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Del Campo EM, Gasulla F, Hell AF, González-Hourcade M, Casano LM. Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont. MICROBIAL ECOLOGY 2023; 86:1725-1739. [PMID: 37039841 PMCID: PMC10497648 DOI: 10.1007/s00248-023-02213-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.
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Affiliation(s)
- Eva M Del Campo
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain.
| | - Francisco Gasulla
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
| | - Aline F Hell
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
- Centre of Natural Sciences and Humanities, Federal University of ABC, 09606-070, São Bernardo Do Campo, SP, Brazil
| | - María González-Hourcade
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
- Department of Forest Biomaterials and Technology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Leonardo M Casano
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
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2
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Carr EC, Harris SD, Herr JR, Riekhof WR. Lichens and biofilms: Common collective growth imparts similar developmental strategies. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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3
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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Tong X, Liu S. CPPred: coding potential prediction based on the global description of RNA sequence. Nucleic Acids Res 2019; 47:e43. [PMID: 30753596 PMCID: PMC6486542 DOI: 10.1093/nar/gkz087] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/26/2019] [Accepted: 02/01/2019] [Indexed: 11/12/2022] Open
Abstract
The rapid and accurate approach to distinguish between coding RNAs and ncRNAs has been playing a critical role in analyzing thousands of novel transcripts, which have been generated in recent years by next-generation sequencing technology. Previously developed methods CPAT, CPC2 and PLEK can distinguish coding RNAs and ncRNAs very well, but poorly distinguish between small coding RNAs and small ncRNAs. Herein, we report an approach, CPPred (coding potential prediction), which is based on SVM classifier and multiple sequence features including novel RNA features encoded by the global description. The CPPred can better distinguish not only between coding RNAs and ncRNAs, but also between small coding RNAs and small ncRNAs than the state-of-the-art methods due to the addition of the novel RNA features. A recent study proposes 1335 novel human coding RNAs from a large number of RNA-seq datasets. However, only 119 transcripts are predicted as coding RNAs by the CPPred. In fact, almost all proposed novel coding RNAs are ncRNAs (91.1%), which is consistent with previous reports. Remarkably, we also reveal that the global description of encoding features (T2, C0 and GC) plays an important role in the prediction of coding potential.
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Affiliation(s)
- Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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5
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Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, McDonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szövényi P, Talbot NJ, Veneault-Fourrey C, Xavier BB. The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 2019; 20:605. [PMID: 31337355 PMCID: PMC6652019 DOI: 10.1186/s12864-019-5629-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.
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Affiliation(s)
| | - Olaf Müller
- Department of Biology, Duke University, Durham, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | | | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Guillaume Blanc
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
| | - Fred Dietrich
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
| | - Suzanne Joneson
- Department of Biology, Duke University, Durham, USA
- College of General Studies, University of Wisconsin - Milwaukee at Waukesha, Waukesha, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, Argonne, & Department of Bioengineering, University of Illinois at Chicago, Chicago, USA
| | | | | | - Francis Martin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Susan P. May
- Department of Biology, Duke University, Durham, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, USA
| | - Tami R. McDonald
- Department of Biology, Duke University, Durham, USA
- Department of Biology, St. Catherine University, St. Paul, USA
| | - Sabeeha S. Merchant
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, USA
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, USA
| | - Vivian Miao
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Emmanuelle Morin
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
| | - Ryoko Oono
- Department of Ecology, Evolution, and Marine Biology, University of California - Santa Barbara, Santa Barbara, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, and DOE Institute for Genomics and Proteomics, University of California, Los Angeles, USA
| | - Nimrod Rubinstein
- National Evolutionary Synthesis Center, Durham, USA
- Calico Life Sciences LLC, South San Francisco, USA
| | | | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Fachbereich Biowissenschaften, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jason C. Slot
