but based on the volatility of the key truffle volatile compounds, supercritical carbon dioxide extraction may offer the best possibility so that a natural truffle-based product that can be used in food applications throughout the year can be made available.
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Affiliation(s)
- Win Nee Phong
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Alan D Payne
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Gary A Dykes
- School of Agriculture and Food Sciences, University of Queensland, Saint Lucia, Queensland, Australia
| | - Ranil Coorey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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3
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Krösser D, Dreyer B, Siebels B, Voß H, Krisp C, Schlüter H. Investigation of the Proteomes of the Truffles Tuber albidum pico, T. aestivum, T. indicum, T. magnatum, and T. melanosporum. Int J Mol Sci 2021; 22:ijms222312999. [PMID: 34884803 PMCID: PMC8658033 DOI: 10.3390/ijms222312999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Truffles of the Tuber species are known as expensive foods, mainly for their distinct aroma and taste. This high price makes them a profitable target of food fraud, e.g., the misdeclaration of cheaper truffle species as expensive ones. While many studies investigated truffles on the metabolomic level or the volatile organic compounds extruded by them, research at the proteome level as a phenotype determining basis is limited. In this study, a bottom-up proteomic approach based on LC-MS/MS measurements in data-independent acquisition mode was performed to analyze the truffle species Tuber aestivum, Tuber albidum pico, Tuber indicum, Tuber magnatum, and Tuber melanosporum, and a protein atlas of the investigated species was obtained. The yielded proteomic fingerprints are unique for each of the of the five truffle species and can now be used in case of suspected food fraud. First, a comprehensive spectral library containing 9000 proteins and 50,000 peptides was generated by two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS). Then, samples of the truffle species were analyzed in data-independent acquisition (DIA) proteomics mode yielding 2715 quantified proteins present in all truffle samples. Individual species were clearly distinguishable by principal component analysis (PCA). Quantitative proteome fingerprints were generated from 2066 ANOVA significant proteins, and side-by-side comparisons of truffles were done by T-tests. A further aim of this study was the annotation of functions for the identified proteins. For Tuber magnatum and Tuber melanosporum conclusive links to their superior aroma were found by enrichment of proteins responsible for sulfur-metabolic processes in comparison with other truffles. The obtained data in this study may serve as a reference library for food analysis laboratories in the future to tackle food fraud by misdeclaration of truffles. Further identified proteins with their corresponding abundance values in the different truffle species may serve as potential protein markers in the establishment of targeted analysis methods. Lastly, the obtained data may serve in the future as a basis for deciphering the biochemistry of truffles more deeply as well, when protein databases of the different truffle species will be more complete.
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4
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Caboni P, Scano P, Sanchez S, Garcia-Barreda S, Corrias F, Marco P. Multi-platform metabolomic approach to discriminate ripening markers of black truffles (Tuber melanosporum). Food Chem 2020; 319:126573. [PMID: 32169760 DOI: 10.1016/j.foodchem.2020.126573] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/16/2022]
Abstract
Black truffle is characterized by a black ascocarp and white veins. This hypogeous fruit body is known for its aroma. Understanding metabolic variation during ripening can shed light on truffle biology. In this work, the comprehensive polar metabolome and the volatile organic compounds of T. melanosporum were studied at different ripening stages by means of a metabolomic approach using GC-MS. Multivariate statistical data analysis indicated that the metabolic profile changed during ripening and that the metabolites that mostly discriminated truffles in the early ripening stages belonged to the classes of carbohydrates, while free fatty acids and amino acids, among which precursors of VOCs, characterized the late stages of ripening. Principal component analysis of the volatilome indicated that dimethylsulfide and dimethyldisulfide characterized most of the samples collected in December-January, while 1-octen-3-ol samples collected in February-March.
