1
|
Ivanova T, Dincheva I, Badjakov I, Iantcheva A. Transcriptional and Metabolic Profiling of Arabidopsis thaliana Transgenic Plants Expressing Histone Acetyltransferase HAC1 upon the Application of Abiotic Stress-Salt and Low Temperature. Metabolites 2023; 13:994. [PMID: 37755274 PMCID: PMC10536276 DOI: 10.3390/metabo13090994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
Augmented knowledge of plant responses upon application of stress could help improve our understanding of plant tolerance under abiotic stress conditions. Histone acetylation plays an important role in gene expression regulation during plant growth and development and in the response of plants to abiotic stress. The current study examines the level of transcripts and free metabolite content in transgenic Arabidopsis thaliana plants expressing a gene encoding histone acetyltransferase from Medicago truncatula (MtHAC1) after its heterologous expression. Stable transgenic plants with HAC1 gain and loss of function were constructed, and their T5 generation was used. Transgenic lines with HAC1-modified expression showed a deviation in root growth dynamics and leaf area compared to the wild-type control. Transcriptional profiles were evaluated after the application of salinity stress caused by 150 mM NaCl at four different time points (0, 24, 48, and 72 h) in treated and non-treated transgenic and control plants. The content and quantity of free metabolites-amino acids, mono- and dicarbohydrates, organic acids, and fatty acids-were assessed at time points 0 h and 72 h in treated and non-treated transgenic and control plants. The obtained transcript profiles of HAC1 in transgenic plants with modified expression and control were assessed after application of cold stress (low temperature, 4 °C).
Collapse
Affiliation(s)
| | | | | | - Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tzankov 8, 1164 Sofia, Bulgaria; (T.I.); (I.D.); (I.B.)
| |
Collapse
|
2
|
Sugar transporter Slc37a2 regulates bone metabolism in mice via a tubular lysosomal network in osteoclasts. Nat Commun 2023; 14:906. [PMID: 36810735 PMCID: PMC9945426 DOI: 10.1038/s41467-023-36484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Osteoclasts are giant bone-digesting cells that harbor specialized lysosome-related organelles termed secretory lysosomes (SLs). SLs store cathepsin K and serve as a membrane precursor to the ruffled border, the osteoclast's 'resorptive apparatus'. Yet, the molecular composition and spatiotemporal organization of SLs remains incompletely understood. Here, using organelle-resolution proteomics, we identify member a2 of the solute carrier 37 family (Slc37a2) as a SL sugar transporter. We demonstrate in mice that Slc37a2 localizes to the SL limiting membrane and that these organelles adopt a hitherto unnoticed but dynamic tubular network in living osteoclasts that is required for bone digestion. Accordingly, mice lacking Slc37a2 accrue high bone mass owing to uncoupled bone metabolism and disturbances in SL export of monosaccharide sugars, a prerequisite for SL delivery to the bone-lining osteoclast plasma membrane. Thus, Slc37a2 is a physiological component of the osteoclast's unique secretory organelle and a potential therapeutic target for metabolic bone diseases.
Collapse
|
3
|
Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
Collapse
Affiliation(s)
- Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Correspondence: (M.K.T.); (N.T.)
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
| |
Collapse
|
4
|
Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
Collapse
Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| |
Collapse
|
5
|
Kuzhiumparambil U, Labeeuw L, Commault A, Vu HP, Nguyen LN, Ralph PJ, Nghiem LD. Effects of harvesting on morphological and biochemical characteristics of microalgal biomass harvested by polyacrylamide addition, pH-induced flocculation, and centrifugation. BIORESOURCE TECHNOLOGY 2022; 359:127433. [PMID: 35680089 DOI: 10.1016/j.biortech.2022.127433] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
The effects of microalgae harvesting methods on microalgal biomass quality were evaluated using three species namely the freshwater green alga Chlorella vulgaris, marine red alga Porphyridium purpureum and marine diatom Phaeodactylum tricornutum. Harvesting efficiencies of polyacrylamide addition, alkaline addition, and centrifugation ranged from 85 to 95, 59-92 and 100%, respectively, across these species. Morphology of the harvested cells (i.e. compromised cell walls) was significantly impacted by alkaline pH-induced flocculation for all three species. Over 50% of C. vulgaris cells were compromised with alkaline pH compared to < 10% with polyacrylamide and centrifugation. The metabolic profiles varied depending on harvesting methods. Species-specific decrease of certain metabolites was observed. These results suggest that the method of harvest can alter the metabolic profile of the biomass amongst the three harvesting methods, polyacrylamide addition showed higher harvesting efficiency with less compromised cells and higher retention of industry important biochemicals.
Collapse
Affiliation(s)
| | - Leen Labeeuw
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Audrey Commault
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Hang P Vu
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Luong N Nguyen
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Peter J Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo, NSW 2007, Australia
| |
Collapse
|
6
|
Gupta SVK, Smith PMC, Natera SHA, Roessner U. Biochemical Changes in Two Barley Genotypes Inoculated With a Beneficial Fungus Trichoderma harzianum Rifai T-22 Grown in Saline Soil. FRONTIERS IN PLANT SCIENCE 2022; 13:908853. [PMID: 35982702 PMCID: PMC9379338 DOI: 10.3389/fpls.2022.908853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
One of the most important environmental factors impacting crop plant productivity is soil salinity. Fungal endophytes have been characterised as biocontrol agents that help in plant productivity and induce resistance responses to several abiotic stresses, including salinity. In the salt-tolerant cereal crop barley (Hordeum vulgare L.), there is limited information about the metabolites and lipids that change in response to inoculation with fungal endophytes in saline conditions. In this study, gas chromatography coupled to mass spectrometry (GC-MS) and LC-electrospray ionisation (ESI)-quadrupole-quadrupole time of flight (QqTOF)-MS were used to determine the metabolite and lipid changes in two fungal inoculated barley genotypes with differing tolerance levels to saline conditions. The more salt-tolerant cultivar was Vlamingh and less salt tolerant was Gairdner. Trichoderma harzianum strain T-22 was used to treat these plants grown in soil under control and saline (200 mM NaCl) conditions. For both genotypes, fungus-colonised plants exposed to NaCl had greater root and shoot biomass, and better chlorophyll content than non-colonised plants, with colonised-Vlamingh performing better than uninoculated control plants. The metabolome dataset using GC-MS consisted of a total of 93 metabolites of which 74 were identified in roots of both barley genotypes as organic acids, sugars, sugar acids, sugar alcohols, amino acids, amines, and a small number of fatty acids. LC-QqTOF-MS analysis resulted in the detection of 186 lipid molecular species, classified into three major lipid classes-glycerophospholipids, glycerolipids, and sphingolipids, from roots of both genotypes. In Cultivar Vlamingh both metabolites and lipids increased with fungus and salt treatment while in Gairdner they decreased. The results from this study suggest that the metabolic pathways by which the fungus imparts salt tolerance is different for the different genotypes.
Collapse
Affiliation(s)
| | | | - Siria H. A. Natera
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
7
|
Chandana BS, Mahto RK, Singh RK, Ford R, Vaghefi N, Gupta SK, Yadav HK, Manohar M, Kumar R. Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea. Front Genet 2022; 13:900253. [PMID: 35937986 PMCID: PMC9355295 DOI: 10.3389/fgene.2022.900253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenomics has become a significant research interest at a time when rapid environmental changes are occurring. Epigenetic mechanisms mainly result from systems like DNA methylation, histone modification, and RNA interference. Epigenetic mechanisms are gaining importance in classical genetics, developmental biology, molecular biology, cancer biology, epidemiology, and evolution. Epigenetic mechanisms play important role in the action and interaction of plant genes during development, and also have an impact on classical plant breeding programs, inclusive of novel variation, single plant heritability, hybrid vigor, plant-environment interactions, stress tolerance, and performance stability. The epigenetics and epigenomics may be significant for crop adaptability and pliability to ambient alterations, directing to the creation of stout climate-resilient elegant crop cultivars. In this review, we have summarized recent progress made in understanding the epigenetic mechanisms in plant responses to biotic and abiotic stresses and have also tried to provide the ways for the efficient utilization of epigenomic mechanisms in developing climate-resilient crop cultivars, especially in chickpea, and other legume crops.
Collapse
Affiliation(s)
- B. S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | | | - Rebecca Ford
- Center for Planetary Health and Food Security, Griffith University, Brisbane, QLD, Australia
| | - Niloofar Vaghefi
- School of Agriculture and Food, University of Melbourne, Parkville, VIC, Australia
| | | | | | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
- *Correspondence: Rajendra Kumar,
| |
Collapse
|
8
|
Arriagada O, Cacciuttolo F, Cabeza RA, Carrasco B, Schwember AR. A Comprehensive Review on Chickpea ( Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience. Int J Mol Sci 2022; 23:ijms23126794. [PMID: 35743237 PMCID: PMC9223724 DOI: 10.3390/ijms23126794] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.
Collapse
Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Felipe Cacciuttolo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
- Correspondence:
| |
Collapse
|
9
|
Xu Y, Fu X. Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View. Int J Mol Sci 2022; 23:ijms23105716. [PMID: 35628526 PMCID: PMC9143615 DOI: 10.3390/ijms23105716] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 12/15/2022] Open
Abstract
Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.
