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Liu F, Yuan L, Zhang Y. The complete chloroplast genome of the Syzygium buxifolium Hook. Et Arn.1833 and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:851-855. [PMID: 38957225 PMCID: PMC11216237 DOI: 10.1080/23802359.2024.2371553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
Syzygium buxifolium. Hook. Et Arn.1833 is a member of the Myrtaceae family. This species is used in traditional Chinese medicines. It possesses numerous synonyms, reflecting the ambiguity in its taxonomy. The chloroplast genome has been widely used for species identification and phylogenetic analysis. Regrettably, there is a lack of information regarding the chloroplast genome of S. buxifolium. Here, we intend to obtain the chloroplast genome of S. buxifolium to resolve its classification problems. In particular, we utilized Illumina sequencing technology to sequence, GetOrganelle to assemble, and CPGAVAS2 to characterize the chloroplast genome of S. buxifolium. The chloroplast genome of S. buxifolium had a length of 158,581 bp and consisted of 111 unique genes, comprising 78 protein-coding genes, 29 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. In addition, we identified 86 Simple Sequence Repeats, 345 tandem repetitive sequences, and 34 dispersed repetitive sequences using modules implemented in CPGAVAS2. Lastly, we carried out phylogenetic analysis using Phylosuite. The results indicated a close relationship between S. buxifolium and S. grijsii. This study offers novel genetic data for the molecular identification and subsequent phylogenetic analysis of the Syzygium genus.
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Affiliation(s)
- Fang Liu
- Xiangnan University, Chenzhou, P.R. China
| | - Lichai Yuan
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
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2
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van der Gulik PTS, Hoff WD, Speijer D. The contours of evolution: In defence of Darwin's tree of life paradigm. Bioessays 2024; 46:e2400012. [PMID: 38436469 DOI: 10.1002/bies.202400012] [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: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.
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Affiliation(s)
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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3
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Goold HD, Moseley JL, Lauersen KJ. The synthetic future of algal genomes. CELL GENOMICS 2024; 4:100505. [PMID: 38395701 PMCID: PMC10943592 DOI: 10.1016/j.xgen.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.
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Affiliation(s)
- Hugh D Goold
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia; ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Phycoil Biotechnology International, Inc., Fremont, CA 94538, USA
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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4
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Zhang S, Zheng T, Zhou M, Niu B, Li Y. Exposure to the mixotrophic dinoflagellate Lepidodinium sp. and its cues increase toxin production of Pseudo-nitzschia multiseries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169812. [PMID: 38181942 DOI: 10.1016/j.scitotenv.2023.169812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The present study examined the defense responses of toxigenic Pseudo-nitzschia species (P. multiseries) to a mixotrophic dinoflagellate, Lepidodinium sp., and its associated cues. We evaluated their responses to different predation risks, including direct physical contact and indirect interactions facilitated by cues from Lepidodinium sp. during active feeding on heterospecific prey (Rhodonomas salina), limited feeding on conspecific prey (P. multiseries) and non-feeding (autotrophic growth in f/2 medium) states. This study is the first investigation of these trophic interactions. Our results demonstrated a significant increase in cellular domoic acid (cDA) in P. multiseries when exposed to Lepidodinium sp. and its associated cues, which was 1.38 to 2.42 times higher than the non-induced group. Notably, this increase was observed regardless of Lepidodinium sp. feeding on this toxic diatom and nutritional modes. However, the most significant increase occurred when they directly interacted. These findings suggest that P. multiseries evaluates predation risk and increases cDA production as a defensive strategy against potential grazing threats. No morphological changes were observed in P. multiseries in response to Lepidodinium sp. or its cues. P. multiseries cultured in flasks of Group L+P-P showed a decrease in growth, but Group L-P and Group L+R-P did not exhibit any decrease. These results suggest a lack of consistent trade-offs between the defense response and growth, thus an increase in cDA production may be a sustainable and efficient defense strategy for P. multiseries. Furthermore, our findings indicate that P. multiseries had no significant impact on the fitness (cell size, growth and/or grazing) of Lepidodinium sp. and R. salina, which suggests no evident toxic or allelopathic impacts on these two phytoplankton species. This study enhances our understanding of the trophic interactions between toxic diatoms and mixotrophic dinoflagellates and helps elucidate the dynamics of Harmful Algal Blooms, toxin transmission, and their impact on ecosystem health.
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Affiliation(s)
- Shuwen Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Tingting Zheng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Muyao Zhou
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Biaobiao Niu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China
| | - Yang Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, South China Normal University, Guangzhou 510631, PR China.
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5
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Li T, Ma Z, Ding T, Yang Y, Wang F, Wan X, Liang F, Chen X, Yao H. Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species. Funct Integr Genomics 2024; 24:45. [PMID: 38429550 DOI: 10.1007/s10142-024-01316-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/03/2024]
Abstract
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.
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Affiliation(s)
- Tingting Li
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Zheng Ma
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Tiemei Ding
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Yanxin Yang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Fei Wang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xinjing Wan
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Fangyun Liang
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Xi Chen
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China
| | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, 625014, Sichuan, People's Republic of China.
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6
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Jinkerson RE, Poveda-Huertes D, Cooney EC, Cho A, Ochoa-Fernandez R, Keeling PJ, Xiang T, Andersen-Ranberg J. Biosynthesis of chlorophyll c in a dinoflagellate and heterologous production in planta. Curr Biol 2024; 34:594-605.e4. [PMID: 38157859 DOI: 10.1016/j.cub.2023.12.068] [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: 11/10/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Chlorophyll c is a key photosynthetic pigment that has been used historically to classify eukaryotic algae. Despite its importance in global photosynthetic productivity, the pathway for its biosynthesis has remained elusive. Here we define the CHLOROPHYLL C SYNTHASE (CHLCS) discovered through investigation of a dinoflagellate mutant deficient in chlorophyll c. CHLCSs are proteins with chlorophyll a/b binding and 2-oxoglutarate-Fe(II) dioxygenase (2OGD) domains found in peridinin-containing dinoflagellates; other chlorophyll c-containing algae utilize enzymes with only the 2OGD domain or an unknown synthase to produce chlorophyll c. 2OGD-containing synthases across dinoflagellate, diatom, cryptophyte, and haptophyte lineages form a monophyletic group, 8 members of which were also shown to produce chlorophyll c. Chlorophyll c1 to c2 ratios in marine algae are dictated in part by chlorophyll c synthases. CHLCS heterologously expressed in planta results in the accumulation of chlorophyll c1 and c2, demonstrating a path to augment plant pigment composition with algal counterparts.