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Affiliation(s)
- Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy.
| | - Paola Scano
- Department of Life and Environmental Sciences, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Sergio Sanchez
- Forest Resources Department, Agrifood Research and Technology Centre of Aragon (CITA), Agrifood Institute of Aragón-IA2 (CITA-Zaragoza University), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Sergi Garcia-Barreda
- Forest Resources Department, Agrifood Research and Technology Centre of Aragon (CITA), Agrifood Institute of Aragón-IA2 (CITA-Zaragoza University), Av. Montañana 930, 50059 Zaragoza, Spain
| | - Francesco Corrias
- Department of Life and Environmental Sciences, University of Cagliari, via Ospedale 72, 09124 Cagliari, Italy
| | - Pedro Marco
- Forest Resources Department, Agrifood Research and Technology Centre of Aragon (CITA), Agrifood Institute of Aragón-IA2 (CITA-Zaragoza University), Av. Montañana 930, 50059 Zaragoza, Spain
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5
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Krajnc B, Bontempo L, Luis Araus J, Giovanetti M, Alegria C, Lauteri M, Augusti A, Atti N, Smeti S, Taous F, Amenzou NE, Podgornik M, Camin F, Reis P, Máguas C, Bučar Miklavčič M, Ogrinc N. Selective Methods to Investigate Authenticity and Geographical Origin of Mediterranean Food Products. FOOD REVIEWS INTERNATIONAL 2020. [DOI: 10.1080/87559129.2020.1717521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Bor Krajnc
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Luana Bontempo
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Jose Luis Araus
- Section of Plant Physiology, Universitat de Barcelona, Barcelona, AGROTECNIO, Lleida, Spain
| | - Manuela Giovanetti
- Centre for Ecology, Evolution and Environmental Changes (cE3c), da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Carla Alegria
- Centre for Ecology, Evolution and Environmental Changes (cE3c), da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Marco Lauteri
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Porano, Italy
| | - Angela Augusti
- Consiglio Nazionale delle Ricerche, Istituto di Ricerca sugli Ecosistemi Terrestri, Porano, Italy
| | - Naziha Atti
- Laboratoire de Production Animale et Fourragère, Institut National de Recherche Agronomique de Tunisie, University of Carthage, Tunis, Tunisia
| | - Samir Smeti
- Laboratoire de Production Animale et Fourragère, Institut National de Recherche Agronomique de Tunisie, University of Carthage, Tunis, Tunisia
| | - Fouad Taous
- Centre National de L’énergie, Des Sciences Et Techniques Nucleaires, Rabat, Morocco
| | - Nour Eddine Amenzou
- Centre National de L’énergie, Des Sciences Et Techniques Nucleaires, Rabat, Morocco
| | - Maja Podgornik
- Science and Research Centre Koper, Institute for Oliveculture, Koper, Slovenia
| | - Federica Camin
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Italy
| | - Pedro Reis
- Sistemas agrários e florestais e sanidade vegetal, Instituto Nacional de Investigação Agrária E Veterinária, Oeiras, Portugal
| | - Cristina Máguas
- Centre for Ecology, Evolution and Environmental Changes (cE3c), da Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | | | - Nives Ogrinc
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
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6
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Vita F, Giuntoli B, Bertolini E, Taiti C, Marone E, D'Ambrosio C, Trovato E, Sciarrone D, Zoccali M, Balestrini R, Scaloni A, Mondello L, Mancuso S, Alessio M, Alpi A. Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments. BMC Genomics 2020; 21:90. [PMID: 31996138 PMCID: PMC6988325 DOI: 10.1186/s12864-020-6522-3] [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: 05/28/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments. RESULTS Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were able to identify proteins specifically linked to the sample origin. We further associated the proteomic results to an RNA-seq profiling, which confirmed the possibility to differentiate samples according to their source and provided a basis for the detailed analysis of genes involved in sulfur metabolism. Finally, geographical specificities were associated with the set of volatile compounds produced by the fruiting bodies, as quantitatively and qualitatively determined through proton transfer reaction-mass spectrometry (PTR-MS) and gas-chromatography-mass spectrometry (GC-MS). In particular, a partial least squares-discriminant analysis (PLS-DA) model built from the latter data was able to return high confidence predictions of sample source. CONCLUSIONS Results provide a characterization of white fruiting bodies by a wide range of different molecules, suggesting the role for specific compounds in the responses and adaptation to distinct environments.
