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Zhou D, Fei Z, Liu G, Jiang Y, Jiang W, Lin CSK, Zhang W, Xin F, Jiang M. The bioproduction of astaxanthin: A comprehensive review on the microbial synthesis and downstream extraction. Biotechnol Adv 2024; 74:108392. [PMID: 38825214 DOI: 10.1016/j.biotechadv.2024.108392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/26/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Astaxanthin is a valuable orange-red carotenoid with wide applications in agriculture, food, cosmetics, pharmaceuticals and nutraceuticals areas. At present, the biological synthesis of astaxanthin mainly relies on Haematococcus pluvialis and Xanthophyllomyces dendrorhous. With the rapid development of synthetic biology, more recombinant microbial hosts have been genetically constructed for astaxanthin production including Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica. As multiple genes (15) were involved in the astaxanthin synthesis, it is particularly important to adopt different strategies to balance the metabolic flow towards the astaxanthin synthesis. Furthermore, astaxanthin is a fat-soluble compound stored intracellularly, hence efficient extraction methods are also essential for the economical production of astaxanthin. Several efficient and green extraction methods of astaxanthin have been reported in recent years, including the superfluid extraction, ionic liquid extraction and microwave-assisted extraction. Accordingly, this review will comprehensively introduce the advances on the astaxanthin production and extraction by using different microbial hosts and strategies to improve the astaxanthin synthesis and extraction efficiency.
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Affiliation(s)
- Dawei Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Zhengyue Fei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Guannan Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, 999077, Hong Kong
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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Acheampong A, Li L, Elsherbiny SM, Wu Y, Swallah MS, Bondzie-Quaye P, Huang Q. A crosswalk on the genetic and conventional strategies for enhancing astaxanthin production in Haematococcus pluvialis. Crit Rev Biotechnol 2023:1-22. [PMID: 37778751 DOI: 10.1080/07388551.2023.2240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023]
Abstract
Astaxanthin is a naturally occurring xanthophyll with powerful: antioxidant, antitumor, and antibacterial properties that are widely employed in food, feed, medicinal and nutraceutical industries. Currently, chemical synthesis dominates the world's astaxanthin market, but the increasing demand for natural products is shifting the market for natural astaxanthin. Haematococcus pluvialis (H. pluvialis) is the factory source of natural astaxanthin when grown in optimal conditions. Currently, various strategies for the production of astaxanthin have been proposed or are being developed in order to meet its market demand. This up-to-date review scrutinized the current approaches or strategies that aim to increase astaxanthin yield from H. pluvialis. We have emphasized the genetic and environmental parameters that increase astaxanthin yield. We also looked at the transcriptomic dynamics caused by environmental factors (phytohormones induction, light, salt, temperature, and nutrient starvation) on astaxanthin synthesizing genes and other metabolic changes. Genetic engineering and culture optimization (environmental factors) are effective approaches to producing more astaxanthin for commercial purposes. Genetic engineering, in particular, is accurate, specific, potent, and safer than conventional random mutagenesis approaches. New technologies, such as CRISPR-Cas9 coupled with omics and emerging computational tools, may be the principal strategies in the future to attain strains that can produce more astaxanthin. This review provides accessible data on the strategies to increase astaxanthin accumulation natively. Also, this review can be a starting point for new scholars interested in H. pluvialis research.
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Affiliation(s)
- Adolf Acheampong
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Lamei Li
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Shereen M Elsherbiny
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Yahui Wu
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Mohammed Sharif Swallah
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Precious Bondzie-Quaye
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
| | - Qing Huang
- CAS Key Laboratory of High Magnetic Field and Iron Beam Physical Biology, Institute of Intelligent Machines, Hefei Institute of Physical Sciences, Chinese Academy of Sciences, Hefei, China
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, China
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3
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Wang L, Zhang S, Fang J, Jin X, Mamut R, Li P. The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13101840. [PMID: 36292725 PMCID: PMC9601494 DOI: 10.3390/genes13101840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (Trebouxiophyceae sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.
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Affiliation(s)
- Lidan Wang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Shenglu Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinjin Fang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
- Correspondence: (R.M.); (P.L.)
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: (R.M.); (P.L.)