Collapse
Affiliation(s)
- Yuan Xu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
| | - Xinyu Fu
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
| |
Collapse
|
10
|
Koley S, Chu KL, Gill SS, Allen DK. An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2938-2952. [PMID: 35560196 DOI: 10.1093/jxb/erac062] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/15/2022] [Indexed: 06/15/2023]
Abstract
Assessing central carbon metabolism in plants can be challenging due to the dynamic range in pool sizes, with low levels of important phosphorylated sugars relative to more abundant sugars and organic acids. Here, we report a sensitive liquid chromatography-mass spectrometry method for analysing central metabolites on a hybrid column, where both anion-exchange and hydrophilic interaction chromatography (HILIC) ligands are embedded in the stationary phase. The liquid chromatography method was developed for enhanced selectivity of 27 central metabolites in a single run with sensitivity at femtomole levels observed for most phosphorylated sugars. The method resolved phosphorylated hexose, pentose, and triose isomers that are otherwise challenging. Compared with a standard HILIC approach, these metabolites had improved peak areas using our approach due to ion enhancement or low ion suppression in the biological sample matrix. The approach was applied to investigate metabolism in high lipid-producing tobacco leaves that exhibited increased levels of acetyl-CoA, a precursor for oil biosynthesis. The application of the method to isotopologue detection and quantification was considered through evaluating 13C-labeled seeds from Camelina sativa. The method provides a means to analyse intermediates more comprehensively in central metabolism of plant tissues.
Collapse
Affiliation(s)
- Somnath Koley
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Kevin L Chu
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Saba S Gill
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
- United States Department of Agriculture-Agriculture Research Service, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| |
Collapse
|
11
|
Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia. Nat Commun 2022; 13:2614. [PMID: 35551192 PMCID: PMC9098909 DOI: 10.1038/s41467-022-30223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The interaction of germline variation and somatic cancer driver mutations is under-investigated. Here we describe the genomic mitochondrial landscape in adult acute myeloid leukaemia (AML) and show that rare variants affecting the nuclear- and mitochondrially-encoded complex I genes show near-mutual exclusivity with somatic driver mutations affecting isocitrate dehydrogenase 1 (IDH1), but not IDH2 suggesting a unique epistatic relationship. Whereas AML cells with rare complex I variants or mutations in IDH1 or IDH2 all display attenuated mitochondrial respiration, heightened sensitivity to complex I inhibitors including the clinical-grade inhibitor, IACS-010759, is observed only for IDH1-mutant AML. Furthermore, IDH1 mutant blasts that are resistant to the IDH1-mutant inhibitor, ivosidenib, retain sensitivity to complex I inhibition. We propose that the IDH1 mutation limits the flexibility for citrate utilization in the presence of impaired complex I activity to a degree that is not apparent in IDH2 mutant cells, exposing a mutation-specific metabolic vulnerability. This reduced metabolic plasticity explains the epistatic relationship between the germline complex I variants and oncogenic IDH1 mutation underscoring the utility of genomic data in revealing metabolic vulnerabilities with implications for therapy. Mitochondrial metabolism has been associated with tumourigenesis in acute myeloid leukaemia (AML) and currently considered as a potential therapeutic target. Here, the authors show, in patients with AML, that germline mutations in mitochondrial complex I are mutually exclusive with somatic mutations in the metabolic enzyme IDH1, and find IDH1 mutant cells have increased sensitivity to complex I inhibitors.
Collapse
|
12
|
Di Minno A, Gelzo M, Caterino M, Costanzo M, Ruoppolo M, Castaldo G. Challenges in Metabolomics-Based Tests, Biomarkers Revealed by Metabolomic Analysis, and the Promise of the Application of Metabolomics in Precision Medicine. Int J Mol Sci 2022; 23:5213. [PMID: 35563604 PMCID: PMC9103094 DOI: 10.3390/ijms23095213] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolomics helps identify metabolites to characterize/refine perturbations of biological pathways in living organisms. Pre-analytical, analytical, and post-analytical limitations that have hampered a wide implementation of metabolomics have been addressed. Several potential biomarkers originating from current targeted metabolomics-based approaches have been discovered. Precision medicine argues for algorithms to classify individuals based on susceptibility to disease, and/or by response to specific treatments. It also argues for a prevention-based health system. Because of its ability to explore gene-environment interactions, metabolomics is expected to be critical to personalize diagnosis and treatment. Stringent guidelines have been applied from the very beginning to design studies to acquire the information currently employed in precision medicine and precision prevention approaches. Large, prospective, expensive and time-consuming studies are now mandatory to validate old, and discover new, metabolomics-based biomarkers with high chances of translation into precision medicine. Metabolites from studies on saliva, sweat, breath, semen, feces, amniotic, cerebrospinal, and broncho-alveolar fluid are predicted to be needed to refine information from plasma and serum metabolome. In addition, a multi-omics data analysis system is predicted to be needed for omics-based precision medicine approaches. Omics-based approaches for the progress of precision medicine and prevention are expected to raise ethical issues.
Collapse
Affiliation(s)
- Alessandro Di Minno
- Dipartimento di Farmacia, University of Naples Federico II, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
| | - Monica Gelzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Marianna Caterino
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Michele Costanzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Margherita Ruoppolo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| |
Collapse
|
13
|
Siddiqui SA, Agrawal S, Brahmbhatt H, Rathore MS. Metabolite expression changes in Kappaphycus alvarezii (a red alga) under hypo- and hyper-saline conditions. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
14
|
Patel MK, Pandey S, Kumar M, Haque MI, Pal S, Yadav NS. Plants Metabolome Study: Emerging Tools and Techniques. PLANTS (BASEL, SWITZERLAND) 2021; 10:2409. [PMID: 34834772 PMCID: PMC8621461 DOI: 10.3390/plants10112409] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 05/06/2023]
Abstract
Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense responses to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted methods. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) matrix-assisted laser desorption/ionization (MALDI), ion mobility spectrometry (IMS) and nuclear magnetic resonance (NMR) have speed up precise metabolic profiling in plants. Further, we provide a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.
Collapse
Affiliation(s)
- Manish Kumar Patel
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Sonika Pandey
- Independent Researcher, Civil Line, Fathepur 212601, India;
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Md Intesaful Haque
- Fruit Tree Science Department, Newe Ya’ar Research Center, Agriculture Research Organization, Volcani Center, Ramat Yishay 3009500, Israel;
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu 180006, India;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
15
|
Gupta S, Smith PMC, Boughton BA, Rupasinghe TWT, Natera SHA, Roessner U. Inoculation of barley with Trichoderma harzianum T-22 modifies lipids and metabolites to improve salt tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7229-7246. [PMID: 34279634 DOI: 10.1093/jxb/erab335] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/17/2021] [Indexed: 05/23/2023]
Abstract
Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in two barley (Hordeum vulgare L.) cultivars, Gairdner and Vlamingh, with contrasting salinity tolerance. GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in sensitive cv. Gairdner and, to a lesser extent, improved root growth in more tolerance cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increased in both cultivars, with ribulose, ribose, and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh, but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.
Collapse
Affiliation(s)
- Sneha Gupta
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Penelope M C Smith
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- Australian National Phenome Centre, Murdoch University, Murdoch, Western Australia, Australia
| | - Thusitha W T Rupasinghe
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- SCIEX, Mulgrave, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
16
|
Rozali NL, Tahir NI, Hassan H, Othman A, Ramli US. Identification of amines, amino and organic acids in oil palm (Elaeis guineensis Jacq.) spear leaf using GC- and LC/Q-TOF MS metabolomics platforms. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
17
|
Schillaci M, Kehelpannala C, Martinez-Seidel F, Smith PMC, Arsova B, Watt M, Roessner U. The Metabolic Response of Brachypodium Roots to the Interaction with Beneficial Bacteria Is Affected by the Plant Nutritional Status. Metabolites 2021; 11:metabo11060358. [PMID: 34205012 PMCID: PMC8228974 DOI: 10.3390/metabo11060358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022] Open
Abstract
The potential of plant growth promoting (PGP) bacteria in improving the performance of plants in suboptimal environments is increasingly acknowledged, but little information is available on the mechanisms underlying this interaction, particularly when plants are subjected to a combination of stresses. In this study, we investigated the effects of the inoculation with the PGP bacteria Azospirillum brasilense (Azospirillum) on the metabolism of the model cereal Brachypodium distachyon (Brachypodium) grown at low temperatures and supplied with insufficient phosphorus. Investigating polar metabolite and lipid fluctuations during early plant development, we found that the bacteria initially elicited a defense response in Brachypodium roots, while at later stages Azospirillum reduced the stress caused by phosphorus deficiency and improved root development of inoculated plants, particularly by stimulating the growth of branch roots. We propose that the interaction of the plant with Azospirillum was influenced by its nutritional status: bacteria were sensed as pathogens while plants were still phosphorus sufficient, but the interaction became increasingly beneficial for the plants as their phosphorus levels decreased. Our results provide new insights on the dynamics of the cereal-PGP bacteria interaction, and contribute to our understanding of the role of beneficial microorganisms in the growth of cereal crops in suboptimal environments.
Collapse
Affiliation(s)
- Martino Schillaci
- School of BioSciences, University of Melbourne, Parkville 3010, Australia; (C.K.); (M.W.); (U.R.)
- Correspondence:
| | - Cheka Kehelpannala
- School of BioSciences, University of Melbourne, Parkville 3010, Australia; (C.K.); (M.W.); (U.R.)
| | - Federico Martinez-Seidel
- School of BioSciences, University of Melbourne, Parkville 3010, Australia; (C.K.); (M.W.); (U.R.)
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany;
| | - Penelope M. C. Smith
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora 3086, Australia;
| | - Borjana Arsova
- Institute for Bio & Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, 52425 Juelich, Germany;
| | - Michelle Watt
- School of BioSciences, University of Melbourne, Parkville 3010, Australia; (C.K.); (M.W.); (U.R.)