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Affiliation(s)
- Robert E Jinkerson
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.
| | - Daniel Poveda-Huertes
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Rocio Ochoa-Fernandez
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Tingting Xiang
- Department of Bioengineering, University of California, Riverside, Riverside, CA 92521, USA.
| | - Johan Andersen-Ranberg
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
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7
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Zhang F, Li Z, Chen C, Luan H, Fang RH, Zhang L, Wang J. Biohybrid Microalgae Robots: Design, Fabrication, Materials, and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2303714. [PMID: 37471001 PMCID: PMC10799182 DOI: 10.1002/adma.202303714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/25/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
The integration of microorganisms and engineered artificial components has shown considerable promise for creating biohybrid microrobots. The unique features of microalgae make them attractive candidates as natural actuation materials for the design of biohybrid microrobotic systems. In this review, microalgae-based biohybrid microrobots are introduced for diverse biomedical and environmental applications. The distinct propulsion and phototaxis behaviors of green microalgae, as well as important properties from other photosynthetic microalga systems (blue-green algae and diatom) that are crucial to constructing powerful biohybrid microrobots, will be described first. Then the focus is on chemical and physical routes for functionalizing the algae surface with diverse reactive materials toward the fabrication of advanced biohybrid microalgae robots. Finally, representative applications of such algae-driven microrobots are presented, including drug delivery, imaging, and water decontamination, highlighting the distinct advantages of these active biohybrid robots, along with future prospects and challenges.
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Affiliation(s)
- Fangyu Zhang
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Zhengxing Li
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Chuanrui Chen
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Hao Luan
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Ronnie H. Fang
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego La Jolla, CA 92093, USA
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8
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Brown AL, Casarez GA, Moeller HV. Acquired Phototrophy as an Evolutionary Path to Mixotrophy. Am Nat 2023; 202:458-470. [PMID: 37792914 DOI: 10.1086/725918] [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] [Indexed: 10/06/2023]
Abstract
AbstractAcquired photosynthesis transforms genotypically heterotrophic lineages into autotrophs. Transient acquisitions of eukaryotic chloroplasts may provide key evolutionary insight into the endosymbiosis process-the hypothesized mechanism by which eukaryotic cells obtained new functions via organelle retention. Here, we use an eco-evolutionary model to study the environmental conditions under which chloroplast retention is evolutionarily favorable. We focus on kleptoplastidic lineages-which steal functional chloroplasts from their prey-as hypothetical evolutionary intermediates. Our adaptive dynamics analysis reveals a spectrum of evolutionarily stable strategies ranging from phagotrophy to phototrophy to obligate kleptoplasty. Our model suggests that a low-light niche and weak (or absent) trade-offs between chloroplast retention and overall digestive ability favor the evolution of phototrophy. In contrast, when consumers experience strong trade-offs, obligate kleptoplasty emerges as an evolutionary end point. Therefore, the preevolved trade-offs that underlie an evolving lineage's physiology will likely constrain its evolutionary trajectory.
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9
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Frangedakis E, Marron AO, Waller M, Neubauer A, Tse SW, Yue Y, Ruaud S, Waser L, Sakakibara K, Szövényi P. What can hornworts teach us? FRONTIERS IN PLANT SCIENCE 2023; 14:1108027. [PMID: 36968370 PMCID: PMC10030945 DOI: 10.3389/fpls.2023.1108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.
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Affiliation(s)
| | - Alan O. Marron
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Sze Wai Tse
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Yuling Yue
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Stephanie Ruaud
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Lucas Waser
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
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10
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Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
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Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
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11
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Evidence for Strand Asymmetry in Different Plastid Genomes. Genes (Basel) 2023; 14:genes14020320. [PMID: 36833247 PMCID: PMC9956171 DOI: 10.3390/genes14020320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. Although this pattern has been reported for a couple of isolated plastid genomes, it is not clear how widespread it is overall in this chromosome. Using a random walk approach, we examine plastid genomes outside of the land plants, which are excluded since they are known not to initiate replication at a single site, for such a pattern of asymmetry. Although it is not a common feature, we find that it is detectable in the plastid genome of species from several diverse lineages. The euglenozoa in particular show a strong skew pattern as do several rhodophytes. There is a weaker pattern in some chlorophytes but it is not apparent in other lineages. The ramifications of this for analyses of plastid evolution are discussed.
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12
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Akhyar O, Mashio AS, Kato Y, Hayashi S, Wong KH, Kosugi C, Hasegawa H. Element pattern in two dominant species of seaweed from Betsukari coastline - Mashike, Hokkaido, Japan. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120473. [PMID: 36273694 DOI: 10.1016/j.envpol.2022.120473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/22/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The present study investigated the monthly of element accumulation in seaweeds. Patterns of As, Ba, Cd, Cu, Fe, Mn, Pb, and Zn concentrations in dominant species of Phaeophyceae and Rhodophyceae, namely Saccharina japonica and Pterocladiella tenuis respectively, collected from the Betsukari coastline-Mashike, Hokkaido, Japan, were investigated. Our results indicated that element accumulation was more related to specific seaweed species than to their supply in seawater concentration. S. japonica was found to be an accumulator of As, whereas P. tenuis notably accumulated Mn. The accumulation of specific elements also affects the coupled patterns between closely related elements. The monthly pattern of Cd was similar to that of As in S. japonica, and it is an element with unknown biological function in the seaweed. The monthly accumulation pattern of Fe and Mn, a well-known closely related element that forms the extracellular surface in seaweed, was found to be similar in P. tenuis. A similar transport mechanism affected the antagonistic pattern of Cd and Zn accumulation in S. japonica. Our data can be employed in the assessment of biomonitoring of element cycles in the environment.
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Affiliation(s)
- Okviyoandra Akhyar
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan; Department of Chemistry Education, Islamic University of Kalimantan Muhammad Arsyad Al Banjari, Jl. Adhyaksa No. 2 Kayu Tangi, Banjarmasin, 70123, Indonesia
| | - Asami Suzuki Mashio
- Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan.
| | - Yusuke Kato
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Syuhei Hayashi
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Kuo Hong Wong
- Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan
| | - Chika Kosugi
- Advanced Technology Research Laboratories, Nippon Steel Corporation, 20-1 Shintomi, Futtsu City, Chiba, 293-8511, Japan
| | - Hiroshi Hasegawa
- Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, 920-1192, Japan.
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13
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Ebenezer TE, Low RS, O'Neill EC, Huang I, DeSimone A, Farrow SC, Field RA, Ginger ML, Guerrero SA, Hammond M, Hampl V, Horst G, Ishikawa T, Karnkowska A, Linton EW, Myler P, Nakazawa M, Cardol P, Sánchez-Thomas R, Saville BJ, Shah MR, Simpson AGB, Sur A, Suzuki K, Tyler KM, Zimba PV, Hall N, Field MC. Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Biol Open 2022; 11:bio059561. [PMID: 36412269 PMCID: PMC9836076 DOI: 10.1242/bio.059561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.