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Affiliation(s)
- Federico Vita
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy. .,A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy.
| | - Beatrice Giuntoli
- Department of Biology, Università di Pisa, via L. Ghini 13, 56126, Pisa, Italy.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.,Present address: Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO, 63132, USA
| | - Cosimo Taiti
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Elettra Marone
- Faculty of Biosciences and Technologies for Agriculture Food and Environment, University of Teramo, Via R. Balzarini 1, 64100, Teramo, Italy
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Emanuela Trovato
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Danilo Sciarrone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Mariosimone Zoccali
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Raffaella Balestrini
- National Research Council of Italy, Institute for Sustainable Plant Protection (CNR-IPSP), Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, I.S.P.A.A.M., National Research Council, 80147, Napoli, Italy
| | - Luigi Mondello
- Chromaleont Srl, c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences Polo Annunziata, University of Messina, viale Annunziata, 98168, Messina, Italy
| | - Stefano Mancuso
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali (DAGRI), University of Florence, Viale delle idee 30, 50019, Florence, Italy
| | - Massimo Alessio
- Division of Genetics and Cell Biology, IRCCS-Ospedale San Raffaele, Milan, Italy
| | - Amedeo Alpi
- A.R.E.A. Foundation, via Tavoleria 28, 56125, Pisa, Italy
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Shah N, Usvalampi A, Chaudhary S, Seppänen-Laakso T, Marathe S, Bankar S, Singhal R, Shamekh S. An investigation on changes in composition and antioxidant potential of mature and immature summer truffle (Tuber aestivum). Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03438-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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8
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Li Q, Fu Y, Sun Q, Sourzat P, Yang M, Liu C, Tan H, Ye L, Zou J, Wu C, Zhang B, Li X. The Uneven Distribution of Mating Type Genes in Natural and Cultivated Truffle Orchards Contributes to the Fructification of Tuber indicum. MYCOBIOLOGY 2018; 46:64-71. [PMID: 29998034 PMCID: PMC6037114 DOI: 10.1080/12298093.2018.1454005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 01/05/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
The aim of this study was to investigate the pattern of distribution of mating type (MAT) genes of Tuber indicum in ectomycorhizosphere soils from natural T. indicum-producing areas and cultivated truffle orchards and ascocarp samples from different regions. Quantitative real-time PCR and multiplex PCR were used to weight the copy numbers of MAT1-1-1 and MAT1-2-1 in natural truffle soils and cultivated orchard soils. The effect of limestone on the pattern of truffle MAT genes and the correlation between soil properties and the proportion of MAT genes were also assessed. These results indicated that an uneven and nonrandom distribution of MAT genes was common in truffle-producing areas, cultivated truffle orchards, and ascocarps gleba. The competition between the two mating type genes and the expansion of unbalanced distribution was found to be closely related to truffle fructification. Limestone treatments failed to alter the proportion of the two mating type genes in the soil. The content of available phosphorus in soil was significantly correlated with the value of MAT1-1-1/MAT1-2-1 in cultivated and natural ectomycorhizosphere soils. The application of real-time quantitative PCR can provide reference for monitoring the dynamic changes of mating type genes in soil. This study investigates the distributional pattern of T. indicum MAT genes in the ectomycorhizosphere soil and ascocarp gleba from different regions, which may provide a foundation for the cultivation of T. indicum.
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Affiliation(s)
- Qiang Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yu Fu
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Qun Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Pierre Sourzat
- Truffle Research Centre of Cahors-Le Montat, Le Montat, France
| | - Mei Yang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, Sichuan, China
| | - Chengyi Liu
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, Sichuan, China
| | - Hao Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Lei Ye
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Jie Zou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Chenguang Wu
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Bo Zhang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Xiaolin Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
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9
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Islam MT, Mohamedali A, Ahn SB, Nawar I, Baker MS, Ranganathan S. A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes. Methods Mol Biol 2017; 1549:163-176. [PMID: 27975291 DOI: 10.1007/978-1-4939-6740-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the past decade, proteomics and mass spectrometry have taken tremendous strides forward, particularly in the life sciences, spurred on by rapid advances in technology resulting in generation and conglomeration of vast amounts of data. Though this has led to tremendous advancements in biology, the interpretation of the data poses serious challenges for many practitioners due to the immense size and complexity of the data. Furthermore, the lack of annotation means that a potential gold mine of relevant biological information may be hiding within this data. We present here a simple and intuitive workflow for the research community to investigate and mine this data, not only to extract relevant data but also to segregate usable, quality data to develop hypotheses for investigation and validation. We apply an MS evidence workflow for verifying peptides of proteins from one's own data as well as publicly available databases. We then integrate a suite of freely available bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology and biochemical pathways. We also provide an example of the functional annotation of missing proteins in human chromosome 7 data from the NeXtProt database, where no evidence is available at the proteomic, antibody, or structural levels. We give examples of protocols, tools and detailed flowcharts that can be extended or tailored to interpret and annotate the proteome of any novel organism.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Abidali Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.,Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ishmam Nawar
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.