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville 3010, Australia; (C.K.); (M.W.); (U.R.)
| |
Collapse
|
18
|
McGuiness PN, Reid JB, Foo E. The influence of ethylene, gibberellins and brassinosteroids on energy and nitrogen-fixation metabolites in nodule tissue. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110846. [PMID: 33691972 DOI: 10.1016/j.plantsci.2021.110846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 05/12/2023]
Abstract
Legume nodules are a unique plant organ that contain nitrogen-fixing rhizobial bacteria. For this interaction to be mutually beneficial, plant and bacterial metabolism must be precisely co-ordinated. Plant hormones are known to play essential roles during the establishment of legume-rhizobial symbioses but their role in subsequent nodule metabolism has not been explored in any depth. The plant hormones brassinosteroids, ethylene and gibberellins influence legume infection, nodule number and in some cases nodule function. In this paper, the influence of these hormones on nodule metabolism was examined in a series of well characterised pea mutants with altered hormone biosynthesis or response. A targeted set of metabolites involved in nutrient exchange and nitrogen fixation was examined in nodule tissue of mutant and wild type plants. Gibberellin-deficiency had a major negative impact on the level of several major dicarboxylates supplied to rhizobia by the plant and also led to a significant deficit in the amino acids involved in glutamine-aspartate transamination, consistent with the limited bacteroid development and low fixation rate of gibberellin-deficient na mutant nodules. In contrast, no major effects of brassinosteroid-deficiency or ethylene-insensitivity on the key metabolites in these pathways were found. Therefore, although all three hormones influence infection and nodule number, only gibberellin is important for the establishment of a functional nodule metabolome.
Collapse
Affiliation(s)
- Peter N McGuiness
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - James B Reid
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - Eloise Foo
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
| |
Collapse
|
19
|
Patel MK, Kumar M, Li W, Luo Y, Burritt DJ, Alkan N, Tran LSP. Enhancing Salt Tolerance of Plants: From Metabolic Reprogramming to Exogenous Chemical Treatments and Molecular Approaches. Cells 2020; 9:E2492. [PMID: 33212751 PMCID: PMC7697626 DOI: 10.3390/cells9112492] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/26/2022] Open
Abstract
Plants grow on soils that not only provide support for root anchorage but also act as a reservoir of water and nutrients important for plant growth and development. However, environmental factors, such as high salinity, hinder the uptake of nutrients and water from the soil and reduce the quality and productivity of plants. Under high salinity, plants attempt to maintain cellular homeostasis through the production of numerous stress-associated endogenous metabolites that can help mitigate the stress. Both primary and secondary metabolites can significantly contribute to survival and the maintenance of growth and development of plants on saline soils. Existing studies have suggested that seed/plant-priming with exogenous metabolites is a promising approach to increase crop tolerance to salt stress without manipulation of the genome. Recent advancements have also been made in genetic engineering of various metabolic genes involved in regulation of plant responses and protection of the cells during salinity, which have therefore resulted in many more basic and applied studies in both model and crop plants. In this review, we discuss the recent findings of metabolic reprogramming, exogenous treatments with metabolites and genetic engineering of metabolic genes for the improvement of plant salt tolerance.
Collapse
Affiliation(s)
- Manish Kumar Patel
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Weiqiang Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China;
- Joint International Laboratory for Multi-Omics Research, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yin Luo
- School of Life Sciences, East China Normal University, Shanghai 200241, China;
| | - David J. Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand;
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| |
Collapse
|
20
|
Bandehagh A, Taylor NL. Can Alternative Metabolic Pathways and Shunts Overcome Salinity Induced Inhibition of Central Carbon Metabolism in Crops? FRONTIERS IN PLANT SCIENCE 2020; 11:1072. [PMID: 32849676 PMCID: PMC7417600 DOI: 10.3389/fpls.2020.01072] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/30/2020] [Indexed: 05/25/2023]
Abstract
The annual cost of lost crop production from exposure to salinity has major impacts on food security in all parts of the world. Salinity stress disturbs energy metabolism and knowledge of the impacts on critical processes controlling plant energy production is key to successfully breeding salt tolerant crops. To date, little progress has been achieved using classic breeding approaches to develop salt tolerance. The hope of some salinity researchers is that through a better understanding of the metabolic responses and adaptation to salinity exposure, new breeding targets can be suggested to help develop salt tolerant crops. Plants sense and react to salinity through a complex system of sensors, receptor systems, transporters, signal transducers, and gene expression regulators in order to control the uptake of salts and to induce tolerant metabolism that jointly leads to changes in growth rate and biomass production. During this response, there must be a balance between supply of energy from mitochondria and chloroplasts and energy demands for water and ion transport, growth, and osmotic adjustment. The photosynthetic response to salinity has been thoroughly researched and generally we see a sharp drop in photosynthesis after exposure to salinity. However, less attention has been given to the effect of salt stress on plant mitochondrial respiration and the metabolic processes that influence respiratory rate. A further complication is the wide range of respiratory responses that have been observed in different plant species, which have included major and minor increases, decreases, and no change in respiratory rate after salt exposure. In this review, we begin by considering physiological and biochemical impacts of salinity on major crop plants. We then summarize and consider recent advances that have characterized changes in abundance of metabolites that are involved in respiratory pathways and their alternative routes and shunts in terms of energy metabolism in crop plants. We will consider the diverse molecular responses of cellular plant metabolism during salinity exposure and suggest how these metabolic responses might aid in salinity tolerance. Finally, we will consider how this commonality and diversity should influence how future research of the salinity responses of crops plants should proceed.
Collapse
Affiliation(s)
- Ali Bandehagh
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Nicolas L. Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| |
Collapse
|
21
|
Cheong BE, Onyemaobi O, Wing Ho Ho W, Biddulph TB, Rupasinghe TWT, Roessner U, Dolferus R. Phenotyping the Chilling and Freezing Responses of Young Microspore Stage Wheat Spikes Using Targeted Metabolome and Lipidome Profiling. Cells 2020; 9:cells9051309. [PMID: 32466096 PMCID: PMC7291281 DOI: 10.3390/cells9051309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
Chilling and frost conditions impose major yield restraints to wheat crops in Australia and other temperate climate regions. Unpredictability and variability of field frost events are major impediments for cold tolerance breeding. Metabolome and lipidome profiling were used to compare the cold response in spikes of cold-tolerant Young and sensitive variety Wyalkatchem at the young microspore (YM) stage of pollen development. We aimed to identify metabolite markers that can reliably distinguish cold-tolerant and sensitive wheat varieties for future cold-tolerance phenotyping applications. We scored changes in spike metabolites and lipids for both varieties during cold acclimation after initial and prolonged exposure to combined chilling and freezing cycles (1 and 4 days, respectively) using controlled environment conditions. The two contrasting wheat varieties showed qualitative and quantitative differences in primary metabolites involved in osmoprotection, but differences in lipid accumulation most distinctively separated the cold response of the two wheat lines. These results resemble what we previously observed in flag leaves of the same two wheat varieties. The fact that this response occurs in tissue types with very different functions indicates that chilling and freezing tolerance in these wheat lines is associated with re-modelling of membrane lipid composition to maintain membrane fluidity.
Collapse
Affiliation(s)
- Bo Eng Cheong
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Olive Onyemaobi
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
| | - William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Thomas Ben Biddulph
- Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151, Australia;
| | - Thusitha W. T. Rupasinghe
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; (B.E.C.); (W.W.H.H.); (T.W.T.R.); (U.R.)
| | - Rudy Dolferus
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601, Australia;
- Correspondence: ; Tel.: +61-2-6246 5010
| |
Collapse
|
22
|
Ho WWH, Hill CB, Doblin MS, Shelden MC, van de Meene A, Rupasinghe T, Bacic A, Roessner U. Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms. PLANT COMMUNICATIONS 2020; 1:100031. [PMID: 33367236 PMCID: PMC7748018 DOI: 10.1016/j.xplc.2020.100031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/02/2020] [Accepted: 02/06/2020] [Indexed: 05/02/2023]
Abstract
The mechanisms underlying rootzone-localized responses to salinity during early stages of barley development remain elusive. In this study, we performed the analyses of multi-root-omes (transcriptomes, metabolomes, and lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) that maintain and restrict seedling root growth under salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEGs) and abundant metabolites (DAMs) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, and maturation Z3). Based on pathway over-representation of the DEGs and DAMs, phenylpropanoid biosynthesis is the most statistically enriched biological pathway among all salinity responses observed. Together with histological evidence, an intense salt-induced lignin impregnation was found only at stelic cell wall of Clipper Z2, compared with a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on the global correlation network of the DEGs and DAMs, callose deposition that potentially adjusted symplastic flow in roots was almost independent of salinity in rootzones of Clipper, and was markedly decreased in Sahara. Taken together, we propose two distinctive salt tolerance mechanisms in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with deteriorating global soil salinization.
Collapse
Affiliation(s)
- William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Camilla B. Hill
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Monika S. Doblin
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Megan C. Shelden
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Allison van de Meene
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Thusitha Rupasinghe
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Metabolomics Australia, The University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author
| |
Collapse
|
23
|
Roorkiwal M, Bharadwaj C, Barmukh R, Dixit GP, Thudi M, Gaur PM, Chaturvedi SK, Fikre A, Hamwieh A, Kumar S, Sachdeva S, Ojiewo CO, Tar'an B, Wordofa NG, Singh NP, Siddique KHM, Varshney RK. Integrating genomics for chickpea improvement: achievements and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1703-1720. [PMID: 32253478 PMCID: PMC7214385 DOI: 10.1007/s00122-020-03584-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/18/2020] [Indexed: 05/19/2023]
Abstract
Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.
