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State of the Art of the Molecular Biology of the Interaction between Cocoa and Witches’ Broom Disease: A Systematic Review. Int J Mol Sci 2023; 24:ijms24065684. [PMID: 36982760 PMCID: PMC10057015 DOI: 10.3390/ijms24065684] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 03/19/2023] Open
Abstract
Significant scientific advances to elucidate the Moniliophthora perniciosa pathosystem have been achieved in recent years, but the molecular biology of this pathogen-host interaction is still a field with many unanswered questions. In order to present insights at the molecular level, we present the first systematic review on the theme. All told, 1118 studies were extracted from public databases. Of these, 109 were eligible for the review, based on the inclusion and exclusion criteria. The results indicated that understanding the transition from the biotrophic-necrotrophic phase of the fungus is crucial for control of the disease. Proteins with strong biotechnological potential or that can be targets for pathosystem intervention were identified, but studies regarding possible applications are still limited. The studies identified revealed important genes in the M. perniciosa-host interaction and efficient molecular markers in the search for genetic variability and sources of resistance, with Theobroma cacao being the most common host. An arsenal of effectors already identified and not explored in the pathosystem were highlighted. This systematic review contributes to the understanding of the pathosystem at the molecular level, offering new insights and proposing different paths for the development of new strategies to control witches’ broom disease.
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Alderdice R, Pernice M, Cárdenas A, Hughes DJ, Harrison PL, Boulotte N, Chartrand K, Kühl M, Suggett DJ, Voolstra CR. Hypoxia as a physiological cue and pathological stress for coral larvae. Mol Ecol 2021; 31:571-587. [PMID: 34716959 DOI: 10.1111/mec.16259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022]
Abstract
Ocean deoxygenation events are intensifying worldwide and can rapidly drive adult corals into a state of metabolic crisis and bleaching-induced mortality, but whether coral larvae are subject to similar stress remains untested. We experimentally exposed apo-symbiotic coral larvae of Acropora selago to deoxygenation stress with subsequent reoxygenation aligned to their night-day light cycle, and followed their gene expression using RNA-Seq. After 12 h of deoxygenation stress (~2 mg O2 /L), coral planulae demonstrated a low expression of HIF-targeted hypoxia response genes concomitant with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult corals. Despite exhibiting a consistent swimming phenotype compared to control samples, the differential gene expression observed in planulae exposed to deoxygenation-reoxygenation suggests a disruption of pathways involved in developmental regulation, mitochondrial activity, lipid metabolism, and O2 -sensitive epigenetic regulators. Importantly, we found that treated larvae exhibited a disruption in the expression of conserved HIF-targeted developmental regulators, for example, Homeobox (HOX) genes, corroborating how changes in external oxygen levels can affect animal development. We discuss how the observed deoxygenation responses may be indicative of a possible acclimation response or alternatively may imply negative latent impacts for coral larval fitness.
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Affiliation(s)
- Rachel Alderdice
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David J Hughes
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Peter L Harrison
- Marine Ecology Research Centre, Southern Cross University, Lismore, NSW, Australia
| | - Nadine Boulotte
- Marine Ecology Research Centre, Southern Cross University, Lismore, NSW, Australia
| | - Katie Chartrand
- Centre of Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, Qld, Australia
| | - Michael Kühl
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia.,Marine Biology Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - David J Suggett
- Faculty of Science, Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
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Heineike BM, El-Samad H. Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:642336. [PMID: 37744115 PMCID: PMC10512328 DOI: 10.3389/ffunb.2021.642336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.
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Affiliation(s)
- Benjamin M. Heineike
- Bioinformatics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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de Souza MR, Teixeira RC, Daúde MM, Augusto ANL, Ságio SA, de Almeida AF, Barreto HG. Comparative assessment of three RNA extraction methods for obtaining high-quality RNA from Candida viswanathii biomass. J Microbiol Methods 2021; 184:106200. [PMID: 33713728 DOI: 10.1016/j.mimet.2021.106200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 11/24/2022]
Abstract
Isolating high quality RNA is a limiting factor in molecular analysis, since it is the base for transcriptional studies. The RNA extraction method can directly affect the RNA quality and quantity, as well as, its overall cost. The industrial importance of the yeast genus Candida in several sectors comes from their capacity to produce Lipases. These enzymes are one of the main metabolites produced by some Candida species, and it has been shown that Candida yeast can biodegrade petroleum hydrocarbons and diesel oil from biosurfactants that they can produce, a feature that turns these organisms into potential combatants for bioremediation techniques. Thus, this study aimed to determine an efficient method for isolating high quality RNA from Candida viswanathii biomass. To achieve this aim, three different RNA extraction methods, TRIzol, Hot Acid Phenol, and CTAB (Cetyltrimethylammonium Bromide), were tested. The three tested methods allowed the isolation of high-quality RNA from C. viswanathii biomass and yielded suitable RNA quantity for carrying out RT-qPCR studies. In addition, all methods displayed high sensitivity for the expression analysis of the CvGPH1 gene through RT-qPCR, with TRIzol and CTAB showing the best results and the CTAB method displaying the best cost-benefit ratio (US$0.35/sample).
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Affiliation(s)
- Micaele Rodrigues de Souza
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Ronan Cristhian Teixeira
- Laboratory of Biotechnology, Food analysis, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Matheus Martins Daúde
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Anderson Neiva Lopes Augusto
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Solange Aparecida Ságio
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil
| | - Alex Fernando de Almeida
- Laboratory of Biotechnology, Food analysis, and Product Purification, Federal University of Tocantins, University Campus of Gurupi, TO, Brazil
| | - Horllys Gomes Barreto
- Laboratory of Molecular Analysis, Department of Life Sciences, Federal University of Tocantins, Palmas, University Campus of Palmas, TO, Brazil.
