1
|
Perez Saura P, Chabi M, Corato A, Cardol P, Remacle C. Cell adaptation of the extremophilic red microalga Galdieria sulphuraria to the availability of carbon sources. FRONTIERS IN PLANT SCIENCE 2022; 13:978246. [PMID: 36186036 PMCID: PMC9520601 DOI: 10.3389/fpls.2022.978246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/16/2022] [Indexed: 06/12/2023]
Abstract
Global energy demand and fossil fuels impact on climate can be partially managed by an increase in the use of biofuels for transports and industries. Biodiesel production is generally preceded by a transesterification process of the green biomass triacylglycerols that generates large amounts of glycerol as a by-product. In this study, the extremophilic red microalga Galdieria sulphuraria 074W was cultivated in heterotrophy. The microalgal growth parameters and biomass composition were compared when grown on an equivalent molar concentration of carbon of either glucose or glycerol as unique carbon source. The maximal biomass reached in these two conditions was not significantly different (∼2.5 g.L-1). Fatty acid profile, protein and storage carbohydrate contents were also statistically similar, irrespectively of the metabolized carbon source. We also observed that the pigment content of G. sulphuraria cells decreased during heterotrophic growth compared to photoautotrophic cultivated cells, and that this diminution was more important in the presence of glucose than glycerol: cells were yellowish in the presence of glucose and green in the presence of glycerol. The pigmentation was restored when glucose was totally consumed in the medium, suggesting that the presence of glucose repressed pigment synthesis. Based on this observation, a transcriptome analysis was performed in order to better understand the mechanisms involved in the loss of color mediated by darkness and by glucose in G. sulphuraria. Three conditions were analyzed: heterotrophy with glycerol or glucose and phototrophy. This allowed us to understand the transcriptional response of cells to light and dark environments both at the nuclear and chloroplast levels, and to show that transcription of gene families, acquired by horizontal gene transfer, such as sugar, amino acid, or acetate transporters, were involved in the response to the availability of different (in)organic sources.
Collapse
|
2
|
Stadnichuk IN, Tropin IV. Cyanidiales as Polyextreme Eukaryotes. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:472-487. [PMID: 35790381 DOI: 10.1134/s000629792205008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/28/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
Cyanidiales were named enigmatic microalgae due to their unique polyextreme properties, considered for a very long time unattainable for eukaryotes. Cyanidiales mainly inhabit hot sulfuric springs with high acidity (pH 0-4), temperatures up to 56°C, and ability to survive in the presence of dissolved heavy metals. Owing to the minimal for eukaryotes genome size, Cyanidiales have become one of the most important research objects in plant cell physiology, biochemistry, molecular biology, phylogenomics, and evolutionary biology. They play an important role in studying many aspects of oxygenic photosynthesis and chloroplasts origin. The ability to survive in stressful habitats and the corresponding metabolic pathways were acquired by Cyanidiales from archaea and bacteria via horizontal gene transfer (HGT). Thus, the possibility of gene transfer from prokaryotes to eukaryotes was discovered, which was a new step in understanding of the origin of eukaryotic cell.
Collapse
Affiliation(s)
- Igor N Stadnichuk
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127726, Russia.