Collapse
Affiliation(s)
- Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
| | | | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Girish P Dixit
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Asnake Fikre
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Supriya Sachdeva
- ICAR-Indian Agricultural Research Institute (IARI), Delhi, India
| | - Chris O Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
| |
Collapse
|
24
|
Sha XM, Wang GY, Li X, Zhang LZ, Tu ZC. Identification and quantification of gelatin by a high-resolution mass spectrometry-based label-free method. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
25
|
Liu Y, Liu J, Abozeid A, Wu KX, Guo XR, Mu LQ, Tang ZH. UV-B Radiation Largely Promoted the Transformation of Primary Metabolites to Phenols in Astragalus mongholicus Seedlings. Biomolecules 2020; 10:E504. [PMID: 32225015 PMCID: PMC7226020 DOI: 10.3390/biom10040504] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022] Open
Abstract
: Ultraviolet-B (UV-B) radiation (280-320 nm) may induce photobiological stress in plants, activate the plant defense system, and induce changes of metabolites. In our previous work, we found that between the two Astragalus varieties prescribed by the Chinese Pharmacopoeia, Astragalus mongholicus has better tolerance to UV-B. Thus, it is necessary to study the metabolic strategy of Astragalus under UV-B radiation further. In the present study, we used untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-mass spectrometry (LC-MS techniques) to investigate the profiles of primary and secondary metabolic. The profiles revealed the metabolic response of Astragalus to UV-B radiation. We then used real-time polymerase chain reaction (RT-PCR) to obtain the transcription level of relevant genes under UV-B radiation (UV-B supplemented in the field, λmax = 313 nm, 30 W, lamp-leaf distance = 60 cm, 40 min·day-1), which annotated the responsive mechanism of phenolic metabolism in roots. Our results indicated that supplemental UV-B radiation induced a stronger shift from carbon assimilation to carbon accumulation. The flux through the phenylpropanoids pathway increased due to the mobilization of carbon reserves. The response of metabolism was observed to be significantly tissue-specific upon the UV-B radiation treatment. Among phenolic compounds, C6C1 carbon compounds (phenolic acids in leaves) and C6C3C6 carbon compounds (flavones in leaves and isoflavones in roots) increased at the expense of C6C3 carbon compounds. Verification experiments show that the response of phenolics in roots to UV-B is activated by upregulation of relevant genes rather than phenylalanine. Overall, this study reveals the tissues-specific alteration and mechanism of primary and secondary metabolic strategy in response to UV-B radiation.
Collapse
Affiliation(s)
- Yang Liu
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jia Liu
- Material Science and Engineering College, Northeast Forestry University, Harbin 150040, China
| | - Ann Abozeid
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, China
- Botany Department, Faculty of Science, Menoufia University, Shebin El-koom 32511, Egypt
| | - Ke-Xin Wu
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, China
| | - Xiao-Rui Guo
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, China
| | - Li-Qiang Mu
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhong-Hua Tang
- Key Laboratory of Plant Ecology, Northeast Forestry University, Harbin 150040, China
| |
Collapse
|
26
|
Afshari R, Pillidge CJ, Read E, Rochfort S, Dias DA, Osborn AM, Gill H. New insights into cheddar cheese microbiota-metabolome relationships revealed by integrative analysis of multi-omics data. Sci Rep 2020; 10:3164. [PMID: 32081987 PMCID: PMC7035325 DOI: 10.1038/s41598-020-59617-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/27/2020] [Indexed: 11/11/2022] Open
Abstract
Cheese microbiota and metabolites and their inter-relationships that underpin specific cheese quality attributes remain poorly understood. Here we report that multi-omics and integrative data analysis (multiple co-inertia analysis, MCIA) can be used to gain deeper insights into these relationships and identify microbiota and metabolite fingerprints that could be used to monitor product quality and authenticity. Our study into different brands of artisanal and industrial cheddar cheeses showed that Streptococcus, Lactococcus and Lactobacillus were the dominant taxa with overall microbial community structures differing not only between industrial and artisanal cheeses but also among different cheese brands. Metabolome analysis also revealed qualitative and semi-quantitative differences in metabolites between different cheeses. This also included the presence of two compounds (3-hydroxy propanoic acid and O-methoxycatechol-O-sulphate) in artisanal cheese that have not been previously reported in any type of cheese. Integrative analysis of multi-omics datasets revealed that highly similar cheeses, identical in age and appearance, could be distinctively clustered according to cheese type and brand. Furthermore, the analysis detected strong relationships, some previously unknown, which existed between the cheese microbiota and metabolome, and uncovered specific taxa and metabolites that contributed to these relationships. These results highlight the potential of this approach for identifying product specific microbe/metabolite signatures that could be used to monitor and control cheese quality and product authenticity.
Collapse
Affiliation(s)
- Roya Afshari
- School of Science, RMIT University, Bundoora, PO Box 71, Bundoora, VIC, 3083, Australia
| | | | - Elizabeth Read
- Biosciences Research Division, Department of Environment and Primary Industries, AgriBiosciences, 5 Ring Road, Bundoora, Victoria VIC, 3083, Australia
| | - Simone Rochfort
- Biosciences Research Division, Department of Environment and Primary Industries, AgriBiosciences, 5 Ring Road, Bundoora, Victoria VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, RMIT University, Bundoora, PO Box 71, Bundoora, VIC, 3083, Australia
| | - A Mark Osborn
- School of Science, RMIT University, Bundoora, PO Box 71, Bundoora, VIC, 3083, Australia
| | - Harsharn Gill
- School of Science, RMIT University, Bundoora, PO Box 71, Bundoora, VIC, 3083, Australia.
| |
Collapse
|
27
|
Wong JWH, Plett KL, Natera SHA, Roessner U, Anderson IC, Plett JM. Comparative metabolomics implicates threitol as a fungal signal supporting colonization of Armillaria luteobubalina on eucalypt roots. PLANT, CELL & ENVIRONMENT 2020; 43:374-386. [PMID: 31797388 DOI: 10.1111/pce.13672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Armillaria root rot is a fungal disease that affects a wide range of trees and crops around the world. Despite being a widespread disease, little is known about the plant molecular responses towards the pathogenic fungi at the early phase of their interaction. With recent research highlighting the vital roles of metabolites in plant root-microbe interactions, we sought to explore the presymbiotic metabolite responses of Eucalyptus grandis seedlings towards Armillaria luteobuablina, a necrotrophic pathogen native to Australia. Using a metabolite profiling approach, we have identified threitol as one of the key metabolite responses in E. grandis root tips specific to A. luteobubalina that were not induced by three other species of soil-borne microbes of different lifestyle strategies (a mutualist, a commensalist, and a hemi-biotrophic pathogen). Using isotope labelling, threitol detected in the Armillaria-treated root tips was found to be largely derived from the fungal pathogen. Exogenous application of d-threitol promoted microbial colonization of E. grandis and triggered hormonal responses in root cells. Together, our results support a role of threitol as an important metabolite signal during eucalypt-Armillaria interaction prior to infection thus advancing our mechanistic understanding on the earliest stage of Armillaria disease development. Comparative metabolomics of eucalypt roots interacting with a range of fungal lifestyles identified threitol enrichment as a specific characteristic of Armillaria pathogenesis. Our findings suggest that threitol acts as one of the earliest fungal signals promoting Armillaria colonization of roots.
Collapse
Affiliation(s)
- Johanna W-H Wong
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Sydney, Australia
| | - Krista L Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Sydney, Australia
| | - Siria H A Natera
- Metabolomics Australia, The University of Melbourne, Parkville, Melbourne, Australia
| | - Ute Roessner
- Metabolomics Australia, The University of Melbourne, Parkville, Melbourne, Australia
- School of BioSciences, The University of Melbourne, Parkville, Melbourne, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Sydney, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, Sydney, Australia
| |
Collapse
|
28
|
Boonchaisri S, Stevenson T, Dias DA. Utilization of GC-MS untargeted metabolomics to assess the delayed response of glufosinate treatment of transgenic herbicide resistant (HR) buffalo grasses (Stenotaphrum secundatum L.). Metabolomics 2020; 16:22. [PMID: 31989303 DOI: 10.1007/s11306-020-1644-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Herbicide resistant (HR) buffalo grasses were genetically engineered to resist the non-selective herbicide, glufosinate in order to facilitate a modern, 'weeding program' which is highly effective in terms of minimizing costs and labor. The resistant trait was conferred by an insertion of the pat gene to allow for the production of the enzyme phosphinothricin acetyltransferase (PAT) to detoxify the glufosinate inhibitive effect. To date, there are only a few reports using metabolomics as well as molecular characterizations published for glufosinate-resistant crops with no reports on HR turfgrass. Therefore, for the first time, this study examines the metabolome of glufosinate-resistant buffalo grasses which not only will be useful to future growers but also the scientific community. OBJECTIVE A major aim of this present work is to characterize and evaluate the metabolic alterations which may arise from a genetic transformation of HR buffalo grasses by comprehensively using gas chromatography-mass spectrometry (GC-MS) based untargeted metabolomics. METHODS Eight-week old plants of 4 HR buffalo grasses, (93-1A, 93-2B, 93-3C and 93-5A) and 3 wild type varieties (WT 8-4A, WT 9-1B and WT 9-1B) were selected for physiological, molecular and metabolomics experiments. Plants were either sprayed with 1, 5, 10 and 15% v/v of glufosinate to evaluate the visual injuries or submerged in 5% v/v of glufosinate 3 days prior to a GC-MS based untargeted metabolomics analysis. In contrast, the control group was treated with distilled water. Leaves were extracted in 1:1 methanol:water and then analysed, using an in-house GC-MS untargeted workflow. RESULTS Results identified 199 metabolites with only 6 of them (cis-aconitic acid, allantoin, cellobiose, glyceric acid, maltose and octadecanoic acid) found to be statistically significant (p < 0.05) between the HR and wild type buffalo grass varieties compared to the control experiment. Among these metabolites, unusual accumulation of allantoin was prominent and was an unanticipated effect of the pat gene insertion. As expected, glufosinate treatment caused significant metabolic alterations in the sensitive wild type, with the up-regulation of several amino acids (e.g. phenylalanine and isoleucine) which was likely due to glufosinate-induced senescence. The aminoacyl-tRNA biosynthetic pathway was identified as the most significant enriched pathway as a result of glufosinate effects because a number of its intermediates were amino acids. CONCLUSION HR buffalo grasses were very similar to its wild type comparator based on a comprehensive GC-MS based untargeted metabolomics and therefore, should guarantee the safe use of these HR buffalo grasses. The current metabolomics analyses not only confirmed the effects of glufosinate to up-regulate free amino acid pools in the sensitive wild type but also several alterations in sugar, sugar phosphate and organic acid metabolism have been reported.
