1
|
Yu B, Zhan R, Hu Y, Lv Z. Mass Spectrometry Imaging: An Emerging Technology in Medical Parasitology. Anal Chem 2024; 96:8011-8020. [PMID: 38579105 DOI: 10.1021/acs.analchem.3c05341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Affiliation(s)
- Bingcheng Yu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510080, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, Guangdong 511493, China
| | - Rongjian Zhan
- Department of Otolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China
| | - Yue Hu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510080, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, Guangdong 511493, China
| | - Zhiyue Lv
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510080, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, Guangdong 511493, China
- Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University Haikou, Haikou, Hainan 571199, China
| |
Collapse
|
2
|
Schrader M. Origins, Technological Advancement, and Applications of Peptidomics. Methods Mol Biol 2024; 2758:3-47. [PMID: 38549006 DOI: 10.1007/978-1-0716-3646-6_1] [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] [Indexed: 04/02/2024]
Abstract
Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.
Collapse
Affiliation(s)
- Michael Schrader
- Department of Bioengineering Sciences, Weihenstephan-Tr. University of Applied Sciences, Freising, Germany.
| |
Collapse
|
3
|
Yu X, Liu Z, Sun X. Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives. PLANT COMMUNICATIONS 2023; 4:100508. [PMID: 36540021 DOI: 10.1016/j.xplc.2022.100508] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 05/11/2023]
Abstract
Plants contain a large number of cell types and exhibit complex regulatory mechanisms. Studies at the single-cell level have gradually become more common in plant science. Single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics techniques have been combined to analyze plant development. These techniques have been used to study the transcriptomes and metabolomes of plant tissues at the single-cell level, enabling the systematic investigation of gene expression and metabolism in specific tissues and cell types during defined developmental stages. In this review, we present an overview of significant breakthroughs in spatial multi-omics in plants, and we discuss how these approaches may soon play essential roles in plant research.
Collapse
Affiliation(s)
- Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, P.R. China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, P.R. China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, P.R. China.
| |
Collapse
|
4
|
Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging. Int J Mol Sci 2021; 22:ijms222212393. [PMID: 34830273 PMCID: PMC8623934 DOI: 10.3390/ijms222212393] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.
Collapse
|
5
|
Hu W, Han Y, Sheng Y, Wang Y, Pan Q, Nie H. Mass spectrometry imaging for direct visualization of components in plants tissues. J Sep Sci 2021; 44:3462-3476. [PMID: 34245221 DOI: 10.1002/jssc.202100138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Mass spectrometry is considered the most informative technique for components identification and has been widely adopted in plant sciences. However, the spatial distribution of compounds in the plant, which is vital for the exploration of plant physiological mechanisms, is missed in MS analysis. In recent years, mass spectrometry imaging has brought a great breakthrough in plant analysis because it can determine both the molecular compositions and spatial distributions, which is conducive to understand functions and regulation pathways of specific components in plants. Mass spectrometry imaging analysis of plant tissue is toward high sensitivity, high spatial resolution, and even single-cell analysis. Despite many challenges and technical barriers, such as difficulties of sample pretreatment caused by morphological diversity of plant tissues, obstacles for high spatial resolution imaging, and so on, lots of researches have contributed to remarkable progress, including improvement in tissue preparation, matrix innovation, and ionization mode development. This review focuses on the advances of mass spectrometry imaging analysis of plants in the last 5 years, including commonly used ionization techniques, technical advances, and recent applications of mass spectrometry imaging in plants.
Collapse
Affiliation(s)
- Wenya Hu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yiqi Sheng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yinghao Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Qiong Pan
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| |
Collapse
|
6
|
Mass spectrometry imaging as a potential technique for diagnostic of Huanglongbing disease using fast and simple sample preparation. Sci Rep 2020; 10:13457. [PMID: 32778716 PMCID: PMC7417563 DOI: 10.1038/s41598-020-70385-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
Huanglongbing (HLB) is a disease of worldwide incidence that affects orange trees, among other commercial varieties, implicating in great losses to the citrus industry. The disease is transmitted through Diaphorina citri vector, which inoculates Candidatus Liberibacter spp. in the plant sap. HLB disease lead to blotchy mottle and fruit deformation, among other characteristic symptoms, which induce fruit drop and affect negatively the juice quality. Nowadays, the disease is controlled by eradication of sick, symptomatic plants, coupled with psyllid control. Polymerase chain reaction (PCR) is the technique most used to diagnose the disease; however, this methodology involves high cost and extensive sample preparation. Mass spectrometry imaging (MSI) technique is a fast and easily handled sample analysis that, in the case of Huanglongbing allows the detection of increased concentration of metabolites associated to the disease, including quinic acid, phenylalanine, nobiletin and sucrose. The metabolites abieta-8,11,13-trien-18-oic acid, suggested by global natural product social molecular networking (GNPS) analysis, and 4-acetyl-1-methylcyclohexene showed a higher distribution in symptomatic leaves and have been directly associated to HLB disease. Desorption electrospray ionization coupled to mass spectrometry imaging (DESI-MSI) allows the rapid and efficient detection of biomarkers in sweet oranges infected with Candidatus Liberibacter asiaticus and can be developed into a real-time, fast-diagnostic technique.
Collapse
|
7
|
Favre-Godal Q, Gourguillon L, Lordel-Madeleine S, Gindro K, Choisy P. Orchids and their mycorrhizal fungi: an insufficiently explored relationship. MYCORRHIZA 2020; 30:5-22. [PMID: 31982950 DOI: 10.1007/s00572-020-00934-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/17/2020] [Indexed: 05/03/2023]
Abstract
Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.
Collapse
Affiliation(s)
- Quentin Favre-Godal
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France.
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France.
| | - Lorène Gourguillon
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
| | - Sonia Lordel-Madeleine
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France
| | - Katia Gindro
- Agroscope, Swiss Federal Research Station, Plant Protection, 60 Route de Duiller, PO Box, 1260, Nyon, Switzerland
| | - Patrick Choisy
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
| |
Collapse
|