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Affiliation(s)
- ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross S. Low
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ishuo Huang
- Office of Regulatory Science, United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Antonio DeSimone
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Scott C. Farrow
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Robert A. Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Sergio Adrián Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral. CCT CONICET Santa Fe, Santa Fe 3000, Argentina
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 25250, Czech Republic
| | - Geoff Horst
- Kemin Industries, Research and Development, Plymouth, MI 48170, USA
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue 690-8504, Japan
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Warsaw 02-089, Poland
| | - Eric W. Linton
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Masami Nakazawa
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, 599-8531, Japan
| | - Pierre Cardol
- Department of Life Sciences, Institut de Botanique, Université de Liège, Liège 4000, Belgium
| | | | - Barry J. Saville
- Forensic Science, Environmental and Life Sciences Graduate Program, Trent University, Peterborough K9L 0G2, Canada
| | - Mahfuzur R. Shah
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Aakash Sur
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Kengo Suzuki
- R&D Company, Euglena Co., Ltd., 2F Yokohama Bio Industry Center (YBIC), 1-6 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kevin M. Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Center of Excellence for Bionanoscience Research, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Paul V. Zimba
- PVZimba, LLC, 12241 Percival St, Chester, VA 23831, USA
- Rice Rivers Center, VA Commonwealth University, Richmond, VA 23284, USA
| | - Neil Hall
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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14
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Corcoran AA, Ohan J, Hanschen ER, Granite A, Martinez H, Holguin F, Hovde BT, Starkenburg SR. Scale-dependent enhancement of productivity and stability in xenic Nannochloropsis cultures. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Wang Q, Yue J, Zhang C, Yan J. Split-Ubiquitin Two-Hybrid Screen for Proteins Interacting with slToc159-1 and slToc159-2, Two Chloroplast Preprotein Import Receptors in Tomato ( Solanum lycopersicum). PLANTS (BASEL, SWITZERLAND) 2022; 11:2923. [PMID: 36365376 PMCID: PMC9654457 DOI: 10.3390/plants11212923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
The post-translational import of nuclear-encoded chloroplast preproteins is critical for chloroplast biogenesis, and the Toc159 family of proteins is the receptor for this process. Our previous work identified and analyzed the Toc GTPase in tomato; however, the tomato-specific transport substrate for Toc159 is still unknown, which limits the study of the function of the TOC receptor in tomato. In this study, we expand the number of preprotein substrates of slToc159 receptor family members using slToc159-1 and slToc159-2 as bait via a split-ubiquitin yeast two-hybrid membrane system. Forty-one specific substrates were identified in tomato for the first time. Using slToc159-1GM and slToc159-2GM as bait, we compared the affinity of the two bait proteins, with and without the A domain, to the precursor protein, which suggested that the A domain endowed the proproteins with subclass specificity. The presence of the A domain enhanced the interaction intensity of slToc159-1 with the photosynthetic preprotein but decreased the interaction intensity of slToc159-2 with the photosynthetic preprotein. Similarly, the presence of the A domain also altered the affinity of slToc159 to non-photosynthetic preproteins. Bimolecular fluorescence complementation (BiFC) analysis showed that A domain had the ability to recognize the preprotein, and the interaction occurred in the chloroplast. Further, the localization of the A domain in Arabidopsis protoplasts showed that the A domain did not contain chloroplast membrane targeting signals. Our data demonstrate the importance of a highly non-conserved A domain, which endows the slToc159 receptor with specificity for different protein types. However, the domain containing the information on targeting the chloroplast needs further study.
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Affiliation(s)
- Qi Wang
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Vegetable Research Academy, Guizhou University, Guiyang 550025, China
| | - Jiang Yue
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Vegetable Research Academy, Guizhou University, Guiyang 550025, China
| | - Chaozhong Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Vegetable Research Academy, Guizhou University, Guiyang 550025, China
| | - Jianmin Yan
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Vegetable Research Academy, Guizhou University, Guiyang 550025, China
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16
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Nowicka B. Heavy metal-induced stress in eukaryotic algae-mechanisms of heavy metal toxicity and tolerance with particular emphasis on oxidative stress in exposed cells and the role of antioxidant response. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:16860-16911. [PMID: 35006558 PMCID: PMC8873139 DOI: 10.1007/s11356-021-18419-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/27/2021] [Indexed: 04/15/2023]
Abstract
Heavy metals is a collective term describing metals and metalloids with a density higher than 5 g/cm3. Some of them are essential micronutrients; others do not play a positive role in living organisms. Increased anthropogenic emissions of heavy metal ions pose a serious threat to water and land ecosystems. The mechanism of heavy metal toxicity predominantly depends on (1) their high affinity to thiol groups, (2) spatial similarity to biochemical functional groups, (3) competition with essential metal cations, (4) and induction of oxidative stress. The antioxidant response is therefore crucial for providing tolerance to heavy metal-induced stress. This review aims to summarize the knowledge of heavy metal toxicity, oxidative stress and antioxidant response in eukaryotic algae. Types of ROS, their formation sites in photosynthetic cells, and the damage they cause to the cellular components are described at the beginning. Furthermore, heavy metals are characterized in more detail, including their chemical properties, roles they play in living cells, sources of contamination, biochemical mechanisms of toxicity, and stress symptoms. The following subchapters contain the description of low-molecular-weight antioxidants and ROS-detoxifying enzymes, their properties, cellular localization, and the occurrence in algae belonging to different clades, as well as the summary of the results of the experiments concerning antioxidant response in heavy metal-treated eukaryotic algae. Other mechanisms providing tolerance to metal ions are briefly outlined at the end.
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Affiliation(s)
- Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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17
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Sanders WB. The photoaerogens: algae and plants reunited conceptually. AMERICAN JOURNAL OF BOTANY 2022; 109:363-365. [PMID: 35257370 DOI: 10.1002/ajb2.1828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Affiliation(s)
- William B Sanders
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL 33965-6565, USA
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18
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Inagaki N. Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen. Int J Mol Sci 2022; 23:ijms23052520. [PMID: 35269663 PMCID: PMC8909930 DOI: 10.3390/ijms23052520] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.
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Affiliation(s)
- Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
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19
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
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20
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Sandmann G. Diversity and origin of carotenoid biosynthesis: its history of coevolution towards plant photosynthesis. THE NEW PHYTOLOGIST 2021; 232:479-493. [PMID: 34324713 DOI: 10.1111/nph.17655] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The development of photosynthesis was a highlight in the progression of bacteria. In addition to the photosystems with their structural proteins, the photosynthesis apparatus consists of different cofactors including essential carotenoids. Thus, the evolution of the carotenoid pathways in relation to the functionality of the resulting structures in photosynthesis is the focus of this review. Analysis of carotenoid pathway genes indicates early evolutionary roots in prokaryotes. The pathway complexity leading to a multitude of structures is a result of gene acquisition, including their functional modifications, emergence of novel genes and gene exchange between species. Along with the progression of photosynthesis, carotenoid pathways coevolved with photosynthesis according to their advancing functionality. Cyanobacteria, with their oxygenic photosynthesis, became a landmark for evolutionary events including carotenogenesis. Concurrent with endosymbiosis, the cyanobacterial carotenoid pathways were inherited into algal plastids. In the lineage leading to Chlorophyta and plants, carotenoids evolved to their prominent role in protection and regulation of light energy input as constituents of a highly efficient light-harvesting complex.
