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Montoya EJO, Dorion S, Atehortua-Garcés L, Rivoal J. Phycobilin heterologous production from the Rhodophyta Porphyridium cruentum. J Biotechnol 2021; 341:30-42. [PMID: 34500003 DOI: 10.1016/j.jbiotec.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/19/2022]
Abstract
Phycobiliproteins are colored, active molecules with potential use in different industries. They are the union of proteins and bilins (Chromophores). The primary source of phycobiliproteins is algae; however, the traditional algae culture has production restrictions. The production in bacterial models can be a more efficient alternative to produce these molecules. However, the lack of knowledge in some steps of the phycobiliprotein metabolic pathway limits this alternative. Porphyridium cruentum is a single cell red alga with a high phycobiliprotein content. Its protein sequences were the basis for phycobilin production in this study. In this study, we cloned and characterized enzymes presumably involved in the chromophore production of P. cruentum. Using sequences obtained from its transcriptome, we characterized two cDNA sequences predicted to code respectively for a ferredoxin-dependent bilin reductase and a bilin lyase-isomerase. We expressed these enzymes in Escherichia coli to obtain in vivo evidence of their enzymatic activity on the substrate biliverdin IXα. Lastly, we analyzed them using thin-layer chromatography, spectrophotometry, and fluorescence spectroscopy. These experiments provided evidence of bilin modification. The expressed bilin lyase-isomerase did not show significant activity over the biliverdin molecule. On the contrary, the expressed ferredoxin-dependent bilin reductase showed activity over the biliverdin.
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Affiliation(s)
- Erika Juliana Obando Montoya
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia.
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Lucía Atehortua-Garcés
- Laboratorio de Biotecnología, Sede de Investigación Universitaria - SIU, Universidad de Antioquia, Carrera 53 # 61 - 30 - SIU. Torre 1 Laboratorio de 210, Medellín 050010, Colombia
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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Gao F, Nan F, Feng J, Xie S. Characterization and Comparative Analysis of MicroRNAs in 3 Representative Red Algae. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2868. [PMID: 35350641 PMCID: PMC8926317 DOI: 10.30498/ijb.2021.247164.2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background MicroRNA (miRNA) is a key regulator at the gene posttranscriptional regulation level. We have previously identified miRNAs and their putative targets in 3 representative red algae, Chondrus crispus, Galdieria sulphurariais and Porphyridium purpureum. Objectives In this study, unique molecular and evolutionary characterization of miRNAs were revealed in the 3 red algae based on the comparative miRNAs profiling. Materials and Methods Genome locations of small RNAs (sRNAs), miRNAs and MIRNAs (MIRs) in the 3 red algae were shown by collinearity analysis. Characterization of miRNAs and MIRs were profiled via bioinformatics analysis. Taken MIR156s and miR156s for examples, red algae miRNAs evolutionary features were demonstrated via phylogenetic and evolutionary information analysis. MiRNA targets main inhibition type was validated via performing data statistics and RLM-RACE PCR. Key target genes and their function were predicted by the common Gene Ontolgoy (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results Quantity, nucleotide bias and common sequences of miRNAs were analyzed in the 3 red algae. Four typical precursor structures and primary molecular features of red algae miRNAs were profiled. Genome-wide collinearity analysis of sRNAs, miRNAs and MIRs in the 3 red algae was performed to show their distribution and interrelation based on the deep sequencing data. Taken red algae MIR156s for example, their family members and sequences divergence were demonstrated. The whole evolutionary processes of miR156s and pre-miR156s in red algae were steady with negative selected pressure though diverse phylogenetic relationships and evolutionary parameters showed. Through 3 red algae miR156 targets validation, cleavage was validated as their main miRNA targets inhibition type. The common target genes (GO:0009536) enriched significantly for plastid formation will provide important insights for red algal biopigment research. The common KEGG pathways (ko01100) enriched significantly were predicted without a detailed reference metabolic map. Conclusions MiRNA plays an essential role in gene expression regulation involved in diverse biological processes of red algae. Comprehensive molecular and evolutionary features of miRNAs in the 3 red algae will provide insights for further utilizing the algae resources at the molecular level.
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Affiliation(s)
| | | | | | - Shulian Xie
- School of Life Science, Shanxi University, Wucheng Road No. 92, Taiyuan 030006, P. R. China
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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Lu Y, Gu X, Lin H, Melis A. Engineering microalgae: transition from empirical design to programmable cells. Crit Rev Biotechnol 2021; 41:1233-1256. [PMID: 34130561 DOI: 10.1080/07388551.2021.1917507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.