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Pánek T, Barcytė D, Treitli SC, Záhonová K, Sokol M, Ševčíková T, Zadrobílková E, Jaške K, Yubuki N, Čepička I, Eliáš M. A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biol 2022; 20:66. [PMID: 35296310 PMCID: PMC8928634 DOI: 10.1186/s12915-022-01263-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
Background The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them. Results We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms, we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes. Conclusions With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01263-w.
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Affiliation(s)
- Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kristína Záhonová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Martin Sokol
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Naoji Yubuki
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic.,Bioimaging Facility, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.
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van Beveren F, Eme L, López-García P, Ciobanu M, Moreira D. OUP accepted manuscript. Genome Biol Evol 2022; 14:6548715. [PMID: 35289373 PMCID: PMC8995046 DOI: 10.1093/gbe/evac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 11/20/2022] Open
Abstract
Proliferation of selfish genetic elements has led to significant genome size expansion in plastid and mitochondrial genomes of various eukaryotic lineages. Within the red algae, such expansion events are only known in the plastid genomes of the Proteorhodophytina, a highly diverse group of mesophilic microalgae. By contrast, they have never been described in the much understudied red algal mitochondrial genomes. Therefore, it remains unclear how widespread such organellar genome expansion events are in this eukaryotic phylum. Here, we describe new mitochondrial and plastid genomes from 25 red algal species, thereby substantially expanding the amount of organellar sequence data available, especially for Proteorhodophytina, and show that genome expansions are common in this group. We confirm that large plastid genomes are limited to the classes Rhodellophyceae and Porphyridiophyceae, which, in part, are caused by lineage-specific expansion events. Independently expanded mitochondrial genomes—up to three times larger than typical red algal mitogenomes—occur across Proteorhodophytina classes and a large shift toward high GC content occurred in the Stylonematophyceae. Although intron proliferation is the main cause of plastid and mitochondrial genome expansion in red algae, we do not observe recent intron transfer between different organelles. Phylogenomic analyses of mitochondrial and plastid genes from our expanded taxon sampling yielded well-resolved phylogenies of red algae with strong support for the monophyly of Proteorhodophytina. Our work shows that organellar genomes followed different evolutionary dynamics across red algal lineages.
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Affiliation(s)
- Fabian van Beveren
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique—CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Laura Eme
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique—CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique—CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique—CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, Centre National de la Recherche Scientifique—CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
- Corresponding author: E-mail:
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Ren Q, Wang YC, Lin Y, Zhen Z, Cui Y, Qin S. The extremely large chloroplast genome of the green alga Haematococcus pluvialis: Genome structure, and comparative analysis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data. BMC Genomics 2021; 22:298. [PMID: 33892645 PMCID: PMC8063479 DOI: 10.1186/s12864-021-07598-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. RESULTS Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. CONCLUSION Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
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Wan X, Zhou XR, Moncalian G, Su L, Chen WC, Zhu HZ, Chen D, Gong YM, Huang FH, Deng QC. Reprogramming microorganisms for the biosynthesis of astaxanthin via metabolic engineering. Prog Lipid Res 2020; 81:101083. [PMID: 33373616 DOI: 10.1016/j.plipres.2020.101083] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022]
Abstract
There is an increasing demand for astaxanthin in food, feed, cosmetics and pharmaceutical applications because of its superior anti-oxidative and coloring properties. However, naturally produced astaxanthin is expensive, mainly due to low productivity and limited sources. Reprogramming of microorganisms for astaxanthin production via metabolic engineering is a promising strategy. We primarily focus on the application of synthetic biology, enzyme engineering and metabolic engineering in enhancing the synthesis and accumulation of astaxanthin in microorganisms in this review. We also discuss the biosynthetic pathways of astaxanthin within natural producers, and summarize the achievements and challenges in reprogramming microorganisms for enhancing astaxanthin production. This review illuminates recent biotechnological advances in microbial production of astaxanthin. Future perspectives on utilization of new technologies for boosting microbial astaxanthin production are also discussed.
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Affiliation(s)
- Xia Wan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China; Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Wuhan 430062, PR China.
| | | | - Gabriel Moncalian
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - Lin Su
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, PR China
| | - Wen-Chao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China; Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Wuhan 430062, PR China
| | - Hang-Zhi Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Dan Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yang-Min Gong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China; Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Wuhan 430062, PR China
| | - Feng-Hong Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China; Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Wuhan 430062, PR China.
| | - Qian-Chun Deng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, PR China; Oil Crops and Lipids Process Technology National & Local Joint Engineering Laboratory, Wuhan 430062, PR China.