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Affiliation(s)
- Gerhard Sandmann
- Institute of Molecular Biosciences, Goethe-University Frankfurt/M, Max von Laue Str. 9, Frankfurt, D-60438, Germany
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21
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Gavalás-Olea A, Siol A, Sakka Y, Köser J, Nentwig N, Hauser T, Filser J, Thöming J, Lang I. Potential of the Red Alga Dixoniella grisea for the Production of Additives for Lubricants. PLANTS (BASEL, SWITZERLAND) 2021; 10:1836. [PMID: 34579369 PMCID: PMC8465309 DOI: 10.3390/plants10091836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
There is an increasing interest in algae-based raw materials for medical, cosmetic or nutraceutical applications. Additionally, the high diversity of physicochemical properties of the different algal metabolites proposes these substances from microalgae as possible additives in the chemical industry. Among the wide range of natural products from red microalgae, research has mainly focused on extracellular polymers for additive use, while this study also considers the cellular components. The aim of the present study is to analytically characterize the extra- and intracellular molecular composition from the red microalga Dixoniella grisea and to evaluate its potential for being used in the tribological industry. D. grisea samples, fractionated into extracellular polymers (EPS), cells and medium, were examined for their molecular composition. This alga produces a highly viscous polymer, mainly composed of polysaccharides and proteins, being secreted into the culture medium. The EPS and biomass significantly differed in their molecular composition, indicating that they might be used for different bio-additive products. We also show that polysaccharides and proteins were the major chemical compounds in EPS, whereas the content of lipids depended on the separation protocol and the resulting product. Still, they did not represent a major group and were thus classified as a potential valuable side-product. Lyophilized algal fractions obtained from D. grisea were found to be not toxic when EPS were not included. Upon implementation of EPS as a commercial product, further assessment on the environmental toxicity to enchytraeids and other soil organisms is required. Our results provide a possible direction for developing a process to gain an environmentally friendly bio-additive for application in the tribological industry based on a biorefinery approach.
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Affiliation(s)
- Antonio Gavalás-Olea
- Algae Biotechnology, Institute of EcoMaterials, Bremerhaven University of Applied Sciences, An der Karlstadt 8, D-27568 Bremerhaven, Germany; (A.G.-O.); (T.H.)
| | - Antje Siol
- Center for Environmental Research and Sustainable Technology (UFT), Department Chemical Process Engineering (CVT), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (A.S.); (J.K.); (J.T.)
| | - Yvonne Sakka
- Center for Environmental Research and sustainable Technology (UFT), Department General and Theoretical Ecology (ÖKO), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (Y.S.); (N.N.); (J.F.)
| | - Jan Köser
- Center for Environmental Research and Sustainable Technology (UFT), Department Chemical Process Engineering (CVT), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (A.S.); (J.K.); (J.T.)
| | - Nina Nentwig
- Center for Environmental Research and sustainable Technology (UFT), Department General and Theoretical Ecology (ÖKO), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (Y.S.); (N.N.); (J.F.)
| | - Thomas Hauser
- Algae Biotechnology, Institute of EcoMaterials, Bremerhaven University of Applied Sciences, An der Karlstadt 8, D-27568 Bremerhaven, Germany; (A.G.-O.); (T.H.)
| | - Juliane Filser
- Center for Environmental Research and sustainable Technology (UFT), Department General and Theoretical Ecology (ÖKO), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (Y.S.); (N.N.); (J.F.)
| | - Jorg Thöming
- Center for Environmental Research and Sustainable Technology (UFT), Department Chemical Process Engineering (CVT), University of Bremen, Leobener Straße 6, D-28359 Bremen, Germany; (A.S.); (J.K.); (J.T.)
| | - Imke Lang
- Algae Biotechnology, Institute of EcoMaterials, Bremerhaven University of Applied Sciences, An der Karlstadt 8, D-27568 Bremerhaven, Germany; (A.G.-O.); (T.H.)
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22
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Starko S, Bringloe TT, Soto Gomez M, Darby H, Graham SW, Martone PT. Genomic Rearrangements and Sequence Evolution across Brown Algal Organelles. Genome Biol Evol 2021; 13:evab124. [PMID: 34061182 PMCID: PMC8290108 DOI: 10.1093/gbe/evab124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Organellar genomes serve as useful models for genome evolution and contain some of the most widely used phylogenetic markers, but they are poorly characterized in many lineages. Here, we report 20 novel mitochondrial genomes and 16 novel plastid genomes from the brown algae. We focused our efforts on the orders Chordales and Laminariales but also provide the first plastid genomes (plastomes) from Desmarestiales and Sphacelariales, the first mitochondrial genome (mitome) from Ralfsiales and a nearly complete mitome from Sphacelariales. We then compared gene content, sequence evolution rates, shifts in genome structural arrangements, and intron distributions across lineages. We confirm that gene content is largely conserved in both organellar genomes across the brown algal tree of life, with few cases of gene gain or loss. We further show that substitution rates are generally lower in plastid than mitochondrial genes, but plastomes are more variable in gene arrangement, as mitomes tend to be colinear even among distantly related lineages (with exceptions). Patterns of intron distribution across organellar genomes are complex. In particular, the mitomes of several laminarialean species possess group II introns that have T7-like ORFs, found previously only in mitochondrial genomes of Pylaiella spp. (Ectocarpales). The distribution of these mitochondrial introns is inconsistent with vertical transmission and likely reflects invasion by horizontal gene transfer between lineages. In the most extreme case, the mitome of Hedophyllum nigripes is ∼40% larger than the mitomes of close relatives because of these introns. Our results provide substantial insight into organellar evolution across the brown algae.
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Affiliation(s)
- Samuel Starko
- Department of Biology, University of Victoria, Victoria, Canada
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Trevor T Bringloe
- Department of BioSciences, University of Melbourne, Melbourne, Australia
| | - Marybel Soto Gomez
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Hayley Darby
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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Skejo J, Garg SG, Gould SB, Hendriksen M, Tria FDK, Bremer N, Franjević D, Blackstone NW, Martin WF. Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction. Genome Biol Evol 2021; 13:evab096. [PMID: 33963405 PMCID: PMC8290118 DOI: 10.1093/gbe/evab096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.