- College of Food, Agricultural, and Environmental Sciences, Department of Plant Pathology, The Ohio State University, Columbus, USA
| | - Darren Soanes
- College of Life & Environmental Sciences, University of Exeter, Exeter, UK
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | | | - Claire Veneault-Fourrey
- INRA, Université de Lorraine, Interactions Arbres-Microorganismes, INRA-Nancy, Champenoux, France
- Université de Lorraine, INRA, Interactions Arbres-Microorganismes, Faculté des Sciences et Technologies, Vandoeuvre les Nancy Cedex, France
| | - Basil B. Xavier
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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6
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Kang YJ, Yang DC, Kong L, Hou M, Meng YQ, Wei L, Gao G. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res 2019; 45:W12-W16. [PMID: 28521017 PMCID: PMC5793834 DOI: 10.1093/nar/gkx428] [Citation(s) in RCA: 836] [Impact Index Per Article: 167.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/03/2017] [Indexed: 12/19/2022] Open
Abstract
With advances in next-generation sequencing technologies, numerous novel transcripts in a large number of organisms have been identified. With the goal of fast, accurate assessment of the coding ability of RNA transcripts, we upgraded the coding potential calculator CPC1 to CPC2. CPC2 runs ∼1000 times faster than CPC1 and exhibits superior accuracy compared with CPC1, especially for long non-coding transcripts. Moreover, the model of CPC2 is species-neutral, making it feasible for ever-growing non-model organism transcriptomes. A mobile-friendly web server, as well as a downloadable standalone package, is freely available at http://cpc2.cbi.pku.edu.cn.
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Affiliation(s)
- Yu-Jian Kang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - De-Chang Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Mei Hou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Yu-Qi Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Liping Wei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
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Shanmugam K, Ramalingam S, Venkataraman G, Hariharan GN. The CRISPR/Cas9 System for Targeted Genome Engineering in Free-Living Fungi: Advances and Opportunities for Lichenized Fungi. Front Microbiol 2019; 10:62. [PMID: 30792699 PMCID: PMC6375251 DOI: 10.3389/fmicb.2019.00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 01/15/2019] [Indexed: 01/01/2023] Open
Abstract
Studies using whole genome sequencing, computational and gene expression, targeted genome engineering techniques for generating site-specific sequence alterations through non-homologous end joining (NHEJ) by genomic double-strand break (DSB) repair pathway with high precision, resulting in gene inactivation have elucidated the complexity of gene expression, and metabolic pathways in fungi. These tools and the data generated are crucial for precise generation of fungal products such as enzymes, secondary metabolites, antibiotics etc. Artificially engineered molecular scissors, zinc finger nucleases (ZFNs), Transcriptional activator-like effector nucleases (TALENs; that use protein motifs for DNA sequence recognition in the genome) and CRISPR associated protein 9 (Cas9;CRISPR/Cas9) system (RNA-DNA recognition) are being used in achieving targeted genome modifications for modifying traits in free-living fungal systems. Here, we discuss the recent research breakthroughs and developments which utilize CRISPR/Cas9 in the metabolic engineering of free-living fungi for the biosynthesis of secondary metabolites, enzyme production, antibiotics and to develop resistance against post-harvest browning of edible mushrooms and fungal pathogenesis. We also discuss the potential and advantages of using targeted genome engineering in lichenized fungal (mycobiont) cultures to enhance their growth and secondary metabolite production in vitro can be complemented by other molecular approaches.
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Affiliation(s)
- Karthik Shanmugam
- M.S. Swaminathan Research Foundation, Chennai, India
- Department of Mycology, University of Bayreuth, Bayreuth, Germany
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8
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Bertrand RL, Abdel-Hameed M, Sorensen JL. Lichen Biosynthetic Gene Clusters. Part I. Genome Sequencing Reveals a Rich Biosynthetic Potential. JOURNAL OF NATURAL PRODUCTS 2018; 81:723-731. [PMID: 29485276 DOI: 10.1021/acs.jnatprod.7b00769] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lichens are symbionts of fungi and algae that produce diverse secondary metabolites with useful properties. Little is known of lichen natural product biosynthesis because of the challenges of working with lichenizing fungi. We describe the first attempt to comprehensively profile the genetic secondary metabolome of a lichenizing fungus. An Illumina platform combined with the Antibiotics and Secondary Metabolites Analysis Shell (FungiSMASH, version 4.0) was used to sequence and annotate assembled contigs of the fungal partner of Cladonia uncialis. Up to 48 putative gene clusters are described comprising type I and type III polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS), hybrid PKS-NRPS, and terpene synthases. The number of gene clusters revealed by this work dwarfs the number of known secondary metabolites from C. uncialis, suggesting that lichenizing fungi have an unexplored biosynthetic potential.
