1
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Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW. Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae. Genome Biol Evol 2021; 13:6402010. [PMID: 34665222 PMCID: PMC8570151 DOI: 10.1093/gbe/evab233] [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] [Accepted: 10/09/2021] [Indexed: 11/12/2022] Open
Abstract
Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | | | - Xia Xu
- Boyce Thompson Institute, Ithaca, New York, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, USA.,Plant Biology Section, Cornell University, USA
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2
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Kuo RC, Zhang H, Stuart JD, Provatas AA, Hannick L, Lin S. Abundant synthesis of long-chain polyunsaturated fatty acids in Eutreptiella sp. (Euglenozoa) revealed by chromatographic and transcriptomic analyses. JOURNAL OF PHYCOLOGY 2021; 57:577-591. [PMID: 33191494 DOI: 10.1111/jpy.13105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/19/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
Algal lipids are important molecules to store energy in algae and transfer energy in the marine food chain, and are potential materials for high value nutraceuticals (e.g., omega-3 fatty acids) or biofuel production. However, how lipid biosynthesis is regulated is not well understood in many species including Eutreptiella from the phylum of Euglenozoa. Here, we characterized the fatty acid (FA) profile of an Eutreptiella species isolated from Long Island Sound, USA, using gas chromatography-tandem mass spectrometry (GC/MS/MS) and investigated their biosynthesis pathways by transcriptome sequencing. We discovered 24 types of FAs including a relatively high proportion of long-chain unsaturated FAs. The abundances of C16, C18, and saturated FAs decreased when phosphate in the culture medium was depleted. Among the 24 FAs, docosahexaenoic acid (C22:6∆4,7,10,13,16,19 ) was most abundant, suggesting that Eutreptiella sp. preferentially invests in the synthesis of long-chain polyunsaturated fatty acids (LC-PFAs). Further transcriptomic analysis revealed that Eutreptiella sp. likely synthesizes LC-PFAs via ∆8 pathway and uses type I and II fatty acid synthases. Using RT-qPCR, we found that some of the lipid synthesis genes, such as β-ketoacyl-ACP reductase, fatty acid desaturase, acetyl-CoA carboxylase, acyl carrier protein, ∆8 desaturase, and Acyl-ACP thioesterase, were more actively expressed during light period, and two carbon fixation genes were up-regulated in the high-lipid illuminated cultures, suggesting a linkage between photosynthesis and lipid production. The lipid profile renders Eutreptiella sp. a nutritional prey and valuable source for nutraceuticals, and the biosynthesis pathway documented here will be useful for future research and applications.
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Affiliation(s)
- Rita C Kuo
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - James D Stuart
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Anthony A Provatas
- Center of Environmental Sciences and Engineering, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Linda Hannick
- SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Rockville, Maryland, 20852, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
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3
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Grigoriev IV, Hayes RD, Calhoun S, Kamel B, Wang A, Ahrendt S, Dusheyko S, Nikitin R, Mondo SJ, Salamov A, Shabalov I, Kuo A. PhycoCosm, a comparative algal genomics resource. Nucleic Acids Res 2021; 49:D1004-D1011. [PMID: 33104790 PMCID: PMC7779022 DOI: 10.1093/nar/gkaa898] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.
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Affiliation(s)
- Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard D Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bishoy Kamel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alice Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Dusheyko
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Roman Nikitin
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor Shabalov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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Gumińska N, Zakryś B, Milanowski R. A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids. J Mol Biol 2020; 433:166758. [PMID: 33316270 DOI: 10.1016/j.jmb.2020.166758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringing together intron ends and placing adjacent exons in proximity. To date, little is known about the mechanism of their excision (e.g. whether it involves the spliceosome or not). The tubA gene of Euglena gracilis harbors three conventional and three nonconventional introns. While the conventional introns are excised as lariats, nonconventional introns are present in the cell solely as circular RNAs with full-length ends. Based on this discovery as well as on previous observations indicating that nonconventional introns are observed frequently at unique positions of genes, we suggest that this new type of intronic circRNA might play a role in intron mobility.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Center, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Center, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Center, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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5
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Novák Vanclová AMG, Zoltner M, Kelly S, Soukal P, Záhonová K, Füssy Z, Ebenezer TE, Lacová Dobáková E, Eliáš M, Lukeš J, Field MC, Hampl V. Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid. THE NEW PHYTOLOGIST 2020; 225:1578-1592. [PMID: 31580486 DOI: 10.1111/nph.16237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 05/20/2023]
Abstract
Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.