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9
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Smith DR. Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms? Genome Biol Evol 2020; 12:3797-3802. [PMID: 31971558 PMCID: PMC7043297 DOI: 10.1093/gbe/evaa012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2020] [Indexed: 12/19/2022] Open
Abstract
A major finding in organelle biology over the past decade is that land plant mitochondrial genomes, which are the largest among eukaryotes, can have a “Jekyll and Hyde” mutational pattern: low for synonymous sites, high for intergenic ones. This has led to the theory that double-strand breaks (DSBs) in the intergenic DNA of plant mitogenomes are repaired by inaccurate mechanisms, such as break-induced replication, which can result in large insertions and, thus, could explain why these genomes are so prone to expansion. But how universal is this theory? Can it apply to other giant organelle DNAs, such as the massive plastid DNAs (ptDNAs) of chlamydomonadalean green algae? Indeed, it can. Analysis of the expanded plastomes from two distinct isolates of the unicellular chlamydomonadalean Chlorosarcinopsis eremi uncovered exceptionally low rates of synonymous substitution in the coding regions but high substitution rates, including frequent indels, in the noncoding ptDNA, mirroring the trend from land plant mitogenomes. Remarkably, nearly all of the substitutions and indels identified in the noncoding ptDNA of C. eremi occur adjacent to or within short inverted palindromic repeats, suggesting that these elements are mutational hotspots. Building upon earlier studies, I propose that these palindromic repeats are predisposed to DSBs and that error-prone repair of these breaks is contributing to genomic expansion. Short palindromic repeats are a common theme among bloated plastomes, including the largest one on record, meaning that these data could have wide-reaching implications for our understanding of ptDNA expansion.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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10
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020; 11:576124. [PMID: 33101394 PMCID: PMC7545089 DOI: 10.3389/fgene.2020.576124] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.,Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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11
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Kumari S, Nesamma AA, Lali AM, Jutur PP, Prakash G. The chloroplast genome of a resilient chlorophycean microalga Asterarcys sp. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Wang K, Cui Y, Wang Y, Gao Z, Liu T, Meng C, Qin S. Chloroplast Genetic Engineering of a Unicellular Green Alga Haematococcus pluvialis with Expression of an Antimicrobial Peptide. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:572-580. [PMID: 32535692 DOI: 10.1007/s10126-020-09978-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/14/2020] [Indexed: 05/18/2023]
Abstract
The purpose of this study was to express an antimicrobial peptide in the chloroplast to further develop the plastid engineering of H. pluvialis. Homologous targeting of the 16S-trnI/trnA-23S region and four endogenous regulatory elements, including the psbA promoter, rbcL promoter, rbcL terminator, and psbA terminator in H. pluvialis, were performed to construct a chloroplast transformation vector for H. pluvialis. The expression of codon-optimized antimicrobial peptide piscidin-4 gene (ant1) and selection marker gene (bar, biolaphos resistance gene) in the chloroplast of H. pluvialis was controlled by the rbcL promoter and psbA promoter, respectively. Upon biolistic transformation and selection with phosphinothricin, integration and expression of ant1 in the chloroplast genome were detected using polymerase chain reaction (PCR), southern blotting, and western blotting. Using this method, we successfully expressed antimicrobial peptide piscidin-4 in H. pluvialis. Hence, our results showed H. pluvialis promises as a platform for expressing recombinant proteins for biotechnological applications, which will further contribute to promoting genetic engineering improvement of this strain.
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Affiliation(s)
- Kang Wang
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong Province, China
| | - Yulin Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yinchu Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong Province, China
| | - Tianzhong Liu
- Microalgal Biotechnology Group, CAS key Laboratory of Biofuels and Shandong Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and bioprocess technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Chunxiao Meng
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, Shandong Province, China.