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Affiliation(s)
- Robert L Bertrand
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - Mona Abdel-Hameed
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - John L Sorensen
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
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9
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Munzi S, Sheppard LJ, Leith ID, Cruz C, Branquinho C, Bini L, Gagliardi A, Cai G, Parrotta L. The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis. PLANTA 2017; 245:819-833. [PMID: 28054148 DOI: 10.1007/s00425-017-2647-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/01/2017] [Indexed: 05/10/2023]
Abstract
Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.
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Affiliation(s)
- Silvana Munzi
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal.
| | - Lucy J Sheppard
- Centre for Ecology and Hydrology (CEH) Edinburgh, Bush Estate, Penicuik, EH26 0QB, UK
| | - Ian D Leith
- Centre for Ecology and Hydrology (CEH) Edinburgh, Bush Estate, Penicuik, EH26 0QB, UK
| | - Cristina Cruz
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal
| | - Cristina Branquinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Bloco C2, 1749-016, Lisbon, Portugal
| | - Luca Bini
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100, Siena, Italy
| | - Assunta Gagliardi
- Department of Life Sciences, University of Siena, Via Aldo Moro, 2, 53100, Siena, Italy
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, Via Pier Andrea Mattioli, 4, 53100, Siena, Italy
| | - Luigi Parrotta
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio, 42, 40126, Bologna, Italy
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10
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Abstract
ABSTRACT
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
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11
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Penha LL, Hoffmann L, Souza SSD, Martins ACDA, Bottaro T, Prosdocimi F, Faffe DS, Motta MCM, Ürményi TP, Silva R. Symbiont modulates expression of specific gene categories in Angomonas deanei. Mem Inst Oswaldo Cruz 2016; 111:686-691. [PMID: 27706380 PMCID: PMC5125052 DOI: 10.1590/0074-02760160228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/10/2016] [Indexed: 11/21/2022] Open
Abstract
Trypanosomatids are parasites that cause disease in humans, animals, and plants. Most
are non-pathogenic and some harbor a symbiotic bacterium. Endosymbiosis is part of
the evolutionary process of vital cell functions such as respiration and
photosynthesis. Angomonas deanei is an example of a
symbiont-containing trypanosomatid. In this paper, we sought to investigate how
symbionts influence host cells by characterising and comparing the transcriptomes of
the symbiont-containing A. deanei (wild type) and the symbiont-free
aposymbiotic strains. The comparison revealed that the presence of the symbiont
modulates several differentially expressed genes. Empirical analysis of differential
gene expression showed that 216 of the 7625 modulated genes were significantly
changed. Finally, gene set enrichment analysis revealed that the largest categories
of genes that downregulated in the absence of the symbiont were those involved in
oxidation-reduction process, ATP hydrolysis coupled proton transport and glycolysis.
