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Matsuda R, Handayani ML, Sasaki H, Takechi K, Takano H, Takio S. Production of indoleacetic acid by strains of the epiphytic bacteria Neptunomonas spp. isolated from the red alga Pyropia yezoensis and the seagrass Zostera marina. Arch Microbiol 2017; 200:255-265. [DOI: 10.1007/s00203-017-1439-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/24/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023]
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Kakinuma M, Nakamoto C, Kishi K, Coury DA, Amano H. Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta). MARINE ENVIRONMENTAL RESEARCH 2017; 128:76-87. [PMID: 27581686 DOI: 10.1016/j.marenvres.2016.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 05/25/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status.
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Affiliation(s)
- Makoto Kakinuma
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
| | - Chika Nakamoto
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Kazuki Kishi
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Daniel A Coury
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
| | - Hideomi Amano
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
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Im S, Lee HN, Jung HS, Yang S, Park EJ, Hwang MS, Jeong WJ, Choi DW. Transcriptome-Based Identification of the Desiccation Response Genes in Marine Red Algae Pyropia tenera (Rhodophyta) and Enhancement of Abiotic Stress Tolerance by PtDRG2 in Chlamydomonas. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:232-245. [PMID: 28421378 DOI: 10.1007/s10126-017-9744-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
Pyropia tenera (Kjellman) are marine red algae that grow in the intertidal zone and lose more than 90% of water during hibernal low tides every day. In order to identify the desiccation response gene (DRG) in P. tenera, we generated 1,444,210 transcriptome sequences using the 454-FLX platform from the gametophyte under control and desiccation conditions. De novo assembly of the transcriptome reads generated 13,170 contigs, covering about 12 Mbp. We selected 1160 differentially expressed genes (DEGs) in response to desiccation stress based on reads per kilobase per million reads (RPKM) expression values. As shown in green higher plants, DEGs under desiccation are composed of two groups of genes for gene regulation networks and functional proteins for carbohydrate metabolism, membrane perturbation, compatible solutes, and specific proteins similar to higher plants. DEGs that show no significant homology with known sequences in public databases were selected as DRGs in P. tenera. PtDRG2 encodes a novel polypeptide of 159 amino acid residues locating chloroplast. When PtDRG2 was overexpressed in Chlamydomonas, the PtDRG2 confer mannitol and salt tolerance in transgenic cells. These results suggest that Pyropia may possess novel genes that differ from green plants, although the desiccation tolerance mechanism in red algae is similar to those of higher green plants. These transcriptome sequences will facilitate future studies to understand the common processes and novel mechanisms involved in desiccation stress tolerance in red algae.
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Affiliation(s)
- Sungoh Im
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Ha-Nul Lee
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Hyun Shin Jung
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Sunghwan Yang
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Eun-Jeong Park
- Seaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 58746, South Korea
| | - Mi Sook Hwang
- Seaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 58746, South Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Dong-Woog Choi
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea.