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10
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Islam MT, Mohamedali A, Fernandes CS, Baker MS, Ranganathan S. De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data. Methods Mol Biol 2017; 1549:119-134. [PMID: 27975288 DOI: 10.1007/978-1-4939-6740-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High resolution mass spectrometry has revolutionized proteomics over the past decade, resulting in tremendous amounts of data in the form of mass spectra, being generated in a relatively short span of time. The mining of this spectral data for analysis and interpretation though has lagged behind such that potentially valuable data is being overlooked because it does not fit into the mold of traditional database searching methodologies. Although the analysis of spectra by de novo sequences removes such biases and has been available for a long period of time, its uptake has been slow or almost nonexistent within the scientific community. In this chapter, we propose a methodology to integrate de novo peptide sequencing using three commonly available software solutions in tandem, complemented by homology searching, and manual validation of spectra. This simplified method would allow greater use of de novo sequencing approaches and potentially greatly increase proteome coverage leading to the unearthing of valuable insights into protein biology, especially of organisms whose genomes have been recently sequenced or are poorly annotated.
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Affiliation(s)
- Mohammad Tawhidul Islam
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Abidali Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Criselda Santan Fernandes
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, 2109, Australia.
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11
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Barbieri E, Ceccaroli P, Agostini D, Zeppa SD, Gioacchini AM, Stocchi V. Truffle-Associated Bacteria: Extrapolation from Diversity to Function. SOIL BIOLOGY 2016. [DOI: 10.1007/978-3-319-31436-5_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Aroma improvement by repeated freeze-thaw treatment during Tuber melanosporum fermentation. Sci Rep 2015; 5:17120. [PMID: 26607288 PMCID: PMC4660818 DOI: 10.1038/srep17120] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/26/2015] [Indexed: 02/05/2023] Open
Abstract
The aroma attributes of sulfurous, mushroom and earthy are the most important characteristics of the aroma of Tuber melanosporum. However, these three aroma attributes are absent in the T. melanosporum fermentation system. To improve the quality of the aroma, repeated freeze-thaw treatment (RFTT) was adopted to affect the interplay of volatile organic compounds (VOCs). Using RFTT, not only was the score on the hedonic scale of the aroma increased from the “liked slightly” to the “liked moderately” grade, but the aroma attributes of sulfurous, mushroom and earthy could also be smelled in the T. melanosporum fermentation system for the first time. A total of 29 VOCs were identified, and 9 compounds were identified as the key discriminative volatiles affected by RFTT. Amino acid analysis revealed that methionine, valine, serine, phenylalanine, isoleucine and threonine were the key substrates associated with the biosynthesis of the 9 key discriminative VOCs. This study noted that amino acid metabolism played an important role in the regulation of the aroma of the T. melanosporum fermentation system.