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Cui K, Zhao Y, He L, Ding J, Li B, Mu W, Liu F. Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole. Front Microbiol 2020; 11:1043. [PMID: 32655508 PMCID: PMC7325989 DOI: 10.3389/fmicb.2020.01043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/27/2020] [Indexed: 12/25/2022] Open
Abstract
Benzothiazole (BT) has a strong inhibitory effect on the growth and development of a wide spectrum of fungi and insects, such as Botrytis cinerea and Bradysia odoriphaga, that cause serious losses in agriculture. To investigate the underlying antifungal and insecticidal mechanisms of BT, RNA-seq analysis was performed for B. cinerea after BT treatment for 12, 24, and 48 h and for B. odoriphaga after BT treatment for 6 and 24 h. In B. cinerea, the pectin degradation process was inhibited, suggesting a low utilization of carbohydrate sources. As the treatment time was extended, the cell walls of B. cinerea thickened, and increases in melanin synthesis and ion transport were observed. In B. odoriphaga, signaling pathways including MAPK, insulin, adipocytokine, forkhead box class O, and peroxisome proliferator-activated receptor were activated at 6 h, and phosphoenolpyruvate carboxykinase was the core gene in the signal transduction pathways that responded to BT; digestive system and melanogenesis genes were obviously altered at 24 h. In addition, we identified several insecticidal target genes, such as trypsin, aminopeptidase N, and tyrosinase. Benzothiazole significantly affected nutrient metabolism, especially carbohydrate metabolism, in both species, and the pentose and glucuronate interconversions pathway was shared by both species, although the individual genes were different in each species. Overall, our results suggested that BT was a melanogenesis disrupter for the insect but an activator for the fungus. Our findings are helpful for deeply exploring the genes targeted by BT and for developing new pesticide compounds with unique mechanisms of action.
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Affiliation(s)
- Kaidi Cui
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yunhe Zhao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Leiming He
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Jinfeng Ding
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Beixing Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Wei Mu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Feng Liu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, China
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Kundu D, Hameed S, Fatima Z, Pasrija R. Phospholipid biosynthesis disruption renders the yeast cells sensitive to antifungals. Folia Microbiol (Praha) 2019; 65:121-131. [DOI: 10.1007/s12223-019-00713-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/25/2019] [Indexed: 10/26/2022]
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Pichler H, Emmerstorfer-Augustin A. Modification of membrane lipid compositions in single-celled organisms – From basics to applications. Methods 2018; 147:50-65. [DOI: 10.1016/j.ymeth.2018.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/18/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
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Di Bartolomeo F, Wagner A, Daum G. Cell biology, physiology and enzymology of phosphatidylserine decarboxylase. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:25-38. [PMID: 27650064 DOI: 10.1016/j.bbalip.2016.09.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/17/2022]
Abstract
Phosphatidylethanolamine is one of the most abundant phospholipids whose major amounts are formed by phosphatidylserine decarboxylases (PSD). Here we provide a comprehensive description of different types of PSDs in the different kingdoms of life. In eukaryotes, type I PSDs are mitochondrial enzymes, whereas other PSDs are localized to other cellular compartments. We describe the role of mitochondrial Psd1 proteins, their function, enzymology, biogenesis, assembly into mitochondria and their contribution to phospholipid homeostasis in much detail. We also discuss briefly the cellular physiology and the enzymology of Psd2. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Francesca Di Bartolomeo
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
| | - Ariane Wagner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, A-8010 Graz, Austria.
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Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures. Appl Microbiol Biotechnol 2015; 100:969-85. [DOI: 10.1007/s00253-015-7038-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 09/14/2015] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
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Gsell M, Fankl A, Klug L, Mascher G, Schmidt C, Hrastnik C, Zellnig G, Daum G. A Yeast Mutant Deleted of GPH1 Bears Defects in Lipid Metabolism. PLoS One 2015; 10:e0136957. [PMID: 26327557 PMCID: PMC4556709 DOI: 10.1371/journal.pone.0136957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
In a previous study we demonstrated up-regulation of the yeast GPH1 gene under conditions of phosphatidylethanolamine (PE) depletion caused by deletion of the mitochondrial (M) phosphatidylserine decarboxylase 1 (PSD1) (Gsell et al., 2013, PLoS One. 8(10):e77380. doi: 10.1371/journal.pone.0077380). Gph1p has originally been identified as a glycogen phosphorylase catalyzing degradation of glycogen to glucose in the stationary growth phase of the yeast. Here we show that deletion of this gene also causes decreased levels of phosphatidylcholine (PC), triacylglycerols and steryl esters. Depletion of the two non-polar lipids in a Δgph1 strain leads to lack of lipid droplets, and decrease of the PC level results in instability of the plasma membrane. In vivo labeling experiments revealed that formation of PC via both pathways of biosynthesis, the cytidine diphosphate (CDP)-choline and the methylation route, is negatively affected by a Δgph1 mutation, although expression of genes involved is not down regulated. Altogether, Gph1p besides its function as a glycogen mobilizing enzyme appears to play a regulatory role in yeast lipid metabolism.
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Affiliation(s)
- Martina Gsell
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Ariane Fankl
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Lisa Klug
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Gerald Mascher
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Claudia Schmidt
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Claudia Hrastnik
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
| | - Günther Zellnig
- Institute of Plant Sciences, Karl Franzens University Graz, NaWi Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, NaWi Graz, Petersgasse 12/2, 8010, Graz, Austria
- * E-mail:
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