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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13
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Zhang X, Bauman N, Brown R, Richardson TH, Akella S, Hann E, Morey R, Smith DR. The mitochondrial and chloroplast genomes of the green alga Haematococcus are made up of nearly identical repetitive sequences. Curr Biol 2020; 29:R736-R737. [PMID: 31386847 DOI: 10.1016/j.cub.2019.06.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The chlamydomonadalean green alga Haematococcus lacustris (strain UTEX 2505) has the largest chloroplast genome on record: 1352 kb with ∼90% non-coding DNA [1,2]. But what of the mitochondrial genome? Here we present sequencing, assembly, and analysis of the mitogenome that shows that it, too, is extremely expanded. What's more, the same repetitive elements have spread throughout the mitochondrial and chloroplast (or plastid) DNA (mtDNA and ptDNA, respectively), resulting in the situation whereby these two distinct organelle genomes are made up of nearly identical sequences.
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Affiliation(s)
- Xi Zhang
- Department of Biology, University of Western Ontario, London, ON, N6A-5B7, Canada
| | | | - Rob Brown
- Synthetic Genomics Inc., La Jolla, California, 92037, USA
| | | | | | - Elizabeth Hann
- Synthetic Genomics Inc., La Jolla, California, 92037, USA
| | - Robert Morey
- Synthetic Genomics Inc., La Jolla, California, 92037, USA
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, N6A-5B7, Canada.
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14
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Smith DR. Common Repeat Elements in the Mitochondrial and Plastid Genomes of Green Algae. Front Genet 2020; 11:465. [PMID: 32477407 PMCID: PMC7235400 DOI: 10.3389/fgene.2020.00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/15/2020] [Indexed: 12/31/2022] Open
Abstract
Despite both originating from endosymbiotic bacteria, one does not typically expect mitochondrial DNA (mtDNA) to show strong sequence identity to plastid DNA (ptDNA). Nevertheless, a recent analysis of Haematococcus lacustris revealed exactly that. A common repeat element has proliferated throughout the mtDNA and ptDNA of this chlamydomonadalean green alga, resulting in the unprecedented situation whereby these two distinct organelle genomes are largely made up of nearly identical sequences. In this short update to the work on H. lacustris, I highlight another chlamydomonadalean species (Stephanosphaera pluvialis) for which matching repeats have spread throughout its organelle genomes (but to a lesser degree than in H. lacustris). What's more, the organelle repeats from S. pluvialis are similar to those from H. lacustris, suggesting that they have a shared origin, and perhaps existed in the mtDNA and ptDNA of the most recent common ancestor of these two species. However, my examination of organelle genomes from other close relatives of H. lacustris and S. pluvialis did not uncover further compelling examples of common organelle repeat elements, meaning that the evolutionary history of these repeats might be more complicated than initially thought.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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15
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Comprehensive genomic analyses with 115 plastomes from algae to seed plants: structure, gene contents, GC contents, and introns. Genes Genomics 2020; 42:553-570. [PMID: 32200544 DOI: 10.1007/s13258-020-00923-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Chloroplasts are a common character in plants. The chloroplasts in each plant lineage have shaped their own genomes, plastomes, by structural changes and transferring many genes to nuclear genomes during plant evolution. Some plastid genes have introns that are mostly group II introns. OBJECTIVE This study aimed to get genomic and evolutionary insights on the plastomes from green algae to flowering plants. METHODS Plastomes of 115 species from green algae, bryophytes, pteridophytes (spore bearing vascular plants), gymnosperms, and angiosperms were mined from NCBI organelle genome database. Plastome structure, gene contents and GC contents were analyzed by the in-house developed Phyton code. Intronic features including presence/absence, length, intron phases were analyzed by manually in the annotated information in NCBI. RESULTS The canonical quadripartite structures were retained in most plastomes except of a few plastomes that had lost an invert repeat (IR). Expansion or reduction or deletion of IRs resulted in the length variation of the plastomes. The number of protein coding genes ranged from 40 to 92 with an average 79.43 ± 5.84 per plastome and gene losses were apparent in specific lineages. The number of trn genes ranged from 13 to 33 with an average 21.19 ± 2.42 per plastome. Ribosomal RNA genes, rrn, were located in the IRs so that they were present in a duplicate except of the species that had lost one of the IR. GC contents were variable from 24.9 to 51.0% with an average 38.21 ± 3.27%, indicating bias to high AT contents. Plastid introns were present in 18 protein coding genes, six trn genes, and one rrn gene. Intron losses occurred among the orthologous genes in different plant lineages. The plastid introns were long compared with the nuclear introns, which might be related with the spliceosome nuclear introns and self-splicing group II plastid introns. The trnK-UUU intron contained the maturase encoding matK gene except in the chlorophyte algae and monilophyte ferns in which the trnK-UUU was lost, but matK retained. There were many annotation artefacts in the intron positions in the NCBI database. In the analysis of intron phases, phase 0 introns were more frequent than those of phase 2 and 3 introns. Phase polymorphism was observed in the introns of clpP which was derived from nucleotide insertion. Plastid trn introns were long compared to the archaeal or eukaryotic nuclear tRNA introns. Of the six plastid trn introns, one was at the D loop and other five were at the anticodon loop. The insertion sites were conserved among the trn genes in archaea, eukaryotic nuclear and plastid tRNA genes. CONCLUSIONS Current study refurbrished the previous findings of structural variations, gene contents, and GC contents of the chloroplast genomes from green algae to flowering plants. The study also included some noble findings and discussions on the plastome introns including their length variations and phase variation. We also presented and corrected some false annotations on the introns in protein coding and tRNA genes in the genome database, which might be confirmed by the chloroplast transcriptome analysis in the future.