In contrast, among the upregulated gene categories were those involved in
proteolysis, microtubule-based movement, and cellular metabolic process. Our results
provide valuable information for dissecting the mechanism of endosymbiosis in
A. deanei.
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Affiliation(s)
- Luciana Loureiro Penha
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Luísa Hoffmann
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Silvanna Sant'Anna de Souza
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | | | - Thayane Bottaro
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Francisco Prosdocimi
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Débora Souza Faffe
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | | | - Turán Péter Ürményi
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
| | - Rosane Silva
- Universidade Federal do Rio de Janeiro, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brasil
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12
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Carniel FC, Gerdol M, Montagner A, Banchi E, De Moro G, Manfrin C, Muggia L, Pallavicini A, Tretiach M. New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PLANT MOLECULAR BIOLOGY 2016; 91:319-339. [PMID: 26992400 DOI: 10.1007/s11103-016-0468-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
Trebouxia is the most common lichen-forming genus of aero-terrestrial green algae and all its species are desiccation tolerant (DT). The molecular bases of this remarkable adaptation are, however, still largely unknown. We applied a transcriptomic approach to a common member of the genus, T. gelatinosa, to investigate the alteration of gene expression occurring after dehydration and subsequent rehydration in comparison to cells kept constantly hydrated. We sequenced, de novo assembled and annotated the transcriptome of axenically cultured T. gelatinosa by using Illumina sequencing technology. We tracked the expression profiles of over 13,000 protein-coding transcripts. During the dehydration/rehydration cycle c. 92 % of the total protein-coding transcripts displayed a stable expression, suggesting that the desiccation tolerance of T. gelatinosa mostly relies on constitutive mechanisms. Dehydration and rehydration affected mainly the gene expression for components of the photosynthetic apparatus, the ROS-scavenging system, Heat Shock Proteins, aquaporins, expansins, and desiccation related proteins (DRPs), which are highly diversified in T. gelatinosa, whereas Late Embryogenesis Abundant Proteins were not affected. Only some of these phenomena were previously observed in other DT green algae, bryophytes and resurrection plants, other traits being distinctive of T. gelatinosa, and perhaps related to its symbiotic lifestyle. Finally, the phylogenetic inference extended to DRPs of other chlorophytes, embryophytes and bacteria clearly pointed out that DRPs of chlorophytes are not orthologous to those of embryophytes: some of them were likely acquired through horizontal gene transfer from extremophile bacteria which live in symbiosis within the lichen thallus.
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Affiliation(s)
- Fabio Candotto Carniel
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
- Institute of Botany, University of Innsbruck, Sternwartestraße, 15, 6020, Innsbruck, Austria
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy.
| | - Alice Montagner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Elisa Banchi
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Gianluca De Moro
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Chiara Manfrin
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Lucia Muggia
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
| | - Mauro Tretiach
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, via L. Giorgieri, 10, 34127, Trieste, Italy
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Expressed sequence tag analysis and annotation of genetic information from the freshwater clam, Pisidium (Neopisidium) coreanum endemic to Korea. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0345-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Grube M, Cernava T, Soh J, Fuchs S, Aschenbrenner I, Lassek C, Wegner U, Becher D, Riedel K, Sensen CW, Berg G. Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. ISME JOURNAL 2014; 9:412-24. [PMID: 25072413 DOI: 10.1038/ismej.2014.138] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 11/09/2022]
Abstract
Symbioses represent a frequent and successful lifestyle on earth and lichens are one of their classic examples. Recently, bacterial communities were identified as stable, specific and structurally integrated partners of the lichen symbiosis, but their role has remained largely elusive in comparison to the well-known functions of the fungal and algal partners. We have explored the metabolic potentials of the microbiome using the lung lichen Lobaria pulmonaria as the model. Metagenomic and proteomic data were comparatively assessed and visualized by Voronoi treemaps. The study was complemented with molecular, microscopic and physiological assays. We have found that more than 800 bacterial species have the ability to contribute multiple aspects to the symbiotic system, including essential functions such as (i) nutrient supply, especially nitrogen, phosphorous and sulfur, (ii) resistance against biotic stress factors (that is, pathogen defense), (iii) resistance against abiotic factors, (iv) support of photosynthesis by provision of vitamin B12, (v) fungal and algal growth support by provision of hormones, (vi) detoxification of metabolites, and (vii) degradation of older parts of the lichen thallus. Our findings showed the potential of lichen-associated bacteria to interact with the fungal as well as algal partner to support health, growth and fitness of their hosts. We developed a model of the symbiosis depicting the functional multi-player network of the participants, and argue that the strategy of functional diversification in lichens supports the longevity and persistence of lichens under extreme and changing ecological conditions.