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Affiliation(s)
- Josip Skejo
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Hendriksen
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Fernando D K Tria
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Nico Bremer
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Damjan Franjević
- Faculty of Science, Division of Zoology, Department of Biology, University of Zagreb, Evolution Lab, Zagreb, Croatia
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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Jiang M, Li Y, Chen H, Wang B, Liu C. Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Lactuca raddeana and Lactuca sativa. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1498-1506. [PMID: 33969207 PMCID: PMC8079048 DOI: 10.1080/23802359.2021.1911700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Lactuca raddeana is a biennial plant of the Lactuca genus belonging to the Asteraceae family. The classification of Lactuca is controversial, and no consistent conclusions have been reached based on the analysis of morphological characters and different molecular markers. Here, we sequenced and assembled the complete chloroplast genome of L. raddeana. This genome has a total length of 152,339 bp, a conservative quartile structure that is composed of a large single-copy (LSC) region of 83,976 bp, a small-copy (SSC) region of 18,521 bp, and a pair of inverted repeats (IRs) of 24,921 bp. The genome contains 112 unique genes, including 79 protein-coding, four rRNA, and 29 tRNA genes. Repeat analysis obtained 17 microsatellite, 16 tandem, and 17 interspersed repeats. Comparison of sequence divergence between L. raddeana and L. sativa found the intergenic spacer trnC-petN exhibited the highest degree of variation. Three phylogenetic trees based on the 72 shared protein, matK gene, and rbcL gene sequences showed that L. raddeana and L. sativa are clustered together. The acquisition and comparative analysis of the chloroplast genome provide a valuable resource for the taxonomic and phylogenetic studies of Lactuca.
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Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Yuning Li
- School of Pharmaceutical Sciences, Xiangnan University, Chenzhou, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Bin Wang
- School of Pharmaceutical Sciences, Xiangnan University, Chenzhou, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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25
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Symbiogenesis is driven through hierarchical reorganization of an ecosystem under closed or semi-closed conditions. Biosystems 2021; 205:104427. [PMID: 33857536 DOI: 10.1016/j.biosystems.2021.104427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022]
Abstract
Ecosystems generate selective environments and function as sources of various metabolic systems for symbiogenesis. In this study, we have explored how symbiogenesis occurs in the living world, from a holistic perspective, by observing a long-term experimental culture of an ecosystem model (CET microcosm) and using related findings in laboratory and field studies of endosymbiosis between auto- (photo-) and heterotrophic organisms. The results obtained suggest that symbiogenesis can occur in the mature stages of semi-closed ecosystems and lead to a new ecosystem-oriented perspective of symbiogenesis. Symbiogenesis is an aspect of ecosystem evolution in which whole ecosystem dynamics generate selective conditions operating on the component species, favoring symbiotic associations among some of them. The development of symbiotic associations then modifies the organization and material/energy flow structure of the ecosystem, which, in turn, modifies their selective environments.
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Ni Y, Jiang M, Chen H, Huang L, Chen P, Liu C. Adaptation of a parasitic lifestyle by Cuscuta gronovii Willd. ex Roem. & Schult.: large scale gene deletion, conserved gene orders, and low intraspecific divergence. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1475-1482. [PMID: 33969200 PMCID: PMC8079069 DOI: 10.1080/23802359.2021.1911702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cuscuta gronovii Willd. ex Roem. & Schult. is a parasitic plant and widely distributed in Europe and North America. Here, we compared the plastome sequences of a C. gronovii plant collected from China and other 16 Cuscuta plastomes, including one C. gronovii plastome from North America. The plastome was 86,727 bp in size with a pair of inverted repeats (IRs) of 14,354 bp, a large single-copy (LSC) region of 50,956 bp, and a small single-copy (SSC) region of 7,063 bp. We predicted 97 genes in the plastome, including 61 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. We detected a total of 21 microsatellite, 16 tandem, and ten interspersed repeats in the genome. Gene contents analysis of 17 Cuscuta plastomes showed the loss of the entire ndh gene family. The phylogenomic analysis using 22 shared protein sequences shows that the two C. gronovii formed a cluster. Thirteen of Cuscuta plastomes showed no rearrangement. The other three showed smaller inversions and smaller numbers of gene deletion. Next, we identified the two INDELs, one SNP site between the two C. gronovii plastomes. And we identified two putative RNA editing sites. Lastly, to distinguish between C. gronovii and two medicinal Cuscuta species, C. chinensis and C. australis, we identified ten molecular markers based on the genome sequences. The overall large-scale gene loss, conserved gene order, low intraspecific divergence are consistent with the adaptation of C. gronovii to a parasitic lifestyle.
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Affiliation(s)
- Yang Ni
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Linfang Huang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
| | - Pinghua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, National Engineering Research Center of Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, P. R. China
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P. R. China
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Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
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Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
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28
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Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics. Microorganisms 2021; 9:microorganisms9020311. [PMID: 33546180 PMCID: PMC7913273 DOI: 10.3390/microorganisms9020311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/26/2021] [Accepted: 01/30/2021] [Indexed: 02/08/2023] Open
Abstract
With more than 156,000 described species, eukaryotic algae (both macro- and micro-algae) are a rich source of biological diversity, however their chemical diversity remains largely unexplored. Specialised metabolites with promising biological activities have been widely reported for seaweeds, and more recently extracts from microalgae have exhibited activity in anticancer, antimicrobial, and antioxidant screens. However, we are still missing critical information on the distinction of chemical profiles between macro- and microalgae, as well as the chemical space these metabolites cover. This study has used an untargeted comparative metabolomics approach to explore the chemical diversity of seven seaweeds and 36 microalgal strains. A total of 1390 liquid chromatography-mass spectrometry (LC-MS) features were detected, representing small organic algal metabolites, with no overlap between the seaweeds and microalgae. An in-depth analysis of four Dunaliella tertiolecta strains shows that environmental factors may play a larger role than phylogeny when classifying their metabolomic profiles.
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29
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Sandmann G. Diversity and Evolution of Carotenoid Biosynthesis from Prokaryotes to Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1261:79-94. [PMID: 33783732 DOI: 10.1007/978-981-15-7360-6_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carotenoids exist in pro- and eukaryotic organisms, but not in animals (with one exception). Their biosynthesis evolved from a common ancestor of Archaea and Bacteria and via the latter by endosymbiosis to algae and plants. The formation of carotenoids in fungi can be regarded as a lineage from the archaea. This review highlights the distribution and evolution of carotenogenic pathways in taxonomic groups of prokaryotes and eukaryotes with a special emphasis on the evolutionary aspects of prominent carotenogenic genes in relation to the assigned function of their corresponding enzymes. The latter aspect includes a focus on paralogs of gene families evolving novel functions and unrelated genes encoding enzymes with the same function.