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Affiliation(s)
| | - Martin Zoltner
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Petr Soukal
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
| | - Kristína Záhonová
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Eva Lacová Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Marek Eliáš
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czechia
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Vladimír Hampl
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
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6
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Mars Brisbin M, Mitarai S. Differential Gene Expression Supports a Resource-Intensive, Defensive Role for Colony Production in the Bloom-Forming Haptophyte, Phaeocystis globosa. J Eukaryot Microbiol 2019; 66:788-801. [PMID: 30860641 PMCID: PMC6766888 DOI: 10.1111/jeu.12727] [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: 11/06/2018] [Revised: 01/23/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Phaeocystis globosa forms dense, monospecific blooms in temperate, northern waters. Blooms are usually dominated by the colonial morphotype—nonflagellated cells embedded in a secreted mucilaginous mass. Colonial Phaeocystis blooms significantly affect food‐web structure and function and negatively impact fisheries and aquaculture, but factors regulating colony formation remain enigmatic. Destructive P. globosa blooms have been reported in tropical and subtropical regions more recently and warm‐water blooms could become more common with continued climate change and coastal eutrophication. We therefore assessed genetic pathways associated with colony formation by investigating differential gene expression between colonial and solitary cells of a warm‐water P. globosa strain. Our results illustrate a transcriptional shift in colonial cells with most of the differentially expressed genes downregulated, supporting a reallocation of resources associated with forming and maintaining colonies. Dimethylsulfide and acrylate production and pathogen interaction pathways were upregulated in colonial cells, suggesting a defensive role for producing colonies. We identify several protein kinase signaling pathways that may influence the transition between morphotypes, providing targets for future research into factors affecting colony formation. This study provides novel insights into genetic mechanisms involved in Phaeocystis colony formation and provides new evidence supporting a defensive role for Phaeocystis colonies.
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Affiliation(s)
- Margaret Mars Brisbin
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-Son, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-Son, Japan
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7
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Boroni M, Sammeth M, Gava SG, Jorge NAN, Macedo AM, Machado CR, Mourão MM, Franco GR. Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. Sci Rep 2018; 8:3877. [PMID: 29497070 PMCID: PMC5832876 DOI: 10.1038/s41598-018-22093-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 02/12/2018] [Indexed: 11/09/2022] Open
Abstract
Spliced leader dependent trans-splicing (SLTS) has been described as an important RNA regulatory process that occurs in different organisms, including the trematode Schistosoma mansoni. We identified more than seven thousand putative SLTS sites in the parasite, comprising genes with a wide spectrum of functional classes, which underlines the SLTS as a ubiquitous mechanism in the parasite. Also, SLTS gene expression levels span several orders of magnitude, showing that SLTS frequency is not determined by the expression level of the target gene, but by the presence of particular gene features facilitating or hindering the trans-splicing mechanism. Our in-depth investigation of SLTS events demonstrates widespread alternative trans-splicing (ATS) acceptor sites occurring in different regions along the entire gene body, highlighting another important role of SLTS generating alternative RNA isoforms in the parasite, besides the polycistron resolution. Particularly for introns where SLTS directly competes for the same acceptor substrate with cis-splicing, we identified for the first time additional and important features that might determine the type of splicing. Our study substantially extends the current knowledge of RNA processing by SLTS in S. mansoni, and provide basis for future studies on the trans-splicing mechanism in other eukaryotes.