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Affiliation(s)
- Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Jung Soh
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Ines Aschenbrenner
- 1] Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria [2] Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Christian Lassek
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Uwe Wegner
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Christoph W Sensen
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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15
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Increasing phytoremediation efficiency and reliability using novel omics approaches. Trends Biotechnol 2014; 32:271-80. [DOI: 10.1016/j.tibtech.2014.02.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 01/19/2023]
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16
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Wang YY, Liu B, Zhang XY, Zhou QM, Zhang T, Li H, Yu YF, Zhang XL, Hao XY, Wang M, Wang L, Wei JC. Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota). BMC Genomics 2014; 15:34. [PMID: 24438332 PMCID: PMC3897900 DOI: 10.1186/1471-2164-15-34] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 01/14/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsuknia as a lichen in the arid regions. RESULTS 454 and Illumina technologies were used to sequence the genome of E. pusillum. A total of 9,285 genes were annotated in the 37.5 Mb genome of E. pusillum. Analyses of the genes provided direct molecular evidence for certain natural characteristics, such as homothallic reproduction and drought-tolerance. Comparative genomics analysis indicated that the expansion and contraction of some protein families in the E. pusillum genome reflect the specific relationship with its photosynthetic partner (D. chodatii). Co-culture experiments using the lichen-forming fungus E. pusillum and its algal partner allowed the functional identification of genes involved in the nitrogen and carbon transfer between both symbionts, and three lectins without signal peptide domains were found to be essential for the symbiotic recognition in the lichen; interestingly, the ratio of the biomass of both lichen-forming fungus and its photosynthetic partner and their contact time were found to be important for the interaction between these two symbionts. CONCLUSIONS The present study lays a genomic analysis of the lichen-forming fungus E. pusillum for demonstrating its general biological features and the traits of the interaction between this fungus and its photosynthetic partner D. chodatii, and will provide research basis for investigating the nature of its drought resistance and symbiosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Junttila S, Laiho A, Gyenesei A, Rudd S. Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. BMC Genomics 2013; 14:870. [PMID: 24325588 PMCID: PMC3878897 DOI: 10.1186/1471-2164-14-870] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 11/14/2013] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Lichens are symbiotic organisms with a fungal and an algal or a cyanobacterial partner. Lichens inhabit some of the harshest climates on earth and most lichen species are desiccation-tolerant. Lichen desiccation-tolerance has been studied at the biochemical level and through proteomics, but the underlying molecular genetic mechanisms remain largely unexplored. The objective of our study was to examine the effects of dehydration and rehydration on the gene expression of Cladonia rangiferina. RESULTS Samples of C. rangiferina were collected at several time points during both the dehydration and rehydration process and the gene expression intensities were measured using a custom DNA microarray. Several genes, which were differentially expressed in one or more time points, were identified. The microarray results were validated using qRT-PCR analysis. Enrichment analysis of differentially expressed transcripts was also performed to identify the Gene Ontology terms most associated with the rehydration and dehydration process. CONCLUSIONS Our data identify differential expression patterns for hundreds of genes that are modulated during dehydration and rehydration in Cladonia rangiferina. These dehydration and rehydration events clearly differ from each other at the molecular level and the largest changes to gene expression are observed within minutes following rehydration. Distinct changes are observed during the earliest stage of rehydration and the mechanisms not appear to be shared with the later stages of wetting or with drying. Several of the most differentially expressed genes are similar to genes identified in previous studies that have investigated the molecular mechanisms of other desiccation-tolerant organisms. We present here the first microarray experiment for any lichen species and have for the first time studied the genetic mechanisms behind lichen desiccation-tolerance at the whole transcriptome level.
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Affiliation(s)
- Sini Junttila
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Attila Gyenesei
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
- The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, Tykistökatu, Turku, Finland
| | - Stephen Rudd
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu, Turku, Finland
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