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Affiliation(s)
- Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe University, Frankfurt, Germany.
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30
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Rono PC, Dong X, Yang JX, Mutie FM, Oulo MA, Malombe I, Kirika PM, Hu GW, Wang QF. Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. Front Genet 2020; 11:560368. [PMID: 33362846 PMCID: PMC7756076 DOI: 10.3389/fgene.2020.560368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
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Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Millicent A Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Paul M Kirika
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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31
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Coleman LJM, Martone PT. Morphological plasticity in the kelp Nereocystis luetkeana (Phaeophyceae) is sensitive to the magnitude, direction, and location of mechanical loading. JOURNAL OF PHYCOLOGY 2020; 56:1414-1427. [PMID: 32602559 DOI: 10.1111/jpy.13043] [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: 12/18/2019] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Nereocystis luetkeana is a canopy-forming kelp that exhibits morphological plasticity across hydrodynamic gradients, producing broad, undulate blades in slow flow and narrow, flattened blades in fast flow, enabling thalli to reduce drag while optimizing photosynthesis. While the functional significance of this phenomenon has been well studied, the developmental and physiological mechanisms that facilitate the plasticity remain poorly understood. In this study, we conducted three experiments to characterize how the (1) magnitude, (2) direction, and (3) location of plasticity-inducing mechanical stimuli affect the morphology of Nereocystis blades. We found that applying a gradient of tensile force caused blades to grow progressively longer, narrower, less ruffled, and heavier in a linear fashion, suggesting that Nereocystis is equally well adapted for all conditions within its hydrodynamic niche. We also found that applying tension transversely across blades caused the growth response to rotate 90°, indicating that there is no substantial separation between the sites of stimulus perception and response and suggesting that a long-distance signaling mechanism, such as a hormone, is unlikely to mediate this phenomenon. Meristoderm cells showed morphological changes that paralleled those of their respective blades in this experiment, implying that tissue-level morphology is influenced by cell growth. Finally, we found that plasticity was only induced when tension was applied directly to the growing tissue, reinforcing that long-distance signaling is probably not involved and possibly indicating that the mechanism on display generally requires an intercalary meristem to facilitate mechanoperception.
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Affiliation(s)
- Liam J M Coleman
- Department of Botany & Biodiversity Research Centre, University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Patrick T Martone
- Department of Botany & Biodiversity Research Centre, University of British Columbia, 6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
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Khan AK, Kausar H, Jaferi SS, Drouet S, Hano C, Abbasi BH, Anjum S. An Insight into the Algal Evolution and Genomics. Biomolecules 2020; 10:E1524. [PMID: 33172219 PMCID: PMC7694994 DOI: 10.3390/biom10111524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/06/2023] Open
Abstract
With the increase in biotechnological, environmental, and nutraceutical importance of algae, about 100 whole genomic sequences of algae have been published, and this figure is expected to double in the coming years. The phenotypic and ecological diversity among algae hints at the range of functional capabilities encoded by algal genomes. In order to explore the biodiversity of algae and fully exploit their commercial potential, understanding their evolutionary, structural, functional, and developmental aspects at genomic level is a pre-requisite. So forth, the algal genomic analysis revealed us that algae evolved through endosymbiotic gene transfer, giving rise to around eight phyla. Amongst the diverse algal species, the unicellular green algae Chlamydomonas reinhardtii has attained the status of model organism as it is an ideal organism to elucidate the biological processes critical to plants and animals, as well as commercialized to produce range of bio-products. For this review, an overview of evolutionary process of algae through endosymbiosis in the light of genomics, as well as the phylogenomic, studies supporting the evolutionary process of algae was reviewed. Algal genomics not only helped us to understand the evolutionary history of algae but also may have an impact on our future by helping to create algae-based products and future biotechnological approaches.
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Affiliation(s)
- Amna Komal Khan
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Syyada Samra Jaferi
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France; (S.D.); (C.H.)
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), INRAE USC1328, Université d’Orléans, 28000 Chartres, France; (S.D.); (C.H.)
| | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Sumaira Anjum
- Department of Biotechnology, Kinnaird College for Women, Lahore 54000, Pakistan; (A.K.K.); (H.K.); (S.S.J.)
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Zachar I, Boza G. Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes. Cell Mol Life Sci 2020; 77:3503-3523. [PMID: 32008087 PMCID: PMC7452879 DOI: 10.1007/s00018-020-03462-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/25/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023]
Abstract
Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.
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Affiliation(s)
- István Zachar
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary.
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary.
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Kirchplatz 1, 82049, Munich, Germany.
| | - Gergely Boza
- Evolutionary Systems Research Group, Institute of Evolution, Centre for Ecological Research, Klebelsberg Kunó str. 3., Tihany, 8237, Hungary
- Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Schlossplatz 1, 2361, Laxenburg, Austria
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34
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Antonov IV. Two Cobalt Chelatase Subunits Can Be Generated from a Single chlD Gene via Programed Frameshifting. Mol Biol Evol 2020; 37:2268-2278. [PMID: 32211852 DOI: 10.1093/molbev/msaa081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Magnesium chelatase chlIDH and cobalt chelatase cobNST enzymes are required for biosynthesis of (bacterio)chlorophyll and cobalamin (vitamin B12), respectively. Each enzyme consists of large, medium, and small subunits. Structural and primary sequence similarities indicate common evolutionary origin of the corresponding subunits. It has been reported earlier that some of vitamin B12 synthesizing organisms utilized unusual cobalt chelatase enzyme consisting of a large cobalt chelatase subunit (cobN) along with a medium (chlD) and a small (chlI) subunits of magnesium chelatase. In attempt to understand the nature of this phenomenon, we analyzed >1,200 diverse genomes of cobalamin and/or chlorophyll producing prokaryotes. We found that, surprisingly, genomes of many cobalamin producers contained cobN and chlD genes only; a small subunit gene was absent. Further on, we have discovered a diverse group of chlD genes with functional programed ribosomal frameshifting signals. Given a high similarity between the small subunit and the N-terminal part of the medium subunit, we proposed that programed translational frameshifting may allow chlD mRNA to produce both subunits. Indeed, in genomes where genes for small subunits were absent, we observed statistically significant enrichment of programed frameshifting signals in chlD genes. Interestingly, the details of the frameshifting mechanisms producing small and medium subunits from a single chlD gene could be prokaryotic taxa specific. All over, this programed frameshifting phenomenon was observed to be highly conserved and present in both bacteria and archaea.