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Affiliation(s)
- Mariana Boroni
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Michael Sammeth
- Bioinformatics in Transcriptomics and Functional Genomics (BITFUN), Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil
| | - Sandra Grossi Gava
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil
| | - Natasha Andressa Nogueira Jorge
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Andréa Mara Macedo
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Carlos Renato Machado
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil.
| | - Glória Regina Franco
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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8
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Zhuang Y, Yang F, Xu D, Chen H, Zhang H, Liu G. Spliced leader-based analyses reveal the effects of polycyclic aromatic hydrocarbons on gene expression in the copepod Pseudodiaptomus poplesia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 183:114-126. [PMID: 28043022 DOI: 10.1016/j.aquatox.2016.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/11/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a group of toxic and carcinogenic pollutants that can adversely affect the development, growth and reproduction of marine organisms including copepods. However, knowledge on the molecular mechanisms regulating the response to PAH exposure in marine planktonic copepods is limited. In this study, we investigated the survival and gene expression of the calanoid copepod Pseudodiaptomus poplesia upon exposure to two PAHs, 1, 2-dimethylnaphthalene (1, 2-NAPH) and pyrene. Acute toxicity responses resulted in 96-h LC50 of 788.98μgL-1 and 54.68μgL-1 for 1, 2-NAPH and pyrene, respectively. Using the recently discovered copepod spliced leader as a primer, we constructed full-length cDNA libraries from copepods exposed to sublethal concentrations and revealed 289 unique genes of diverse functions, including stress response genes and novel genes previously undocumented for this species. Eighty-three gene families were specifically expressed in PAH exposure libraries. We further analyzed the expression of seven target genes by reverse transcription-quantitative PCR in a time-course test with three sublethal concentrations. These target genes have primary roles in detoxification, oxidative defense, and signal transduction, and include different forms of glutathione S-transferase (GST), glutathione peroxidases (GPX), peroxiredoxin (PRDX), methylmalonate-semialdehyde dehydrogenase (MSDH) and ras-related C3 botulinum toxin substrate (RAC1). Expression stability of seven candidate reference genes were evaluated and the two most stable ones (RPL15 and RPS20 for 1, 2-NAPH exposure, RPL15 and EF1D for pyrene exposure) were used to normalize the expression levels of the target genes. Significant upregulation was detected in GST-T, GST-DE, GPX4, PRDX6 and RAC1 upon 1, 2-NAPH exposure, and GST-DE and MSDH upon pyrene exposure. These results indicated that the oxidative stress was induced and that signal transduction might be affected by PAH exposure in P. poplesia. However, gene upregulation was followed by a reduction in expression level towards 96h, indicating a threshold value of exposure time that leads to depressed gene expression. Prolonged exposure may cause dysfunction of detoxification and antioxidant machinery in P. poplesia. The transcriptional responses of GST-T, GPX2 and GPX4 upon pyrene exposure were minimal. Our results reveal the different sensitivity of P. poplesia to two PAHs at both the individual and transcriptional levels. As the first attempt, this study proved that copepod spliced leader is useful for obtaining full-length cDNA in P. poplesia exposed to PAHs and provided a valuable gene resource for this non-model species. This approach can be applied to other calanoid copepods exposed to various stressors, particularly under field conditions.
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Affiliation(s)
- Yunyun Zhuang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China
| | - Feifei Yang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China; Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Donghui Xu
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China
| | - Hongju Chen
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China
| | - Huan Zhang
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Guangxing Liu
- Key Laboratory of Marine Environment and Ecology, Ministry of Education,Ocean University of China, Qingdao 266100, China.