| | - Ivan V Tropin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
3
|
Curien G, Lyska D, Guglielmino E, Westhoff P, Janetzko J, Tardif M, Hallopeau C, Brugière S, Dal Bo D, Decelle J, Gallet B, Falconet D, Carone M, Remacle C, Ferro M, Weber AP, Finazzi G. Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism. THE NEW PHYTOLOGIST 2021; 231:326-338. [PMID: 33764540 PMCID: PMC8252106 DOI: 10.1111/nph.17359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/18/2021] [Indexed: 05/04/2023]
Abstract
Galdieria sulphuraria is a cosmopolitan microalga found in volcanic hot springs and calderas. It grows at low pH in photoautotrophic (use of light as a source of energy) or heterotrophic (respiration as a source of energy) conditions, using an unusually broad range of organic carbon sources. Previous data suggested that G. sulphuraria cannot grow mixotrophically (simultaneously exploiting light and organic carbon as energy sources), its photosynthetic machinery being repressed by organic carbon. Here, we show that G. sulphuraria SAG21.92 thrives in photoautotrophy, heterotrophy and mixotrophy. By comparing growth, biomass production, photosynthetic and respiratory performances in these three trophic modes, we show that addition of organic carbon to cultures (mixotrophy) relieves inorganic carbon limitation of photosynthesis thanks to increased CO2 supply through respiration. This synergistic effect is lost when inorganic carbon limitation is artificially overcome by saturating photosynthesis with added external CO2 . Proteomic and metabolic profiling corroborates this conclusion suggesting that mixotrophy is an opportunistic mechanism to increase intracellular CO2 concentration under physiological conditions, boosting photosynthesis by enhancing the carboxylation activity of Ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and decreasing photorespiration. We discuss possible implications of these findings for the ecological success of Galdieria in extreme environments and for biotechnological applications.
Collapse
Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Dagmar Lyska
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Erika Guglielmino
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Phillip Westhoff
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Janina Janetzko
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Marianne Tardif
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Clément Hallopeau
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Sabine Brugière
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Davide Dal Bo
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Benoit Gallet
- Institut de Biologie StructuraleUniversité Grenoble AlpesCNRSCEA71 Avenue des MartyrsGrenoble38044France
| | - Denis Falconet
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| | - Michele Carone
- Genetics and Physiology of MicroalgaeInBios/Phytosystems Research UnitUniversity of LiegeLiège4000Belgium
| | - Claire Remacle
- Genetics and Physiology of MicroalgaeInBios/Phytosystems Research UnitUniversity of LiegeLiège4000Belgium
| | - Myriam Ferro
- EdyP Laboratoire Biologie à Grande Echelle, Université Grenoble AlpesCEAInsermBGE U1038Grenoble Cedex 938054France
| | - Andreas P.M. Weber
- Institute of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale. Université Grenoble AlpesCNRSCEAINRAeGrenoble Cedex 938054France
| |
Collapse
|
4
|
Peng Z, Liu G, Huang K. Cold Adaptation Mechanisms of a Snow Alga Chlamydomonas nivalis During Temperature Fluctuations. Front Microbiol 2021; 11:611080. [PMID: 33584575 PMCID: PMC7874021 DOI: 10.3389/fmicb.2020.611080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Cold environments, such as glaciers and alpine regions, constitute unique habitats for organisms living on Earth. In these harsh ecosystems, snow algae survive, florish, and even become primary producers for microbial communities. How the snow algae maintain physiological activity during violent ambient temperature changes remains unsolved. To explore the cold adaptation mechanisms of the unicellular snow alga Chlamydomonas nivalis, we compared its physiological responses to a model organism from the same genus, Chlamydomonas reinhardtii. When both cell types were exposed to a shift from 22°C to 4°C, C. nivalis exhibited an apparent advantage in cold tolerance over C. reinhardtii, as C. nivalis had both a higher growth rate and photosynthetic efficiency. To determine the cold tolerance mechanisms of C. nivalis, RNA sequencing was used to compare transcriptomes of both species after 1 h of cold treatment, mimicking temperature fluctuations in the polar region. Differential expression analysis showed that C. nivalis had fewer transcriptomic changes and was more stable during rapid temperature decrease relative to C. reinhardtii, especially for the expression of photosynthesis related genes. Additionally, we found that transcription in C. nivalis was precisely regulated by the cold response network, consisting of at least 12 transcription factors and 3 RNA-binding proteins. Moreover, genes participating in nitrogen metabolism, the pentose phosphate pathway, and polysaccharide biosynthesis were upregulated, indicating that increasing resource assimilation and remodeling of metabolisms were critical for cold adaptation in C. nivalis. Furthermore, we identified horizontally transferred genes differentially expressed in C. nivalis, which are critical for cold adaptation in other psychrophiles. Our results reveal that C. nivalis adapts rapid temperature decrease by efficiently regulating transcription of specific genes to optimize resource assimilation and metabolic pathways, providing critical insights into how snow algae survive and propagate in cold environments.