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Affiliation(s)
- Ivan V Antonov
- Institute of Bioengineering, Federal Research Centre Fundamentals of Biotechnology, Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
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Pinevich AV. Chloroplast history clarified by the criterion of light-harvesting complex. Biosystems 2020; 196:104173. [PMID: 32534171 DOI: 10.1016/j.biosystems.2020.104173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 01/13/2023]
Abstract
Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. In particular, the rrn operon, which is the key phylogeny marker, locates chloroplasts on the tree of Cyanobacteria. Chloroplast ancestry and diversity can be also traced with the rpoС and psbA genes, rbc operon, and other molecular criteria of prime importance. Another criterion, also highly reliable, is light-harvesting complex (LHC). LHC pigment and protein moieties specify light acclimation strategies in evolutionary retrospect and modern biosphere. The onset of symbiosis between eukaryotic host and pre-chloroplast, as well as further mutual adjustment of partners depended on physiological competence of LHC. In this review, the criterion of LHC is applied to the origin and diversity of chloroplasts. In particular, ancient cyanobacterium possessing tandem antenna (encoded by the cbp genes and the pbp genes, correspondingly), and defined as a prochlorophyte, is argued to be chloroplast ancestor.
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Affiliation(s)
- Alexander V Pinevich
- St. Petersburg State University, Department of Microbiology, St. Petersburg, Russia.
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Comparing Early Eukaryotic Integration of Mitochondria and Chloroplasts in the Light of Internal ROS Challenges: Timing is of the Essence. mBio 2020; 11:mBio.00955-20. [PMID: 32430475 PMCID: PMC7240161 DOI: 10.1128/mbio.00955-20] [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] [Indexed: 12/27/2022] Open
Abstract
When trying to reconstruct the evolutionary trajectories during early eukaryogenesis, one is struck by clear differences in the developments of two organelles of endosymbiotic origin: the mitochondrion and the chloroplast. From a symbiogenic perspective, eukaryotic development can be interpreted as a process in which many of the defining eukaryotic characteristics arose as a result of mutual adaptions of both prokaryotes (an archaeon and a bacterium) involved. This implies that many steps during the bacterium-to-mitochondrion transition trajectory occurred in an intense period of dramatic and rapid changes. In contrast, the subsequent cyanobacterium-to-chloroplast development in a specific eukaryotic subgroup, leading to the photosynthetic lineages, occurred in a full-fledged eukaryote. The commonalities and differences in the two trajectories shed an interesting light on early, and ongoing, eukaryotic evolutionary driving forces, especially endogenous reactive oxygen species (ROS) formation. Differences between organellar ribosomes, changes to the electron transport chain (ETC) components, and mitochondrial codon reassignments in nonplant mitochondria can be understood when mitochondrial ROS formation, e.g., during high energy consumption in heterotrophs, is taken into account.IMPORTANCE The early eukaryotic evolution was deeply influenced by the acquisition of two endosymbiotic organelles - the mitochondrion and the chloroplast. Here we discuss the possibly important role of reactive oxygen species in these processes.
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Ly SN, Garavito A, De Block P, Asselman P, Guyeux C, Charr JC, Janssens S, Mouly A, Hamon P, Guyot R. Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae. PLoS One 2020; 15:e0232295. [PMID: 32353023 PMCID: PMC7192488 DOI: 10.1371/journal.pone.0232295] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/11/2020] [Indexed: 11/19/2022] Open
Abstract
In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.
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Affiliation(s)
- Serigne Ndiawar Ly
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Andrea Garavito
- Departamento Ciencias Biológicas, Universidad de Caldas, Manizales, Colombia
| | | | - Pieter Asselman
- Meise Botanic Garden, Meise, Belgium
- University of Ghent, Ghent, Belgium
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Arnaud Mouly
- Laboratory Chrono-Environment, UMR CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France
- Besançon Botanic Garden, Université de Bourgogne Franche-Comté, Besançon, France
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France
- Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
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Djemiel C, Plassard D, Terrat S, Crouzet O, Sauze J, Mondy S, Nowak V, Wingate L, Ogée J, Maron PA. µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria. Sci Rep 2020; 10:5915. [PMID: 32246067 PMCID: PMC7125122 DOI: 10.1038/s41598-020-62555-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/09/2020] [Indexed: 11/29/2022] Open
Abstract
Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | | | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Olivier Crouzet
- Univ. Paris Saclay, AgroParisTech, UMR ECOSYS, INRA, F-78206, Versailles, France
| | - Joana Sauze
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Samuel Mondy
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Lisa Wingate
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Jérôme Ogée
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France.
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Barton S, Jenkins J, Buckling A, Schaum CE, Smirnoff N, Raven JA, Yvon-Durocher G. Evolutionary temperature compensation of carbon fixation in marine phytoplankton. Ecol Lett 2020; 23:722-733. [PMID: 32059265 PMCID: PMC7078849 DOI: 10.1111/ele.13469] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/11/2020] [Indexed: 12/01/2022]
Abstract
The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short‐term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long‐term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short‐term increases in temperature. Long‐term experimental evolution under high temperature reversed the short‐term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump.
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Affiliation(s)
- Samuel Barton
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - James Jenkins
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
| | - C-Elisa Schaum
- Institute for Hydrobiology and Fisheries, Section Oceanography, Hamburg University, 22767, Hamburg, Germany
| | - Nicholas Smirnoff
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building University of Exeter, Exeter, EX4 4QD, UK
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.,School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Gabriel Yvon-Durocher
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
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40
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Green Biological Synthesis of Nanoparticles and Their Biomedical Applications. NANOTECHNOLOGY IN THE LIFE SCIENCES 2020. [DOI: 10.1007/978-3-030-44176-0_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hasegawa H, Tsurumaki T, Kobayashi I, Imamura S, Tanaka K. Identification and analysis of a principal sigma factor interacting protein SinA, essential for growth at high temperatures in a cyanobacterium Synechococcus elongatus PCC 7942. J GEN APPL MICROBIOL 2020; 66:66-72. [DOI: 10.2323/jgam.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hazuki Hasegawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Tatsuhiro Tsurumaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Ikki Kobayashi
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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42
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Khalid M. Nanotechnology and chemical engineering as a tool to bioprocess microalgae for its applications in therapeutics and bioresource management. Crit Rev Biotechnol 2019; 40:46-63. [DOI: 10.1080/07388551.2019.1680599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Muneeba Khalid
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
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43
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Zheng F, Colasante C, Voncken F. Characterisation of a mitochondrial iron transporter of the pathogen Trypanosoma brucei. Mol Biochem Parasitol 2019; 233:111221. [DOI: 10.1016/j.molbiopara.2019.111221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022]
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44
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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Yang Y, Zhang Y, Chen Y, Gul J, Zhang J, Liu Q, Chen Q. Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species. PeerJ 2019; 7:e7713. [PMID: 31579601 PMCID: PMC6756139 DOI: 10.7717/peerj.7713] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022] Open
Abstract
As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.