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9
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Smith DR, Keeling PJ. Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits. Annu Rev Microbiol 2016; 70:161-78. [PMID: 27359218 DOI: 10.1146/annurev-micro-102215-095448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The DNA double helix has been called one of life's most elegant structures, largely because of its universality, simplicity, and symmetry. The expression of information encoded within DNA, however, can be far from simple or symmetric and is sometimes surprisingly variable, convoluted, and wantonly inefficient. Although exceptions to the rules exist in certain model systems, the true extent to which life has stretched the limits of gene expression is made clear by nonmodel systems, particularly protists (microbial eukaryotes). The nuclear and organelle genomes of protists are subject to the most tangled forms of gene expression yet identified. The complicated and extravagant picture of the underlying genetics of eukaryotic microbial life changes how we think about the flow of genetic information and the evolutionary processes shaping it. Here, we discuss the origins, diversity, and growing interest in noncanonical protist gene expression and its relationship to genomic architecture.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7;
| | - Patrick J Keeling
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4;
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10
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Yang F, Xu D, Zhuang Y, Yi X, Huang Y, Chen H, Lin S, Campbell DA, Sturm NR, Liu G, Zhang H. Spliced leader RNA trans-splicing discovered in copepods. Sci Rep 2015; 5:17411. [PMID: 26621068 PMCID: PMC4664967 DOI: 10.1038/srep17411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/29/2015] [Indexed: 11/13/2022] Open
Abstract
Copepods are one of the most abundant metazoans in the marine ecosystem, constituting a critical link in aquatic food webs and contributing significantly to the global carbon budget, yet molecular mechanisms of their gene expression are not well understood. Here we report the detection of spliced leader (SL) trans-splicing in calanoid copepods. We have examined nine species of wild-caught copepods from Jiaozhou Bay, China that represent the major families of the calanoids. All these species contained a common 46-nt SL (CopepodSL). We further determined the size of CopepodSL precursor RNA (slRNA; 108-158 nt) through genomic analysis and 3′-RACE technique, which was confirmed by RNA blot analysis. Structure modeling showed that the copepod slRNA folded into typical slRNA secondary structures. Using a CopepodSL-based primer set, we selectively enriched and sequenced copepod full-length cDNAs, which led to the characterization of copepod transcripts and the cataloging of the complete set of 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for a single copepod species. We uncovered the SL trans-splicing in copepod natural populations, and demonstrated that CopepodSL was a sensitive and specific tool for copepod transcriptomic studies at both the individual and population levels and that it would be useful for metatranscriptomic analysis of copepods.
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Affiliation(s)
- Feifei Yang
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Donghui Xu
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yunyun Zhuang
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Xiaoyan Yi
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yousong Huang
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Hongju Chen
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA
| | - David A Campbell
- Department of Microbiology, Immunology &Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Nancy R Sturm
- Department of Microbiology, Immunology &Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Guangxing Liu
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Huan Zhang
- The Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.,Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA
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Guo Z, Zhang H, Lin S. Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina. PLoS One 2014; 9:e114941. [PMID: 25506945 PMCID: PMC4266641 DOI: 10.1371/journal.pone.0114941] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 11/16/2014] [Indexed: 11/18/2022] Open
Abstract
The discovery of microbial rhodopsins in marine proteobacteria changed the dogma that photosynthesis is the only pathway to use the solar energy for biological utilization in the marine environment. Although homologs of these rhodopsins have been identified in dinoflagellates, the diversity of the encoding genes and their physiological roles remain unexplored. As an initial step toward addressing the gap, we conducted high-throughput transcriptome sequencing on Oxyrrhis marina to retrieve rhodopsin transcripts, rapid amplification of cDNA ends to isolate full-length cDNAs of dominant representatives, and quantitative reverse-transcription PCR to investigate their expression under varying conditions. Our phylogenetic analyses showed that O. marina contained both the proton-pumping type (PR) and sensory type (SR) rhodopsins, and the transcriptome data showed that the PR type dominated over the SR type. We compared rhodopsin gene expression for cultures kept under light: dark cycle and continuous darkness in a time course of 24 days without feeding. Although both types of rhodopsin were expressed under the two conditions, the expression levels of PR were much higher than SR, consistent with the transcriptomic data. Furthermore, relative to cultures kept in the dark, rhodopsin expression levels and cell survival rate were both higher in cultures grown in the light. This is the first report of light-dependent promotion of starvation survival and concomitant promotion of PR expression in a eukaryote. While direct evidence needs to come from functional test on rhodopsins in vitro or gene knockout/knockdown experiments, our results suggest that the proton-pumping rhodopsin might be responsible for the light-enhanced survival of O. marina, as previously demonstrated in bacteria.