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Affiliation(s)
- Yandu Lu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Xinping Gu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Hanzhi Lin
- Institute of Marine & Environmental Technology, Center for Environmental Science, University of Maryland, College Park, MD, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Knopp M, Garg SG, Handrich M, Gould SB. Major Changes in Plastid Protein Import and the Origin of the Chloroplastida. iScience 2020; 23:100896. [PMID: 32088393 PMCID: PMC7038456 DOI: 10.1016/j.isci.2020.100896] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/09/2020] [Accepted: 02/04/2020] [Indexed: 12/26/2022] Open
Abstract
Core components of plastid protein import and the principle of using N-terminal targeting sequences are conserved across the Archaeplastida, but lineage-specific differences exist. Here we compare, in light of plastid protein import, the response to high-light stress from representatives of the three archaeplastidal groups. Similar to land plants, Chlamydomonas reinhardtii displays a broad response to high-light stress, not observed to the same degree in the glaucophyte Cyanophora paradoxa or the rhodophyte Porphyridium purpureum. We find that only the Chloroplastida encode both Toc75 and Oep80 in parallel and suggest that elaborate high-light stress response is supported by changes in plastid protein import. We propose the origin of a phenylalanine-independent import pathway via Toc75 allowed higher import rates to rapidly service high-light stress, but with the cost of reduced specificity. Changes in plastid protein import define the origin of the green lineage, whose greatest evolutionary success was arguably the colonization of land. Chloroplastida evolved a dual system, Toc75/Oep80, for high throughput protein import Loss of F-based targeting led to dual organelle targeting using a single ambiguous NTS Relaxation of functional constraints allowed a wider Toc/Tic modification A broad response to high-light stress appears unique to Chloroplastida
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Affiliation(s)
- Michael Knopp
- Institute for Molecular Evolution, HH-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sriram G Garg
- Institute for Molecular Evolution, HH-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Maria Handrich
- Institute for Molecular Evolution, HH-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, HH-University Düsseldorf, 40225 Düsseldorf, Germany.
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Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169. Int J Mol Sci 2019; 20:ijms20143448. [PMID: 31337051 PMCID: PMC6678167 DOI: 10.3390/ijms20143448] [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: 06/11/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/01/2023] Open
Abstract
Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO2 supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO2 revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs’ target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.
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Chen F, Zhang J, Chen J, Li X, Dong W, Hu J, Lin M, Liu Y, Li G, Wang Z, Zhang L. realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5055577. [PMID: 30020436 PMCID: PMC6051438 DOI: 10.1093/database/bay072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 06/15/2018] [Indexed: 11/28/2022]
Abstract
With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development. Database URL: http://realdb.algaegenome.org/
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Affiliation(s)
- Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiawei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junhao Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Xiaojiang Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meigui Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guowei Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China.,College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Lou S, Sun T, Li H, Hu Z. Mechanisms of microRNA-mediated gene regulation in unicellular model alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:244. [PMID: 30202439 PMCID: PMC6129010 DOI: 10.1186/s13068-018-1249-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/31/2018] [Indexed: 05/30/2023]
Abstract
MicroRNAs are a class of endogenous non-coding RNAs that play a vital role in post-transcriptional gene regulation in eukaryotic cells. In plants and animals, miRNAs are implicated in diverse roles ranging from immunity against viral infections, developmental pathways, molecular pathology of cancer and regulation of protein expression. However, the role of miRNAs in the unicellular model green alga Chlamydomonas reinhardtii remains unclear. The mode of action of miRNA-induced gene silencing in C. reinhardtii is very similar to that of higher eukaryotes, in terms of the activation of the RNA-induced silencing complex and mRNA targeting. Certain studies indicate that destabilization of mRNAs and mRNA turnover could be the major possible functions of miRNAs in eukaryotic algae. Here, we summarize recent findings that have advanced our understanding of miRNA regulatory mechanisms in C. reinhardtii.
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Affiliation(s)
- Sulin Lou
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Ting Sun
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
- Key Laboratory of Optoeletronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoeletronic Engineering, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Hui Li
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
| | - Zhangli Hu
- Guangdong Key Laboratory of Plant Epigenetics, Guangdong Engineering Research Center for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 People’s Republic of China
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