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Inoue A, Mashino C, Uji T, Saga N, Mikami K, Ojima T. Characterization of an Eukaryotic PL-7 Alginate Lyase in the Marine Red Alga Pyropia yezoensis. ACTA ACUST UNITED AC 2015; 4:240-248. [PMID: 28553576 PMCID: PMC5436490 DOI: 10.2174/2211550104666150915210434] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alginate lyases belonging to polysaccharide lyase family-7 (PL-7) are the most well studied on their structures and functions among whole alginate lyases. However, all characterized PL-7 alginate lyases are from prokaryotic bacteria cells. Here we report the first identification of eukaryotic PL-7 alginate lyase from marine red alga Pyropia yezoensis. METHODS The cDNA encoding an alginate lyase PyAly was cloned and was used for the construction of recombinant PyAly (rPyAly) expression system in Escherichia coli. Purified rPyAly was assayed to identify its enzymatic properties. Its expression pattern in P. yessoensis was also investigated. RESULTS PyAly is likely a secreted protein consisting of an N-terminal signal peptide of 25 residues and a catalytic domain of 216 residues. The amino-acid sequence of the catalytic domain showed 19-29% identities to those of bacterial characterized alginate lyases classified into family PL-7. Recombinant PyAly protein, rPyAly, which was produced with E. coli BL21(DE3) by cold-inducible expression system, drastically decreased the viscosity of alginate solution in the early stage of reaction. The most preferable substrate for rPyAly was the poly(M) of alginate with an optimal temperature and pH at 35oC and 8.0, respectively. After reaction, unsaturated tri- and tetra-saccharides were produced from poly(M) as major end products. These enzymatic properties indicated that PyAly is an endolytic alginate lyase belonging to PL-7. Moreover, we found that the PyAly gene is split into 4 exons with 3 introns. PyAly was also specifically expressed in the gametophytic haplopid stage. CONCLUSION This study demonstrates that PyAly in marine red alga P. yezoensis is a novel PL-7 alginate lyase with an endolytic manner. PyAly is a gametophyte-specifically expressed protein and its structural gene is composed of four exons and three introns. Thus, PyAly is the first enzymatically characterized eukaryotic PL-7 alginate lyase.
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Affiliation(s)
- Akira Inoue
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Chieco Mashino
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Toshiki Uji
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Naotsune Saga
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Koji Mikami
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Takao Ojima
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
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Qiu H, Price DC, Yang EC, Yoon HS, Bhattacharya D. Evidence of ancient genome reduction in red algae (Rhodophyta). JOURNAL OF PHYCOLOGY 2015; 51:624-36. [PMID: 26986787 DOI: 10.1111/jpy.12294] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/30/2015] [Indexed: 05/27/2023]
Abstract
Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiotic or parasitic lifestyle or adaptation to an extreme or oligotrophic environment. We gathered genome and transcriptome data from a total of 14 red algal genera that represent the major branches of this phylum to study genome evolution in Rhodophyta. Analysis of orthologous gene gains and losses identifies two putative major phases of genome reduction: (i) in the stem lineage leading to all red algae resulting in the loss of major functions such as flagellae and basal bodies, the glycosyl-phosphatidylinositol anchor biosynthesis pathway, and the autophagy regulation pathway; and (ii) in the common ancestor of the extremophilic Cyanidiophytina. Red algal genomes are also characterized by the recruitment of hundreds of bacterial genes through horizontal gene transfer that have taken on multiple functions in shared pathways and have replaced eukaryotic gene homologs. Our results suggest that Rhodophyta may trace their origin to a gene depauperate ancestor. Unlike plants, it appears that a limited gene inventory is sufficient to support the diversification of a major eukaryote lineage that possesses sophisticated multicellular reproductive structures and an elaborate triphasic sexual cycle.
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Affiliation(s)
- Huan Qiu
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Dana C Price
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Sciences & Technology, 787 Haeanro, Ansan, 426-744, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
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Matsuda R, Ozgur R, Higashi Y, Takechi K, Takano H, Takio S. Preferential expression of a bromoperoxidase in sporophytes of a red alga, Pyropia yezoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015; 17:199-210. [PMID: 25407492 DOI: 10.1007/s10126-014-9608-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
A 2,158 bp cDNA (PyBPO1) encoding a bromoperoxidase (BPO) of 625 amino acids was isolated from Pyropia yezoensis. Phylogenetic analysis using amino acid sequences of BPOs suggested that P. yezoensis and cyanobacteria were grouped in the same clade and separated from brown algae. Genomic Southern blot analysis suggested that PyBPO1 existed as a single copy per haploid genome. RT-PCR revealed that PyBPO1 was actively expressed in filamentous sporophytes but repressed in leafy gametophytes under normal growth conditions. High expression levels of PyBPO1 in sporophytes were observed when sporophytes were grown under gametophyte conditions, suggesting that preferential expression of PyBPO1 occurs during the sporophyte phase. BPO activity of cell-free extracts from sporophytes and gametophytes was examined by activity staining on native PAGE gel using o-dianisidine. One activity band was detected in sporophyte sample, but not in gametophyte sample. In addition, we found that bromide and iodide were effective substrate, but chloride was not. BPO activity was observed-likely in chloroplasts-when sporophyte cells were incubated with o-dianisidine and hydrogen peroxide. Cellular BPO staining showed the same halogen preference identified by in-gel BPO staining. Based on GS-MS analysis, bromoform was detected in medium containing sporophytes. Bromoform was not detected under dark culture conditions but was detected in the culture exposed to low light intensity (5 μmol m(-2) s(-1)) and increased under a moderate light intensity (30 μmol m(-2) s(-1)).