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Affiliation(s)
- Zhiling Guo
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, United States of America
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, United States of America
- Department of Environmental Science, Ocean University of China, Qingdao, Shandong 266100, China
- * E-mail: (SL); (HZ)
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, United States of America
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian 361005, China
- * E-mail: (SL); (HZ)
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Santoferrara LF, Guida S, Zhang H, McManus GB. De novo transcriptomes of a mixotrophic and a heterotrophic ciliate from marine plankton. PLoS One 2014; 9:e101418. [PMID: 24983246 PMCID: PMC4077812 DOI: 10.1371/journal.pone.0101418] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/06/2014] [Indexed: 11/19/2022] Open
Abstract
Studying non-model organisms is crucial in the context of the current development of genomics and transcriptomics for both physiological experimentation and environmental characterization. We investigated the transcriptomes of two marine planktonic ciliates, the mixotrophic oligotrich Strombidium rassoulzadegani and the heterotrophic choreotrich Strombidinopsis sp., and their respective algal food using Illumina RNAseq. Our aim was to characterize the transcriptomes of these contrasting ciliates and to identify genes potentially involved in mixotrophy. We detected approximately 10,000 and 7,600 amino acid sequences for S. rassoulzadegani and Strombidinopsis sp., respectively. About half of these transcripts had significant BLASTP hits (E-value <10−6) against previously-characterized sequences, mostly from the model ciliate Oxytricha trifallax. Transcriptomes from both the mixotroph and the heterotroph species provided similar annotations for GO terms and KEGG pathways. Most of the identified genes were related to housekeeping activity and pathways such as the metabolism of carbohydrates, lipids, amino acids, nucleotides, and vitamins. Although S. rassoulzadegani can keep and use chloroplasts from its prey, we did not find genes clearly linked to chloroplast maintenance and functioning in the transcriptome of this ciliate. While chloroplasts are known sources of reactive oxygen species (ROS), we found the same complement of antioxidant pathways in both ciliates, except for one enzyme possibly linked to ascorbic acid recycling found exclusively in the mixotroph. Contrary to our expectations, we did not find qualitative differences in genes potentially related to mixotrophy. However, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in oligotrichs and choreotrichs and experimental investigation of the costs and benefits of mixotrophy.
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Affiliation(s)
- Luciana F. Santoferrara
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- * E-mail:
| | - Stephanie Guida
- The National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - George B. McManus
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
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Zhang H, Campbell DA, Sturm NR, Rosenblad MA, Dungan CF, Lin S. Signal recognition particle RNA in dinoflagellates and the Perkinsid Perkinsus marinus. Protist 2013; 164:748-61. [PMID: 23994724 DOI: 10.1016/j.protis.2013.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 11/16/2022]
Abstract
In dinoflagellates and perkinsids, the molecular structure of the protein translocating machinery is unclear. Here, we identified several types of full-length signal recognition particle (SRP) RNA genes from Karenia brevis (dinoflagellate) and Perkinsus marinus (perkinsid). We also identified the four SRP S-domain proteins, but not the two Alu domain proteins, from P. marinus and several dinoflagellates. We mapped both ends of SRP RNA transcripts from K. brevis and P. marinus, and obtained the 3' end from four other dinoflagellates. The lengths of SRP RNA are predicted to be ∼260-300 nt in dinoflagellates and 280-285 nt in P. marinus. Although these SRP RNA sequences are substantially variable, the predicted structures are similar. The genomic organization of the SRP RNA gene differs among species. In K. brevis, this gene is located downstream of the spliced leader (SL) RNA, either as SL RNA-SRP RNA-tRNA gene tandem repeats, or within a SL RNA-SRP RNA-tRNA-U6-5S rRNA gene cluster. In other dinoflagellates, SRP RNA does not cluster with SL RNA or 5S rRNA genes. The majority of P. marinus SRP RNA genes array as tandem repeats without the above-mentioned small RNA genes. Our results capture a snapshot of a potentially complex evolutionary history of SRP RNA in alveolates.
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Affiliation(s)
- Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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Tandem repeats, high copy number and remarkable diel expression rhythm of form II RuBisCO in Prorocentrum donghaiense (Dinophyceae). PLoS One 2013; 8:e71232. [PMID: 23976999 PMCID: PMC3747160 DOI: 10.1371/journal.pone.0071232] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/27/2013] [Indexed: 11/24/2022] Open
Abstract
Gene structure and expression regulation of form II RuBisCO (rbcII) in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc) and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU); the 5′ region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU) are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR) we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1) undergoes duplication or sequence purification within species, 2) is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3) is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates.
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