Collapse
Affiliation(s)
| | - Trevor Stevenson
- School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, VIC, 3083, Australia.
| |
Collapse
|
29
|
Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
Collapse
Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
30
|
Menéndez AB, Calzadilla PI, Sansberro PA, Espasandin FD, Gazquez A, Bordenave CD, Maiale SJ, Rodríguez AA, Maguire VG, Campestre MP, Garriz A, Rossi FR, Romero FM, Solmi L, Salloum MS, Monteoliva MI, Debat JH, Ruiz OA. Polyamines and Legumes: Joint Stories of Stress, Nitrogen Fixation and Environment. FRONTIERS IN PLANT SCIENCE 2019; 10:1415. [PMID: 31749821 PMCID: PMC6844238 DOI: 10.3389/fpls.2019.01415] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/11/2019] [Indexed: 05/31/2023]
Abstract
Polyamines (PAs) are natural aliphatic amines involved in many physiological processes in almost all living organisms, including responses to abiotic stresses and microbial interactions. On other hand, the family Leguminosae constitutes an economically and ecologically key botanical group for humans, being also regarded as the most important protein source for livestock. This review presents the profuse evidence that relates changes in PAs levels during responses to biotic and abiotic stresses in model and cultivable species within Leguminosae and examines the unreviewed information regarding their potential roles in the functioning of symbiotic interactions with nitrogen-fixing bacteria and arbuscular mycorrhizae in this family. As linking plant physiological behavior with "big data" available in "omics" is an essential step to improve our understanding of legumes responses to global change, we also examined integrative MultiOmics approaches available to decrypt the interface legumes-PAs-abiotic and biotic stress interactions. These approaches are expected to accelerate the identification of stress tolerant phenotypes and the design of new biotechnological strategies to increase their yield and adaptation to marginal environments, making better use of available plant genetic resources.
Collapse
Affiliation(s)
- Ana Bernardina Menéndez
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, UBA-CONICET, Buenos Aires, Argentina
| | | | | | | | - Ayelén Gazquez
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | | | | | | | | | | | - Andrés Garriz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | - Franco Rubén Rossi
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | | | - Leandro Solmi
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | - Maria Soraya Salloum
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Mariela Inés Monteoliva
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Julio Humberto Debat
- Instituto de Patología Vegetal (IPAVE) Ing “Sergio Nome,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| | - Oscar Adolfo Ruiz
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
- Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV) Ing “Victorio S Trippi,” Instituto Nacional de Tecnología Agropecuaria (INTA), Córdoba, Argentina
| |
Collapse
|
31
|
Chang J, Cheong BE, Natera S, Roessner U. Morphological and metabolic responses to salt stress of rice (Oryza sativa L.) cultivars which differ in salinity tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:427-435. [PMID: 31639558 DOI: 10.1016/j.plaphy.2019.10.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 05/25/2023]
Abstract
Salinization is one of the most important abiotic stressors for crop growth and productivity. Rice (Oryza sativa L.), as the major food source around the world, is very sensitive to salt, especially at seedling stage. In order to examine how salt stress influences the metabolism of rice, we compared the levels of a range of sugars and organic acids in three rice cultivars with different tolerance under salt stress over time. According to the morphological result, the shoot length and root fresh weight were only affected by salinity in the salt sensitive cultivar (Nipponbare). The responses of metabolites to salinity were time-, tissue- and cultivar-dependent. Shikimate and quinate, involved in the shikimate pathway, were dramatically decreased in the leaves of all three cultivars, which was regarded as a response to salinity. Many sugars in the leaves of the salt tolerant cultivar (Dendang and Fatmawati) showed earlier increases to salt stress compared to Nipponbare leaves. Moreover, only in the leaves of tolerant cultivars (Dendang and Fatimawati), malate was significantly decreased while sucrose was significantly increased. In Dendang roots, mannitol levels were significantly higher than in Nipponbare roots after 14 days of salt treatment, which may be attributed to its higher salt tolerance. It is proposed that these responses in the more tolerant cultivars are involved in their resistance to high salt stress which may lay the foundation for breeding tolerant rice cultivars.
Collapse
Affiliation(s)
- Jing Chang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Bo Eng Cheong
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia
| | - Siria Natera
- Metabolomics Australia, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Victoria, 3010, Australia; Metabolomics Australia, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| |
Collapse
|
32
|
Cheong BE, Ho WWH, Biddulph B, Wallace X, Rathjen T, Rupasinghe TWT, Roessner U, Dolferus R. Phenotyping reproductive stage chilling and frost tolerance in wheat using targeted metabolome and lipidome profiling. Metabolomics 2019; 15:144. [PMID: 31630279 PMCID: PMC6800866 DOI: 10.1007/s11306-019-1606-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Frost events lead to A$360 million of yield losses annually to the Australian wheat industry, making improvement of chilling and frost tolerance an important trait for breeding. OBJECTIVES This study aimed to use metabolomics and lipidomics to explore genetic variation in acclimation potential to chilling and to identify metabolite markers for chilling tolerance in wheat. METHODS We established a controlled environment screening assay that is able to reproduce field rankings of wheat germplasm for chilling and frost tolerance. This assay, together with targeted metabolomics and lipidomics approaches, were used to compare metabolite and lipid levels in flag leaves of two wheat varieties with contrasting chilling tolerance. RESULTS The sensitive variety Wyalkatchem showed a strong reduction in amino acids after the first cold night, followed by accumulation of osmolytes such as fructose, glucose, putrescine and shikimate over a 4-day period. Accumulation of osmolytes is indicative of acclimation to water stress in Wyalkatchem. This response was not observed for tolerant variety Young. The two varieties also displayed significant differences in lipid accumulation. Variation in two lipid clusters, resulted in a higher unsaturated to saturated lipid ratio in Young after 4 days cold treatment and the lipids PC(34:0), PC(34:1), PC(35:1), PC(38:3), and PI(36:4) were the main contributors to the unsaturated to saturated ratio change. This indicates that Young may have superior ability to maintain membrane fluidity following cold exposure, thereby avoiding membrane damage and water stress observed for Wyalkatchem. CONCLUSION Our study suggests that metabolomics and lipidomics markers could be used as an alternative phenotyping method to discriminate wheat varieties with differences in cold acclimation.
Collapse
Affiliation(s)
- Bo Eng Cheong
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - William Wing Ho Ho
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
- Melbourne Integrative Genomics, Schools of Mathematics and Statistics and of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ben Biddulph
- Department of Primary Industries and Regional Development, 3 Baron Hay Court, South Perth, WA 6151 Australia
| | - Xiaomei Wallace
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601 Australia
| | - Tina Rathjen
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601 Australia
| | - Thusitha W. T. Rupasinghe
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Rudy Dolferus
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT 2601 Australia
| |
Collapse
|
33
|
Sinclair GM, O'Brien AL, Keough M, de Souza DP, Dayalan S, Kanojia K, Kouremenos K, Tull DL, Coleman RA, Jones OAH, Long SM. Metabolite Changes in an Estuarine Annelid Following Sublethal Exposure to a Mixture of Zinc and Boscalid. Metabolites 2019; 9:metabo9100229. [PMID: 31618973 PMCID: PMC6835977 DOI: 10.3390/metabo9100229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/08/2019] [Accepted: 10/12/2019] [Indexed: 12/14/2022] Open
Abstract
Environmental pollutants such as heavy metals and fungicides pose a serious threat to waterways worldwide. Toxicological assessment of such contaminants is usually conducted using single compound exposures, as it is challenging to understand the effect of mixtures on biota using standard ecotoxicological methods; whereas complex chemical mixtures are more probable in ecosystems. This study exposed Simplisetia aequisetis (an estuarine annelid) to sublethal concentrations of a metal (zinc) and a fungicide (boscalid), both singly and as a mixture, for two weeks. Metabolomic analysis via gas and liquid chromatography-mass spectrometry was used to measure the stress response(s) of the organism following exposure. A total of 75 metabolites, including compounds contributing to the tricarboxylic acid cycle, the urea cycle, and a number of other pathways, were identified and quantified. The multiplatform approach identified distinct metabolomic responses to each compound that differed depending on whether the substance was presented singly or as a mixture, indicating a possible antagonistic effect. The study demonstrates that metabolomics is able to elucidate the effects and mode of action of contaminants and can identify possible outcomes faster than standard ecotoxicological endpoints, such as growth and reproduction. Metabolomics therefore has a possible future role in biomonitoring and ecosystem health assessments.
Collapse
Affiliation(s)
- Georgia M Sinclair
- School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria, 3010, Australia.
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria 3010, Australia.
| | - Allyson L O'Brien
- School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria, 3010, Australia.
| | - Michael Keough
- School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria, 3010, Australia.
| | - David P de Souza
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Komal Kanojia
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Konstantinos Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Dedreia L Tull
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia.
| | - Rhys A Coleman
- Melbourne Water Corporation, 990 La Trobe Street, Docklands, Victoria 3008, Australia.
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT, University, GPO Box 2476, Melbourne, Victoria 3001, Australia.
| | - Sara M Long
- School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria, 3010, Australia.