Collapse
Affiliation(s)
- Zhao Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gai Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
5
|
Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Hempen M, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 12: suitability of taxonomic units notified to EFSA until March 2020. EFSA J 2020; 18:e06174. [PMID: 32760463 PMCID: PMC7331632 DOI: 10.2903/j.efsa.2020.6174] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. It is based on an assessment of the taxonomic identity, the body of knowledge, safety concerns and antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs of the 39 microorganisms notified to EFSA between October 2019 and March 2020, 33 were excluded, including five filamentous fungi, five Escherichia coli, two Enterococcus faecium, two Streptomyces spp. and 19 TUs already evaluated. Six TUs were evaluated. Akkermansia muciniphila was not recommended for QPS status due to safety concerns. Clostridium butyricum was not recommended because some strains contain pathogenicity factors. This TU was excluded for further QPS evaluation. Galdieria sulphuraria and Pseudomonas chlororaphis were also rejected due to a lack of body of knowledge. The QPS status of Corynebacterium ammoniagenes (with the qualification 'for production purposes only') and of Komagataella pastoris (with the qualification 'for enzyme production') was confirmed. In relation to the taxonomic revision of the Lactobacillus genus, previously designated Lactobacillus species will be reassigned to the new species and both the old and new names will be retained in the QPS list.
Collapse
|
6
|
Time-Course Transcriptome of Parageobacillus thermoglucosidasius DSM 6285 Grown in the Presence of Carbon Monoxide and Air. Int J Mol Sci 2020; 21:ijms21113870. [PMID: 32485888 PMCID: PMC7312162 DOI: 10.3390/ijms21113870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Parageobacillus thermoglucosidasius is a metabolically versatile, facultatively anaerobic thermophile belonging to the family Bacillaceae. Previous studies have shown that this bacterium harbours co-localised genes coding for a carbon monoxide (CO) dehydrogenase (CODH) and Ni-Fe hydrogenase (Phc) complex and oxidises CO and produces hydrogen (H2) gas via the water-gas shift (WGS) reaction. To elucidate the genetic events culminating in the WGS reaction, P. thermoglucosidasius DSM 6285 was cultivated under an initial gas atmosphere of 50% CO and 50% air and total RNA was extracted at ~8 (aerobic phase), 20 (anaerobic phase), 27 and 44 (early and late hydrogenogenic phases) hours post inoculation. The rRNA-depleted fraction was sequenced using Illumina NextSeq, v2.5, 1x75bp chemistry. Differential expression revealed that at 8 vs.. 20, 20 vs.. 27 and 27 vs.. 44 h post inoculation, 2190, 2118 and 231 transcripts were differentially (FDR < 0.05) expressed. Cluster analysis revealed 26 distinct gene expression trajectories across the four time points. Of these, two similar clusters, showing overexpression at 20 relative to 8 h and depletion at 27 and 44 h, harboured the CODH and Phc transcripts, suggesting possible regulation by O2. The transition between aerobic respiration and anaerobic growth was marked by initial metabolic deterioration, as reflected by up-regulation of transcripts linked to sporulation and down-regulation of transcripts linked to flagellar assembly and metabolism. However, the transcriptome and growth profiles revealed the reversal of this trend during the hydrogenogenic phase.