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Zarivi O, Cesare P, Ragnelli AM, Aimola P, Leonardi M, Bonfigli A, Colafarina S, Poma AM, Miranda M, Pacioni G. Validation of reference genes for quantitative real-time PCR in Périgord black truffle (Tuber melanosporum) developmental stages. PHYTOCHEMISTRY 2015; 116:78-86. [PMID: 25778998 DOI: 10.1016/j.phytochem.2015.02.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/12/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
The symbiotic fungus Tuber melanosporum Vittad. (Périgord black truffle) belongs to the Ascomycota and forms mutualistic symbiosis with tree and shrub roots. This truffle has a high value in a global market and is cultivated in many countries of both hemispheres. The publication of the T. melanosporum genome has given researchers unique opportunities to learn more about the biology of the fungus. Real-time quantitative PCR (qRT-PCR) is a definitive technique for quantitating differences in transcriptional gene expression levels between samples. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. These housekeeping genes must show stable expression under given experimental conditions for the qRT-PCR results to be accurate. Unfortunately, there are no studies on the stability of housekeeping genes used in T. melanosporum development. In this study, we present a morphological and microscopical classification of the developmental stages of T. melanosporum fruit body, and investigate the expression levels of 12 candidate reference genes (18S rRNA; 5.8S rRNA; Elongation factor 1-alpha; Elongation factor 1-beta; α-tubulin; 60S ribosomal protein L29; β-tubulin; 40S ribosomal protein S1; 40S ribosomal protein S3; Glucose-6-phosphate dehydrogenase; β-actin; Ubiquitin-conjugating enzyme). To evaluate the suitability of these genes as endogenous controls, five software-based approaches and one web-based comprehensive tool (RefFinder) were used to analyze and rank the tested genes. We demonstrate here that the 18S rRNA gene shows the most stable expression during T. melanosporum development and that a set of three genes, 18S rRNA, Elongation factor 1-alpha and 40S ribosomal protein S3, is the most suitable to normalize qRT-PCR data from all the analyzed developmental stages; conversely, 18S rRNA, Glucose-6-phosphate dehydrogenase and Elongation factor 1-alpha are the most suitable genes for fruiting body developmental stages.
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Affiliation(s)
- Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Maria Ragnelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Pierpaolo Aimola
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Marco Leonardi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Maria Poma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Michele Miranda
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Giovanni Pacioni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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Tang YJ, Liu RS, Li HM. Current progress on truffle submerged fermentation: a promising alternative to its fruiting bodies. Appl Microbiol Biotechnol 2015; 99:2041-53. [PMID: 25616528 DOI: 10.1007/s00253-015-6379-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/28/2014] [Accepted: 12/31/2014] [Indexed: 10/24/2022]
Abstract
Truffle (Tuber spp.), also known as "underground gold," is popular in various cuisines because of its unique and characteristic aroma. Currently, truffle fruiting bodies are mostly obtained from nature and semi-artificial cultivation. However, the former source is scarce, and the latter is time-consuming, usually taking 4 to 12 years before harvest of the fruiting body. The truffle submerged fermentation process was first developed in Tang's lab as an alternative to its fruiting bodies. To the best of our knowledge, most reports of truffle submerged fermentation come from Tang's group. This review examines the current state of the truffle submerged fermentation process. First, the strategy to optimize the truffle submerged fermentation process is summarized; the final conditions yielded not only the highest reported truffle biomass but also the highest production of extracellular and intracellular polysaccharides. Second, the comparison of metabolites produced by truffle fermentation and fruiting bodies is presented, and the former were superior to the latter. Third, metabolites (i.e., volatile organic compounds, equivalent umami concentration, and sterol) derived from truffle fermentation could be regulated by fermentation process optimization. These findings indicated that submerged fermentation of truffles can be used for commercial production of biomass and metabolites as a promising alternative to generating its fruiting bodies in bioreactor.
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Affiliation(s)
- Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068, China,
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Kuo A, Kohler A, Martin FM, Grigoriev IV. Expanding genomics of mycorrhizal symbiosis. Front Microbiol 2014; 5:582. [PMID: 25408690 PMCID: PMC4219462 DOI: 10.3389/fmicb.2014.00582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/15/2014] [Indexed: 12/11/2022] Open
Abstract
The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.
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Affiliation(s)
- Alan Kuo
- United States Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
| | - Annegret Kohler
- UMR, Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems, Tree-Microbe Interactions, Institut National de la Recherche Agronomique, Université de LorraineNancy, France
| | - Francis M. Martin
- UMR, Lab of Excellence for Advanced Research on the Biology of TRee and Forest Ecosystems, Tree-Microbe Interactions, Institut National de la Recherche Agronomique, Université de LorraineNancy, France
| | - Igor V. Grigoriev
- United States Department of Energy Joint Genome InstituteWalnut Creek, CA, USA
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Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S. Protannotator: A Semiautomated Pipeline for Chromosome-Wise Functional Annotation of the “Missing” Human Proteome. J Proteome Res 2013; 13:76-83. [DOI: 10.1021/pr400794x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - William S. Hancock
- Barnett
Institute, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Brian A. Risk
- College
of Arts and Sciences, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | | | - Shoba Ranganathan
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599 Singapore
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