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16
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Lu Z, Dai J, Zheng L, Teng Z, Zhang Q, Qiu D, Song L. Disodium 2-oxoglutarate promotes carbon flux into astaxanthin and fatty acid biosynthesis pathways in Haematococcus. BIORESOURCE TECHNOLOGY 2020; 299:122612. [PMID: 31874452 DOI: 10.1016/j.biortech.2019.122612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
Improving carbon availability in astaxanthin production is pivotal in Haematococcus industry. In this study, disodium 2-oxoglutarate (2-OG-2Na) was observed to be a potential carbon regulator to increase the astaxanthin content. To illustrate its efficacy in astaxanthin production, key genes and enzyme were analyzed. Upon 2-OG-2Na treatment, genes ipi, bkt and crtR-b were up regulated, concomitantly, carotenoids and astaxanthin content increased by 15.4% and 14.0% at 120 h, respectively; additionally, Acetyl-CoA carboxylase was activated, consistent with 1.27-fold increase in fatty acids content. PUFAs increased earlier as fatty acids assembly gene fad was up-regulated to 20.56. It was also found that cell division was not compromised. Altogether, it was suggested that increased carbon skeletons were re-directed into the astaxanthin and fatty acids biosynthesis pathway. Furthermore, 2-OG-2Na was applied in ten Haematococcus strains. Of these strains, astaxanthin contents were accelerated with average net increase of 10.48%, exhibiting a scalable paradigm for commercial production.
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Affiliation(s)
- Zhe Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jingcheng Dai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - LingLing Zheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Zhuoran Teng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Qi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Dongru Qiu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Lirong Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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17
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Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A. Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes. Front Genet 2020. [PMID: 33101394 DOI: 10.3389/fgene.576124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at https://irscope.shinyapps.io/chloroplot/.
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Affiliation(s)
- Shuyu Zheng
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Peter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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18
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Smith DR. Revisiting published genomes with fresh eyes and new data: Revising old sequencing data can yield unexpected insights and identify errors. EMBO Rep 2019; 20:e49482. [PMID: 31680386 DOI: 10.15252/embr.201949482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Old data are like yesterday's leftovers: sapped of novelty and excitement. But revisiting old sequence data with a fresh mind and new techniques can yield new and unexpected results.