Collapse
|
7
|
Xiang N, Hu J, Wen T, Brennan MA, Brennan CS, Guo X. Effects of temperature stress on the accumulation of ascorbic acid and folates in sweet corn (Zea mays L.) seedlings. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1694-1701. [PMID: 31803938 DOI: 10.1002/jsfa.10184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Extreme temperatures are among the primary abiotic stresses that affect plant growth and development. Ascorbic acid (AsA) is an efficient antioxidant for scavenging relative oxygen species accumulated under stress. Folates play a significant role in DNA synthesis and protect plants against oxidative stress. Sweet corn (Zea mays L.), a crop grown worldwide, is sensitive to extreme temperatures at seedling stage, which may cause yield loss. This study was conducted to explore the biosynthetic regulative mechanism of AsA and folates in sweet corn seedlings under temperature stress. RESULTS The AsA and folate composition and relative gene expression in sweet corn seedlings grown under different temperature stresses (10, 25, and 40 °C) were evaluated. The imposition of temperature stress altered the AsA content mainly by modulating the expression of Zm DHAR, whose encoded enzyme dehydroascorbic reductase (DHAR) is essential in the AsA recycle pathway. Low temperature stress raised the expressions of relative genes, leading to folate accumulation. High temperature stress modulated the folate content by influencing the expression of the correspondence gene for aminodeoxychorismate synthase, Zm ADCS, as well as downstream genes that connected with DNA methylation. CONCLUSION These results provided a theoretical basis, at a genetic level, for understanding the stress responses mechanism in sweet corn seedlings, offering guidance for sweet corn cultivation. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
- Nan Xiang
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Jianguang Hu
- Key Laboratory of Crops Genetics Improvement of Guangdong Province, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tianxiang Wen
- Key Laboratory of Crops Genetics Improvement of Guangdong Province, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Margaret Anne Brennan
- Department of Wine, Food Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Charles Stephen Brennan
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
- Department of Wine, Food Molecular Biosciences, Lincoln University, Lincoln, New Zealand
| | - Xinbo Guo
- School of Food Science and Engineering, South China University of Technology, Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| |
Collapse
|
8
|
Rossoni AW, Price DC, Seger M, Lyska D, Lammers P, Bhattacharya D, Weber APM. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 2019; 8:e45017. [PMID: 31149898 PMCID: PMC6629376 DOI: 10.7554/elife.45017] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.
Collapse
Affiliation(s)
- Alessandro W Rossoni
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Dana C Price
- Department of Plant BiologyRutgers UniversityNew BrunswickUnited States
| | - Mark Seger
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | - Dagmar Lyska
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Peter Lammers
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | | | - Andreas PM Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| |
Collapse
|
9
|
Rossoni AW, Weber APM. Systems Biology of Cold Adaptation in the Polyextremophilic Red Alga Galdieria sulphuraria. Front Microbiol 2019; 10:927. [PMID: 31118926 PMCID: PMC6504705 DOI: 10.3389/fmicb.2019.00927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
Rapid fluctuation of environmental conditions can impose severe stress upon living organisms. Surviving such episodes of stress requires a rapid acclimation response, e.g., by transcriptional and post-transcriptional mechanisms. Persistent change of the environmental context, however, requires longer-term adaptation at the genetic level. Fast-growing unicellular aquatic eukaryotes enable analysis of adaptive responses at the genetic level in a laboratory setting. In this study, we applied continuous cold stress (28°C) to the thermoacidophile red alga G. sulphuraria, which is 14°C below its optimal growth temperature of 42°C. Cold stress was applied for more than 100 generations to identify components that are critical for conferring thermal adaptation. After cold exposure for more than 100 generations, the cold-adapted samples grew ∼30% faster than the starting population. Whole-genome sequencing revealed 757 variants located on 429 genes (6.1% of the transcriptome) encoding molecular functions involved in cell cycle regulation, gene regulation, signaling, morphogenesis, microtubule nucleation, and transmembrane transport. CpG islands located in the intergenic region accumulated a significant number of variants, which is likely a sign of epigenetic remodeling. We present 20 candidate genes and three putative cis-regulatory elements with various functions most affected by temperature. Our work shows that natural selection toward temperature tolerance is a complex systems biology problem that involves gradual reprogramming of an intricate gene network and deeply nested regulators.
Collapse
Affiliation(s)
| | - Andreas P. M. Weber
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|