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, The University of Melbourne, Royal Parade, Parkville Victoria 3010, Australia.
| |
Collapse
|
34
|
Salloum MS, Insani M, Monteoliva MI, Menduni MF, Silvente S, Carrari F, Luna C. Metabolic responses to arbuscular mycorrhizal fungi are shifted in roots of contrasting soybean genotypes. MYCORRHIZA 2019; 29:459-473. [PMID: 31410554 DOI: 10.1007/s00572-019-00909-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Modern breeding programs have reduced genetic variability and might have caused a reduction in plant colonization by arbuscular mycorrhizal fungi (AM). In our previous studies, mycorrhizal colonization was affected in improved soybean genotypes, mainly arbuscule formation. Despite substantial knowledge of the symbiosis-related changes of the transcriptome and proteome, only sparse clues regarding metabolite alterations are available. Here, we evaluated metabolite changes between improved (I-1) and unimproved (UI-4) soybean genotypes and also compare their metabolic responses after AM root colonization. Soybean genotypes inoculated or not with AM were grown in a chamber under controlled light and temperature conditions. At 20 days after inoculation, we evaluated soluble metabolites of each genotype and treatment measured by GC-MS. In this analysis, when comparing non-AM roots between genotypes, I-1 had a lower amount of 31 and higher amount of only 4 metabolites than the UI-4 genotype. When comparing AM roots, I-1 had a lower amount of 36 and higher amount of 4 metabolites than UI-4 (different to those found altered in non-AM treated plants). Lastly, comparing the AM vs non-AM treatments, I-1 had increased levels of three and reduced levels of 24 metabolites, while UI-4 only had levels of 12 metabolites reduced by the effect of mycorrhizas. We found the major changes in sugars, polyols, amino acids, and carboxylic acids. In a targeted analysis, we found lower levels of isoflavonoids and alpha-tocopherol and higher levels of malondialdehyde in the I-1 genotype that can affect soybean-AM symbiosis. Our studies have the potential to support improving soybean with a greater capacity to be colonized and responsive to AM interaction.
Collapse
Affiliation(s)
- María Soraya Salloum
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigación Agropecuaria (CIAP),, Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km. 5.5, CP 5119, Córdoba, Argentina.
| | - Marina Insani
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y de los Reseros s/n, 1686, Hurlingham, Buenos Aires, Argentina
| | - Mariela Inés Monteoliva
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigación Agropecuaria (CIAP),, Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km. 5.5, CP 5119, Córdoba, Argentina
| | - María Florencia Menduni
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Fondo para la Investigación Científica y Tecnológica (FONCyT), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigación Agropecuaria (CIAP),, Instituto Nacional de Tecnología Agropecuaria (INTA),, Camino 60 Cuadras km. 5.5, CP 5119, Córdoba, Argentina
| | - Sonia Silvente
- Instituto de Ambiente de Montaña y Regiones Áridas (IAMRA), Universidad Nacional de Chilecito (UNdeC), Av Los Peregrinos s/n, Chilecito, F5360CKB, La Rioja, Argentina
| | - Fernando Carrari
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
- Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Celina Luna
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisiología y Recursos Genéticos Vegetales (IFRGV), Centro de Investigación Agropecuaria (CIAP),, Instituto Nacional de Tecnología Agropecuaria (INTA), Camino 60 Cuadras km. 5.5, CP 5119, Córdoba, Argentina
| |
Collapse
|
35
|
Soh PXY, Marin Cely JM, Mortlock SA, Jara CJ, Booth R, Natera S, Roessner U, Crossett B, Cordwell S, Singh Khatkar M, Williamson P. Genome-wide association studies of 74 plasma metabolites of German shepherd dogs reveal two metabolites associated with genes encoding their enzymes. Metabolomics 2019; 15:123. [PMID: 31493001 DOI: 10.1007/s11306-019-1586-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION German shepherd dogs (GSDs) are a popular breed affected by numerous disorders. Few studies have explored genetic variations that influence canine blood metabolite levels. OBJECTIVES To investigate genetic variants affecting the natural metabolite variation in GSDs. METHODS A total of 82 healthy GSDs were genotyped on the Illumina CanineHD Beadchip, assaying 173,650 markers. For each dog, 74 metabolites were measured through liquid and gas chromatography mass spectrometry (LC-MS and GC-MS) and were used as phenotypes for genome-wide association analyses (GWAS). Sliding window and homozygosity analyses were conducted to fine-map regions of interest, and to identify haplotypes and gene dosage effects. RESULTS Summary statistics for 74 metabolites in this population of GSDs are reported. Forty-one metabolites had significant associations at a false discovery rate of 0.05. Two associations were located around genes which encode for enzymes for the relevant metabolites: 4-hydroxyproline was significantly associated to D-amino acid oxidase (DAO), and threonine to L-threonine 3-dehydrogenase (LOC477365). Three of the top ten haplotypes associated to 4-hydroxyproline included at least one SNP on DAO. These haplotypes occurred only in dogs with the highest 15 measurements of 4-hydroxyproline, ranging in frequency from 16.67 to 20%. None of the dogs were homozygous for these haplotypes. The top two haplotypes associated to threonine included SNPs on LOC477365 and were also overrepresented in dogs with the highest 15 measurements of threonine. These haplotypes occurred at a frequency of 90%, with 80% of these dogs homozygous for the haplotypes. In dogs with the lowest 15 measurements of threonine, the haplotypes occurred at a frequency of 26.67% and 0% homozygosity. CONCLUSION DAO and LOC477365 were identified as candidate genes affecting the natural plasma concentration of 4-hydroxyproline and threonine, respectively. Further investigations are needed to validate the effects of the variants on these genes.
Collapse
Affiliation(s)
- Pamela Xing Yi Soh
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Juliana Maria Marin Cely
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Sally-Anne Mortlock
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Christopher James Jara
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Rachel Booth
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
| | - Siria Natera
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Stuart Cordwell
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia
- Sydney Mass Spectrometry, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Mehar Singh Khatkar
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, Australia
| | - Peter Williamson
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia.
| |
Collapse
|
36
|
Sedlacko EM, Jahn CE, Heuberger AL, Sindt NM, Miller HM, Borch T, Blaine AC, Cath TY, Higgins CP. Potential for Beneficial Reuse of Oil and Gas-Derived Produced Water in Agriculture: Physiological and Morphological Responses in Spring Wheat (Triticum aestivum). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:1756-1769. [PMID: 31017691 DOI: 10.1002/etc.4449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/15/2019] [Accepted: 04/19/2019] [Indexed: 05/23/2023]
Abstract
Produced water (PW) from oil and gas operations is considered a potential resource for food crop irrigation because of increasing water scarcity in dryland agriculture. However, efforts to employ PW for agriculture have been met with limited success. A greenhouse study was performed to evaluate the effects of PW on physiological and morphological traits of spring wheat (Triticum aestivum). Plants were irrigated with water treatments containing 10 and 50% PW (PW10 and PW50, respectively) and compared to a matching 50% salinity (NaCl50) and 100% tap water controls. Compared to controls, plants watered with PW10 and PW50 exhibited developmental arrest and reductions in aboveground and belowground biomass, photosynthetic efficiency, and reproductive growth. Decreases in grain yield ranged from 70 to 100% in plants irrigated with PW compared to the tap water control. Importantly, the PW10 and NaCl50 treatments were comparable for morphophysiological effects, even though NaCl50 contained 5 times the total dissolved solids, suggesting that constituents other than NaCl in PW contributed to plant stress. These findings indicate that despite discharge and reuse requirements focused on total dissolved solids, salinity stress may not be the primary factor affecting crop health. The results of the present study are informative for developing guidelines for the use of PW in agriculture to ensure minimal effects on crop morphology and physiology. Environ Toxicol Chem 2019;38:1756-1769. © 2019 SETAC.
Collapse
Affiliation(s)
- Erin M Sedlacko
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Courtney E Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Adam L Heuberger
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, Colorado, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Nathan M Sindt
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Hannah M Miller
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Andrea C Blaine
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Tzahi Y Cath
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Christopher P Higgins
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| |
Collapse
|
37
|
Pinu FR, Goldansaz SA, Jaine J. Translational Metabolomics: Current Challenges and Future Opportunities. Metabolites 2019; 9:E108. [PMID: 31174372 PMCID: PMC6631405 DOI: 10.3390/metabo9060108] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
Metabolomics is one of the latest omics technologies that has been applied successfully in many areas of life sciences. Despite being relatively new, a plethora of publications over the years have exploited the opportunities provided through this data and question driven approach. Most importantly, metabolomics studies have produced great breakthroughs in biomarker discovery, identification of novel metabolites and more detailed characterisation of biological pathways in many organisms. However, translation of the research outcomes into clinical tests and user-friendly interfaces has been hindered due to many factors, some of which have been outlined hereafter. This position paper is the summary of discussion on translational metabolomics undertaken during a peer session of the Australian and New Zealand Metabolomics Conference (ANZMET 2018) held in Auckland, New Zealand. Here, we discuss some of the key areas in translational metabolomics including existing challenges and suggested solutions, as well as how to expand the clinical and industrial application of metabolomics. In addition, we share our perspective on how full translational capability of metabolomics research can be explored.