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Affiliation(s)
- Ryuya Matsuda
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto, 860-8555, Japan
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Ho CL. Phylogeny of Algal Sequences Encoding Carbohydrate Sulfotransferases, Formylglycine-Dependent Sulfatases, and Putative Sulfatase Modifying Factors. FRONTIERS IN PLANT SCIENCE 2015; 6:1057. [PMID: 26635861 PMCID: PMC4659905 DOI: 10.3389/fpls.2015.01057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/13/2015] [Indexed: 05/07/2023]
Abstract
Many algae are rich sources of sulfated polysaccharides with biological activities. The physicochemical/rheological properties and biological activities of sulfated polysaccharides are affected by the pattern and number of sulfate moieties. Sulfation of carbohydrates is catalyzed by carbohydrate sulfotransferases (CHSTs) while modification of sulfate moieties on sulfated polysaccharides was presumably catalyzed by sulfatases including formylglycine-dependent sulfatases (FGly-SULFs). Post-translationally modification of Cys to FGly in FGly-SULFs by sulfatase modifiying factors (SUMFs) is necessary for the activity of this enzyme. The aims of this study are to mine for sequences encoding algal CHSTs, FGly-SULFs and putative SUMFs from the fully sequenced algal genomes and to infer their phylogenetic relationships to their well characterized counterparts from other organisms. Algal sequences encoding CHSTs, FGly-SULFs, SUMFs, and SUMF-like proteins were successfully identified from green and brown algae. However, red algal FGly-SULFs and SUMFs were not identified. In addition, a group of SUMF-like sequences with different gene structure and possibly different functions were identified for green, brown and red algae. The phylogeny of these putative genes contributes to the corpus of knowledge of an unexplored area. The analyses of these putative genes contribute toward future production of existing and new sulfated carbohydrate polymers through enzymatic synthesis and metabolic engineering.
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Choi YH, Yamaguchi K, Oda T, Nam TJ. Chemical and mass spectrometry characterization of the red alga Pyropia yezoensis chemoprotective protein (PYP): protective activity of the N-terminal fragment of PYP1 against acetaminophen-induced cell death in Chang liver cells. Int J Mol Med 2014; 35:271-6. [PMID: 25374159 DOI: 10.3892/ijmm.2014.1992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/31/2014] [Indexed: 11/06/2022] Open
Abstract
In the present study, the chemical structure and chemoprotective activity of Pyropia yezoensis protein (PYP) were investigated using sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, automated protein sequencing, matrix-assisted laser desorption/ionization-quadrupole ion trap-time-of-flight mass spectrometry and a chemoprotective assay using a synthetic peptide. The PYP fraction was demonstrated to contain two proteins: PYP1 (10 kDa, SDS-resistant dimer) and PYP2 (10 kDa). PYP1 is a novel protein showing sequence homology with the hypothetical function-unknown proteins of Chondrus crispus (Rhodophyta) and Emiliania huxleyi (Haptophyceae). PYP2 is a paralog of an extrinsic protein of photosystem II found in other Rhodophyta. The synthetic peptide PYP1 (1-20), corresponding to the N-terminal 20 residues of PYP1 (ALEGGKSSGGGEATRDPEPT), exhibits chemoprotective activity against acetaminophen-induced cell death in Chang liver cells, indicating that PYP1 is a chemoprotectant of the PYP fraction. A possible association between the structure of PYP and its chemoprotective activity is discussed.