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Affiliation(s)
- David R Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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19
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Cvetkovska M, Orgnero S, Hüner NPA, Smith DR. The enigmatic loss of light-independent chlorophyll biosynthesis from an Antarctic green alga in a light-limited environment. THE NEW PHYTOLOGIST 2019; 222:651-656. [PMID: 30506801 DOI: 10.1111/nph.15623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Shane Orgnero
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Norman P A Hüner
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
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20
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Lee J. Plasmid-Associated Organelle Genome Evolution In Red Algae. JOURNAL OF PHYCOLOGY 2018; 54:772-774. [PMID: 30614001 DOI: 10.1111/jpy.12797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, 16419, Korea
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21
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Lukeš J, Wheeler R, Jirsová D, David V, Archibald JM. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life 2018; 70:1267-1274. [PMID: 30291814 PMCID: PMC6334171 DOI: 10.1002/iub.1894] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 11/25/2022]
Abstract
The mitochondrial DNA of diplonemid and kinetoplastid protists is known for its suite of bizarre features, including the presence of concatenated circular molecules, extensive trans‐splicing and various forms of RNA editing. Here we report on the existence of another remarkable characteristic: hyper‐inflated DNA content. We estimated the total amount of mitochondrial DNA in four kinetoplastid species (Trypanosoma brucei, Trypanoplasma borreli, Cryptobia helicis, and Perkinsela sp.) and the diplonemid Diplonema papillatum. Staining with 4′,6‐diamidino‐2‐phenylindole and RedDot1 followed by color deconvolution and quantification revealed massive inflation in the total amount of DNA in their organelles. This was further confirmed by electron microscopy. The most extreme case is the ∼260 Mbp of DNA in the mitochondrion of Diplonema, which greatly exceeds that in its nucleus; this is, to our knowledge, the largest amount of DNA described in any organelle. Perkinsela sp. has a total mitochondrial DNA content ~6.6× greater than its nuclear genome. This mass of DNA occupies most of the volume of the Perkinsela cell, despite the fact that it contains only six protein‐coding genes. Why so much DNA? We propose that these bloated mitochondrial DNAs accumulated by a ratchet‐like process. Despite their excessive nature, the synthesis and maintenance of these mtDNAs must incur a relatively low cost, considering that diplonemids are one of the most ubiquitous and speciose protist groups in the ocean. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology., 70(12):1267–1274, 2018
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Affiliation(s)
- Julius Lukeš
- Institute of ParasitologyBiology Centre, Czech Academy of SciencesČeské Budějovice (Budweis)Czech Republic
- Faculty of ScienceUniversity of South BohemiaČeské Budějovice (Budweis)Czech Republic
| | - Richard Wheeler
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Dagmar Jirsová
- Institute of ParasitologyBiology Centre, Czech Academy of SciencesČeské Budějovice (Budweis)Czech Republic
| | - Vojtěch David
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
| | - John M. Archibald
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
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22
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Smith DR. Haematococcus lacustris: the makings of a giant-sized chloroplast genome. AOB PLANTS 2018; 10:ply058. [PMID: 30393516 PMCID: PMC6205361 DOI: 10.1093/aobpla/ply058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/27/2018] [Indexed: 05/23/2023]
Abstract
Recent work on the chlamydomonadalean green alga Haematococcus lacustris uncovered the largest plastid genome on record: a whopping 1.35 Mb with >90 % non-coding DNA. A 500-word description of this genome was published in the journal Genome Announcements. But such a short report for such a large genome leaves many unanswered questions. For instance, the H. lacustris plastome was found to encode only 12 tRNAs, less than half that of a typical plastome, it appears to have a non-standard genetic code, and is one of only a few known plastid DNAs (ptDNAs), out of thousands of available sequences, not biased in adenine and thymine. Here, I take a closer look at the H. lacustris plastome, comparing its size, content and architecture to other large organelle DNAs, including those from close relatives in the Chlamydomonadales. I show that the H. lacustris plastid coding repertoire is not as unusual as initially thought, representing a standard set of rRNAs, tRNAs and protein-coding genes, where the canonical stop codon UGA appears to sometimes signify tryptophan. The intergenic spacers are dense with repeats, and it is within these regions where potential answers to the source of such extreme genomic expansion lie. By comparing ptDNA sequences of two closely related strains of H. lacustris, I argue that the mutation rate of the non-coding DNA is high and contributing to plastome inflation. Finally, by exploring publicly available RNA-sequencing data, I find that most of the intergenic ptDNA is transcriptionally active.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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23
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Gaouda H, Hamaji T, Yamamoto K, Kawai-Toyooka H, Suzuki M, Noguchi H, Minakuchi Y, Toyoda A, Fujiyama A, Nozaki H, Smith DR. Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae. Genome Biol Evol 2018; 10:2248-2254. [PMID: 30102347 PMCID: PMC6128376 DOI: 10.1093/gbe/evy175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbors extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.
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Affiliation(s)
- Hager Gaouda
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Takashi Hamaji
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, Kyoto University, Japan
| | - Kayoko Yamamoto
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - Masahiro Suzuki
- Kobe University Research Center for Inland Seas, Awaji, Hyogo, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yohei Minakuchi
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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