Collapse
Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant and Food Research, Private Bag 92169, Auckland 1142, New Zealand.
| | - Seyed Ali Goldansaz
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Jacob Jaine
- Analytica Laboratories Ltd., Ruakura Research Centre, Hamilton 3216, New Zealand.
| |
Collapse
|
38
|
Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
| |
Collapse
|
39
|
Lohr KE, Camp EF, Kuzhiumparambil U, Lutz A, Leggat W, Patterson JT, Suggett DJ. Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling. J Exp Biol 2019; 222:jeb.195982. [DOI: 10.1242/jeb.195982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/11/2019] [Indexed: 11/20/2022]
Abstract
Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
Collapse
Affiliation(s)
- Kathryn E. Lohr
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Emma F. Camp
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Adrian Lutz
- Metabolomics Australia, University of Melbourne, Parkville, VIC, Australia
| | - William Leggat
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, Australia
| | - Joshua T. Patterson
- Program in Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
- Center for Conservation, The Florida Aquarium, Apollo Beach, FL, USA
| | - David J. Suggett
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, NSW, Australia
| |
Collapse
|
40
|
Shaar‐Moshe L, Hayouka R, Roessner U, Peleg Z. Phenotypic and metabolic plasticity shapes life-history strategies under combinations of abiotic stresses. PLANT DIRECT 2019; 3:e00113. [PMID: 31245755 PMCID: PMC6508786 DOI: 10.1002/pld3.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/11/2018] [Accepted: 12/23/2018] [Indexed: 05/23/2023]
Abstract
Plants developed various reversible and non-reversible acclimation mechanisms to cope with the multifaceted nature of abiotic-stress combinations. We hypothesized that in order to endure these stress combinations, plants elicit distinctive acclimation strategies through specific trade-offs between reproduction and defense. To investigate Brachypodium distachyon acclimation strategies to combinations of salinity, drought and heat, we applied a system biology approach, integrating physiological, metabolic, and transcriptional analyses. We analyzed the trade-offs among functional and performance traits, and their effects on plant fitness. A combination of drought and heat resulted in escape strategy, while under a combination of salinity and heat, plants exhibited an avoidance strategy. On the other hand, under combinations of salinity and drought, with or without heat stress, plant fitness (i.e., germination rate of subsequent generation) was severely impaired. These results indicate that under combined stresses, plants' life-history strategies were shaped by the limits of phenotypic and metabolic plasticity and the trade-offs between traits, thereby giving raise to distinct acclimations. Our findings provide a mechanistic understanding of plant acclimations to combinations of abiotic stresses and shed light on the different life-history strategies that can contribute to grass fitness and possibly to their dispersion under changing environments.
Collapse
Affiliation(s)
- Lidor Shaar‐Moshe
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Ruchama Hayouka
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
| | - Ute Roessner
- School of BioSciencesThe University of MelbourneMelbourneAustralia
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in AgricultureThe Hebrew University of JerusalemRehovotIsrael
| |
Collapse
|
41
|
Richter JA, Behr JH, Erban A, Kopka J, Zörb C. Ion-dependent metabolic responses of Vicia faba L. to salt stress. PLANT, CELL & ENVIRONMENT 2019; 42:295-309. [PMID: 29940081 DOI: 10.1111/pce.13386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
Salt-affected farmlands are increasingly burdened by chlorides, carbonates, and sulfates of sodium, calcium, and magnesium. Intriguingly, the underlying physiological processes are studied almost always under NaCl stress. Two faba bean cultivars were subjected to low- and high-salt treatments of NaCl, Na2 SO4 , and KCl. Assimilation rate and leaf water vapor conductance were reduced to approximately 25-30% without biomass reduction after 7 days salt stress, but this did not cause severe carbon shortage. The equimolar treatments of Na+ , K+ , and Cl- showed comparable accumulation patterns in leaves and roots, except for SO42- which did not accumulate. To gain a detailed understanding of the effects caused by the tested ion combinations, we performed nontargeted gas chromatography-mass spectrometry-based metabolite profiling. Metabolic responses to various salts were in part highly linearly correlated, but only a few metabolite responses were common to all salts and in both cultivars. At high salt concentrations, only myo-inositol, allantoin, and glycerophosphoglycerol were highly significantly increased in roots under all tested conditions. We discovered several metabolic responses that were preferentially associated with the presence of Na+ , K+ , or Cl- . For example, increases of leaf proline and decreases of leaf fumaric acid and malic acid were apparently associated with Cl- accumulation.
Collapse
Affiliation(s)
- Julia A Richter
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Jan H Behr
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Christian Zörb
- Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
42
|
Meher HC, Singh G, Chawla G. Metabolic Alternations of Amino Acids, γ-Aminobutyric Acid, and Salicylic Acid in Solanum lycopersicum (L.) Following Preplanting Seedling Spray with Salicylic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12236-12248. [PMID: 30418772 DOI: 10.1021/acs.jafc.8b04098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Preplanting foliar spray of salicylic acid (SA) (0.0, 5.0, and 10.0 μg/mL) to Solanum lycopersicum (L.) altered the metabolite profile of amino acids, γ-aminobutyric acid (GABA), and SA in leaf, root, and fruits. Free amino acid pools increased; bound amino acid pools reduced. In vegetative tissues, amino acid biosyntheses linked to osmo-compatibility (Pro, Leu, Val and GABA); N (Arg, Asn, Asp, Gln, and Glu); C (Pro, Ser, and Tyr); S (Cys) assimilation; stress tolerance (Ala, Gly, Hyp, His, Lys, Met, and Thr); and central metabolism (Phe, Trp, and Tyr) enhanced for 60-120 days. Concentrations of Ala, Arg, Gln, Gly, Leu, and Ser in leaf and of Asp, Cys, Glu, His, Hyp, Lys, Met, Pro, and Val in root predominated. In planta SA and GABA biosynthesis increased concurrently. SA affected GABA biosynthesis via Glu, Pro, and Arg metabolism. SA, GABA, Glu, and Pro were key canonical variables. This study first reported SA-induced metabolites promoting health (SA/GABA; Cys/Met) and palatability (Glu/Asp; Gln) in table tomato.
Collapse
Affiliation(s)
- Hari C Meher
- Indian Agricultural Research Institute , New Delhi 110012 , India
| | - Ghanendra Singh
- Indian Agricultural Research Institute , New Delhi 110012 , India
| | - Gautam Chawla
- Indian Agricultural Research Institute , New Delhi 110012 , India
| |
Collapse
|
43
|
Parvin S, Uddin S, Bourgault M, Roessner U, Tausz-Posch S, Armstrong R, O'Leary G, Fitzgerald G, Tausz M. Water availability moderates N 2 fixation benefit from elevated [CO 2 ]: A 2-year free-air CO 2 enrichment study on lentil (Lens culinaris MEDIK.) in a water limited agroecosystem. PLANT, CELL & ENVIRONMENT 2018; 41:2418-2434. [PMID: 29859018 DOI: 10.1111/pce.13360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 05/09/2023]
Abstract
Increased biomass and yield of plants grown under elevated [CO2 ] often corresponds to decreased grain N concentration ([N]), diminishing nutritional quality of crops. Legumes through their symbiotic N2 fixation may be better able to maintain biomass [N] and grain [N] under elevated [CO2 ], provided N2 fixation is stimulated by elevated [CO2 ] in line with growth and yield. In Mediterranean-type agroecosystems, N2 fixation may be impaired by drought, and it is unclear whether elevated [CO2 ] stimulation of N2 fixation can overcome this impact in dry years. To address this question, we grew lentil under two [CO2 ] (ambient ~400 ppm and elevated ~550 ppm) levels in a free-air CO2 enrichment facility over two growing seasons sharply contrasting in rainfall. Elevated [CO2 ] stimulated N2 fixation through greater nodule number (+27%), mass (+18%), and specific fixation activity (+17%), and this stimulation was greater in the high than in the low rainfall/dry season. Elevated [CO2 ] depressed grain [N] (-4%) in the dry season. In contrast, grain [N] increased (+3%) in the high rainfall season under elevated [CO2 ], as a consequence of greater post-flowering N2 fixation. Our results suggest that the benefit for N2 fixation from elevated [CO2 ] is high as long as there is enough soil water to continue N2 fixation during grain filling.
Collapse
Affiliation(s)
- Shahnaj Parvin
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, Australia
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Shihab Uddin
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
| | - Maryse Bourgault
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
- Northern Agricultural Research Centre, Montana State University, Havre, Montana, USA
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sabine Tausz-Posch
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Roger Armstrong
- Department of Economic Development, Jobs, Transport and Resources, Horsham, Victoria, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Garry O'Leary
- Department of Economic Development, Jobs, Transport and Resources, Horsham, Victoria, Australia
| | - Glenn Fitzgerald
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Creswick, Victoria, Australia
- Department of Economic Development, Jobs, Transport and Resources, Horsham, Victoria, Australia
| | - Michael Tausz
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, Victoria, Australia
- Birmingham Institute of Forest Research, University of Birmingham, Edgbaston, Birmingham, UK
| |
Collapse
|
44
|
Debnath M, Ashwath N, Hill CB, Callahan DL, Dias DA, Jayasinghe NS, Midmore DJ, Roessner U. Comparative metabolic and ionomic profiling of two cultivars of Stevia rebaudiana Bert. (Bertoni) grown under salinity stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:56-70. [PMID: 29800808 DOI: 10.1016/j.plaphy.2018.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 04/01/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
This study provides a comprehensive investigation on the impact of increasing NaCl concentrations on hydroponically grown Stevia rebaudiana cultivars (Shoutian-2 and Fengtian). Growth parameters including plant height, biomass and physiological responses including osmotic potential were measured. In addition, the levels of steviol glycosides, elements and primary metabolites were measured and statistically evaluated. The cultivar Fengtian grew faster, accumulated less Na+ and compatible organic solutes, and more K+ in the leaves, as compared to the cv. Shoutian-2. Metabolite analysis identified 81 differentially accumulated metabolites, indicating an alteration in the metabolite phenotype of both cultivars upon exposure to salinity A general increase in many amino acids, amines, sugars and sugar phosphates with a concurrent decrease in most organic acids; including tricarboxylic acid (TCA) cycle intermediates, was observed. In the more salt tolerant cv. Fengtian, the levels of hexose phosphates and metabolites involved in cellular protection increased in response to salinity. These metabolites remained unchanged in the sensitive cv. Shoutian-2. Interestingly, salt treatment notably increased the rebaudioside A concentration by 53% while at the same time stevioside decreased by 38% in Fengtian which has important implications for controlling the relative amounts of reboudioside A and stevioside. The findings of this study leads to the conclusion that mild salinity stress can increase the yield of sweetener compounds, which is dependent on the cultivar and the level of salinity stress.