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Affiliation(s)
- Yong Yang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ying Zhang
- Life Sciences and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Juma Gul
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jingwen Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qiang Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qing Chen
- Bawangling National Nature Reserve, Changjiang, Hainan Province, China
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46
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Oborník M. Endosymbiotic Evolution of Algae, Secondary Heterotrophy and Parasitism. Biomolecules 2019; 9:E266. [PMID: 31288476 PMCID: PMC6681372 DOI: 10.3390/biom9070266] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/01/2019] [Accepted: 07/05/2019] [Indexed: 12/15/2022] Open
Abstract
Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the machinery of the photosynthetic electron transport chain is quite complex and is unlikely to have evolved multiple independent times, it is believed that this machinery has been transferred to diverse eukaryotic organisms by endosymbiotic events involving a eukaryotic host and a phototrophic endosymbiont. Thus, photoautotrophy, as a benefit, is transmitted through the evolution of plastids. However, many eukaryotes became secondarily heterotrophic, reverting to hetero-osmotrophy, phagotrophy, or parasitism. Here, I briefly review the constructive evolution of plastid endosymbioses and the consequential switch to reductive evolution involving losses of photosynthesis and plastids and the evolution of parasitism from a photosynthetic ancestor.
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Affiliation(s)
- Miroslav Oborník
- Institute of Parasitology, Biology Centre CAS, 37005 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic.
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47
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Hossain N, Mahlia TMI. Progress in physicochemical parameters of microalgae cultivation for biofuel production. Crit Rev Biotechnol 2019; 39:835-859. [DOI: 10.1080/07388551.2019.1624945] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Nazia Hossain
- Department of Civil and Infrastructure Engineering, School of Engineering, RMIT University, Melbourne, VIC, Australia
| | - Teuku Meurah Indra Mahlia
- School of Information, Systems and Modelling, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, Australia
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Antoshvili M, Caspy I, Hippler M, Nelson N. Structure and function of photosystem I in Cyanidioschyzon merolae. PHOTOSYNTHESIS RESEARCH 2019; 139:499-508. [PMID: 29582227 DOI: 10.1007/s11120-018-0501-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/21/2018] [Indexed: 05/19/2023]
Abstract
The evolution of photosynthesis from primitive photosynthetic bacteria to higher plants has been driven by the need to adapt to a wide range of environmental conditions. The red alga Cyanidioschyzon merolae is a primitive organism, which is capable of performing photosynthesis in extreme acidic and hot environments. The study of its photosynthetic machinery may provide new insight on the evolutionary path of photosynthesis and on light harvesting and its regulation in eukaryotes. With that aim, the structural and functional properties of the PSI complex were investigated by biochemical characterization, mass spectrometry, and X-ray crystallography. PSI was purified from cells grown at 25 and 42 °C, crystallized and its crystal structure was solved at 4 Å resolution. The structure of C. merolae reveals a core complex with a crescent-shaped structure, formed by antenna proteins. In addition, the structural model shows the position of PsaO and PsaM. PsaG and PsaH are present in plant complex and are missing from the C. merolae model as expected. This paper sheds new light onto the evolution of photosynthesis, which gives a strong indication for the chimerical properties of red algae PSI. The subunit composition of the PSI core from C. merolae and its associated light-harvesting antennae suggests that it is an evolutionary and functional intermediate between cyanobacteria and plants.
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Affiliation(s)
- Maya Antoshvili
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ido Caspy
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, 48143, Münster, Germany
| | - Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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Decelle J, Stryhanyuk H, Gallet B, Veronesi G, Schmidt M, Balzano S, Marro S, Uwizeye C, Jouneau PH, Lupette J, Jouhet J, Maréchal E, Schwab Y, Schieber NL, Tucoulou R, Richnow H, Finazzi G, Musat N. Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis. Curr Biol 2019; 29:968-978.e4. [PMID: 30827917 DOI: 10.1016/j.cub.2019.01.073] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/03/2018] [Accepted: 01/28/2019] [Indexed: 01/12/2023]
Abstract
Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.
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Affiliation(s)
- Johan Decelle
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany.
| | - Hryhoriy Stryhanyuk
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Benoit Gallet
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Giulia Veronesi
- Laboratoire de Chimie et Biologie des Métaux UMR 5249, Université Grenoble Alpes, CNRS, CEA, 17 Avenue des Martyrs, 38054 Grenoble, France; ESRF, The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Sergio Balzano
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, the Netherlands
| | - Sophie Marro
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche UMR7093, Observatoire Océanologique, 06230 Villefranche-sur-Mer, France
| | - Clarisse Uwizeye
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Pierre-Henri Jouneau
- Institut Nanosciences et Cryogénie, Université Grenoble Alpes, CEA, 38054 Grenoble, France
| | - Josselin Lupette
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Juliette Jouhet
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Eric Maréchal
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Rémi Tucoulou
- ESRF, The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Hans Richnow
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
| | - Giovanni Finazzi
- Cell & Plant Physiology Laboratory, University of Grenoble Alpes, CNRS, CEA, INRA, 38054 Grenoble Cedex 9, France
| | - Niculina Musat
- Helmholtz Centre for Environmental Research - UFZ, Department of Isotope Biogeochemistry, 04318 Leipzig, Germany
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50
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Li-Beisson Y, Thelen JJ, Fedosejevs E, Harwood JL. The lipid biochemistry of eukaryotic algae. Prog Lipid Res 2019; 74:31-68. [PMID: 30703388 DOI: 10.1016/j.plipres.2019.01.003] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 02/06/2023]
Abstract
Algal lipid metabolism fascinates both scientists and entrepreneurs due to the large diversity of fatty acyl structures that algae produce. Algae have therefore long been studied as sources of genes for novel fatty acids; and, due to their superior biomass productivity, algae are also considered a potential feedstock for biofuels. However, a major issue in a commercially viable "algal oil-to-biofuel" industry is the high production cost, because most algal species only produce large amounts of oils after being exposed to stress conditions. Recent studies have therefore focused on the identification of factors involved in TAG metabolism, on the subcellular organization of lipid pathways, and on interactions between organelles. This has been accompanied by the development of genetic/genomic and synthetic biological tools not only for the reference green alga Chlamydomonas reinhardtii but also for Nannochloropsis spp. and Phaeodactylum tricornutum. Advances in our understanding of enzymes and regulatory proteins of acyl lipid biosynthesis and turnover are described herein with a focus on carbon and energetic aspects. We also summarize how changes in environmental factors can impact lipid metabolism and describe present and potential industrial uses of algal lipids.
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Affiliation(s)
- Yonghua Li-Beisson
- Aix-Marseille Univ, CEA, CNRS, BIAM, UMR7265, CEA Cadarache, Saint-Paul-lez Durance F-13108, France.
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, United States.
| | - Eric Fedosejevs
- Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, United States.
| | - John L Harwood
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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