Collapse
Affiliation(s)
- Mousumi Debnath
- Department of Biosciences, Manipal University Jaipur, Rajasthan 303007, India; Central Queensland University, Institute for Future Farming Systems, Rockhampton, Queensland 4702, Australia
| | - Nanjappa Ashwath
- Central Queensland University, Institute for Future Farming Systems, Rockhampton, Queensland 4702, Australia
| | - Camilla Beate Hill
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Damien L Callahan
- Deakin University, Geelong, Australia, School of Life and Environmental Sciences, Centre for Chemistry and Biotechnology (Burwood Campus), 221 Burwood Highway, Burwood VIC 3125, Australia
| | - Daniel Anthony Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, Victoria 3083, Australia
| | | | - David James Midmore
- Central Queensland University, Institute for Future Farming Systems, Rockhampton, Queensland 4702, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia; Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
45
|
Morris L, O'Brien A, Natera SHA, Lutz A, Roessner U, Long SM. Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management. MARINE POLLUTION BULLETIN 2018; 131:525-529. [PMID: 29886978 DOI: 10.1016/j.marpolbul.2018.04.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/16/2018] [Accepted: 04/22/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional diversity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less diverse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.
Collapse
Affiliation(s)
- Liz Morris
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia.
| | - Allyson O'Brien
- School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ute Roessner
- Metabolomics Australia, School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Sara M Long
- Centre for Aquatic Pollution Identification and Management (CAPIM), School of Biosciences, University of Melbourne, Parkville 3010, Victoria, Australia
| |
Collapse
|
46
|
Liu J, Xu M, Estavillo GM, Delhaize E, White RG, Zhou M, Ryan PR. Altered Expression of the Malate-Permeable Anion Channel OsALMT4 Reduces the Growth of Rice Under Low Radiance. FRONTIERS IN PLANT SCIENCE 2018; 9:542. [PMID: 29774038 PMCID: PMC5943490 DOI: 10.3389/fpls.2018.00542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/06/2018] [Indexed: 05/08/2023]
Abstract
We examined the function of OsALMT4 in rice (Oryza sativa L.) which is a member of the aluminum-activated malate transporter family. Previous studies showed that OsALMT4 localizes to the plasma membrane and that expression in transgenic rice lines results in a constitutive release of malate from the roots. Here, we show that OsALMT4 is expressed widely in roots, shoots, flowers, and grain but not guard cells. Expression was also affected by ionic and osmotic stress, light and to the hormones ABA, IAA, and salicylic acid. Malate efflux from the transgenic plants over-expressing OsALMT4 was inhibited by niflumate and salicylic acid. Growth of transgenic lines with either increased OsALMT4 expression or reduced expression was measured in different environments. Light intensity caused significant differences in growth between the transgenic lines and controls. When day-time light was reduced from 700 to 300 μmol m-2s-1 independent transgenic lines with either increased or decreased OsALMT4 expression accumulated less biomass compared to their null controls. This response was not associated with differences in photosynthetic capacity, stomatal conductance or sugar concentrations in tissues. We propose that by disrupting malate fluxes across the plasma membrane carbon partitioning and perhaps signaling are affected which compromises growth under low light. We conclude that OsALMT4 is expressed widely in rice and facilitates malate efflux from different cell types. Altering OsALMT4 expression compromises growth in low-light environments.
Collapse
Affiliation(s)
- Jie Liu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Muyun Xu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Gonzalo M. Estavillo
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Emmanuel Delhaize
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Rosemary G. White
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Meixue Zhou
- School of Land and Food and Tasmanian Institute for Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Peter R. Ryan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| |
Collapse
|
47
|
Jiao Y, Bai Z, Xu J, Zhao M, Khan Y, Hu Y, Shi L. Metabolomics and its physiological regulation process reveal the salt-tolerant mechanism in Glycine soja seedling roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 126:187-196. [PMID: 29525442 DOI: 10.1016/j.plaphy.2018.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/01/2018] [Accepted: 03/01/2018] [Indexed: 12/17/2023]
Abstract
Wild soybean (Glycine soja) is an excellent germplasm resource and has strong resistance and wide adaptability to different environments. Hence, the physiology and metabolomics characteristics of wild soybean under different types of salt stress were determined to improve understanding of salt-tolerant mechanisms of wild soybean in the field. Two types of wild soybean seedlings were exposed to two different types of salt stress for 14 d. The photosynthesis of wild soybean seedling extracts were analyzed using metabolomics based on gas chromatography-mass spectrometry. The wild soybean root extracts used metabolomics to quantify the metabolic changes and ion contents. The assimilative function of photosynthesis in salt-tolerant wild soybean was less inhibited than in common wild soybean, and it regulated accumulation of toxic ions and maintained the accumulation of K+ and Mg2+ to alleviate salt stress. Moreover, in resisting salt stress the salt-tolerant wild soybean has showed improved amino acid and carbohydrate and polyol metabolisms under neutral-salt stress and organic acid, amino acid and tricarboxylic acid metabolisms under alkali-salt stress. Our results provide valuable insights into the response of salt-tolerant wild soybean to two types of salt stress by linking stress-related physiological responses to changes in metabolites.
Collapse
Affiliation(s)
- Yang Jiao
- School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Zhenzi Bai
- Department of Infectious Diseases, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Jingyu Xu
- School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Mingli Zhao
- School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yaseen Khan
- School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yongjun Hu
- School of Life Sciences, ChangChun Normal University, Changchun 130024, China.
| | - Lianxuan Shi
- School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| |
Collapse
|
48
|
Behrendt L, Raina JB, Lutz A, Kot W, Albertsen M, Halkjær-Nielsen P, Sørensen SJ, Larkum AW, Kühl M. In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina. THE ISME JOURNAL 2018; 12:556-567. [PMID: 29087375 PMCID: PMC5776471 DOI: 10.1038/ismej.2017.192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 01/20/2023]
Abstract
The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.
Collapse
Affiliation(s)
- Lars Behrendt
- Department of Civil, Environmental and Geomatic Engineering, Swiss Federal Institute of Technology, Zürich, Switzerland.
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark.
- Department of Biology, Microbiology Section, University of Copenhagen, Copenhagen, Denmark.
| | - Jean-Baptiste Raina
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, New South Wales, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Witold Kot
- Department of Environmental Science-Enviromental Microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær-Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Søren J Sørensen
- Department of Biology, Microbiology Section, University of Copenhagen, Copenhagen, Denmark
| | - Anthony Wd Larkum
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, New South Wales, Australia
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, New South Wales, Australia
| |
Collapse
|
49
|
Cui F, Sui N, Duan G, Liu Y, Han Y, Liu S, Wan S, Li G. Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut. FRONTIERS IN PLANT SCIENCE 2018; 9:217. [PMID: 29520289 PMCID: PMC5827294 DOI: 10.3389/fpls.2018.00217] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
HIGHLIGHTS Metabolites and transcripts related to plant physiology in salt stress conditions, especially to the recovery process were disclosed in peanut. Peanut (Arachis hypogaea L.) is considered as a moderately salt-sensitive species and thus soil salinity can be a limiting factor for peanut cultivation. To gain insights into peanut plant physiology in response to salt stress and alleviation, we comprehensively characterized leaf relative electrolyte leakage (REC), photosynthesis, leaf transpiration, and metabolism of plants under salt stress and plants that were subjected to salt stress followed by salt alleviation period. As expected, we found that REC levels were higher when plants were subjected to salt stress compared with the untreated plants. However, in contrast to expectations, REC was even higher compared with salt treated plants when plants were transferred from salt stress to standard conditions. To decipher REC variation in response to salt stress, especial during the recovery, metabolite, and transcript variations were analyzed by GC/MS and RNA-seq method, respectively. Ninety two metabolites, among total 391 metabolites identified, varied in response to salt and 42 metabolites responded to recovery specially. Transcriptomics data showed 1,742 in shoots and 3,281 in roots transcript varied in response to salt stress and 372 in shoots and 1,386 transcripts in roots responded specifically to recovery, but not salt stress. Finally, 95 transcripts and 1 metabolite are indicated as candidates involved in REC, photosynthesis, transpiration, and Na+ accumulation variation were revealed by using the principal component analysis (PCA) and correlation analysis. This study provides valuable information on peanut response to salt stress and recovery and may inspire further study to improve salt tolerance in peanut germplasm innovation.
Collapse
Affiliation(s)
- Feng Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Na Sui
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, China
| | - Yiyang Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yan Han
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Shanshan Liu
- College of Life Science, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- *Correspondence: Shubo Wan
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- Guowei Li
| |
Collapse
|
50
|
Jayasinghe NS, Mendis H, Roessner U, Dias DA. Quantification of Sugars and Organic Acids in Biological Matrices Using GC-QqQ-MS. Methods Mol Biol 2018; 1778:207-223. [PMID: 29761441 DOI: 10.1007/978-1-4939-7819-9_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Gas chromatography coupled with triple quadrupole mass spectrometry (GC-QqQ-MS) can be used to accurately quantify endogenous small molecules extracted from biological samples such as plants and human fluids including sera and urine. In order to quantify primary metabolites typically from central carbon metabolism such as sugars from glycolysis and the pentose phosphate pathway; and organic acids involved in the tricarboxylic acid (TCA) cycle; polar endogenous metabolites must be extracted from the samples of interest, chemically derivatized and quantified against a linear calibration curve to a corresponding authentic standard. This chapter describes how to quantify a combination of 48 primary metabolites belonging to classes of sugars, sugar alcohols, sugar acids, sugar phosphates, and organic acids using a robust, optimized, multiple reaction monitoring (MRM)-based GC-QqQ-MS method.
Collapse
Affiliation(s)
- Nirupama Samanmalie Jayasinghe
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
- Racing Analytical Services Ltd., Flemington, VIC, Australia.
| | - Himasha Mendis
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel Anthony Dias
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, Bundoora, VIC, Australia
| |
Collapse
|