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Affiliation(s)
- Youn Hee Choi
- Institute of Fisheries Sciences, Pukyong National University, Busan 619‑911, Republic of Korea
| | - Kenichi Yamaguchi
- Graduate School of Science and Technology, Nagasaki University, Nagasaki 852‑8521, Japan
| | - Tatsuya Oda
- Graduate School of Science and Technology, Nagasaki University, Nagasaki 852‑8521, Japan
| | - Taek Jeong Nam
- Institute of Fisheries Sciences, Pukyong National University, Busan 619‑911, Republic of Korea
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Kaneko K, Washio K, Umezawa T, Matsuda F, Morikawa M, Okino T. cDNA cloning and characterization of vanadium-dependent bromoperoxidases from the red alga Laurencia nipponica. Biosci Biotechnol Biochem 2014; 78:1310-9. [DOI: 10.1080/09168451.2014.918482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
The marine red alga genus Laurencia is one of the richest producers of unique brominated compounds in the marine environment. The cDNAs for two Laurencia nipponica vanadium-dependent bromoperoxidases (LnVBPO1 and LnVBPO2) were cloned and expressed in Escherichia coli. Enzyme assays of recombinant LnVBPO1 and LnVBPO2 using monochlorodimedone revealed that they were thermolabile but their Km values for Br− were significantly lower than other red algal VBPOs. The bromination reaction was also assessed using laurediol, the predicted natural precursor of the brominated ether laurencin. Laurediol, protected by trimethylsilyl at the enyne, was converted to deacetyllaurencin by the LnVBPOs, which was confirmed by tandem mass spectrometry. Native LnVBPO partially purified from algal bodies was active, suggesting that LnVBPO is functional in vivo. These results contributed to our knowledge of the biosynthesis of Laurencia brominated metabolites.
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Affiliation(s)
- Kensuke Kaneko
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Kenji Washio
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Taiki Umezawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Fuyuhiko Matsuda
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Tatsufumi Okino
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
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Uji T, Hirata R, Fukuda S, Mizuta H, Saga N. A codon-optimized bacterial antibiotic gene used as selection marker for stable nuclear transformation in the marine red alga Pyropia yezoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:251-255. [PMID: 24149658 PMCID: PMC3996358 DOI: 10.1007/s10126-013-9549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 09/17/2013] [Indexed: 06/02/2023]
Abstract
Marine macroalgae play an important role in marine coastal ecosystems and are widely used as sea vegetation foodstuffs and for industrial purposes. Therefore, there have been increased demands for useful species and varieties of these macroalgae. However, genetic transformation in macroalgae has not yet been established. We have developed a dominant selection marker for stable nuclear transformation in the red macroalga Pyropia yezoensis. We engineered the coding region of the aminoglycoside phosphotransferase gene aph7″ from Streptomyces hygroscopicus to adapt codon usage of the nuclear genes of P. yezoensis. We designated this codon-optimized aph7″ gene as PyAph7. After bombarding P. yezoensis cells with plasmids containing PyAph7 under the control of their endogenous promoter, 1.9 thalli (or individuals) of hygromycin-resistant strains were isolated from a 10-mm square piece of the bombarded thallus. These transformants were stably maintained throughout the asexual life cycle. Stable expression of PyAph7was verified using Southern blot analysis and genomic PCR and RT-PCR analyses. PyAph7 proved to be a new versatile tool for stable nuclear transformation in P. yezoensis.
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Affiliation(s)
- Toshiki Uji
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611 Japan
| | - Ryo Hirata
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611 Japan
| | - Satoru Fukuda
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611 Japan
| | - Hiroyuki Mizuta
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611 Japan
| | - Naotsune Saga
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611 Japan
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Zhang W, Sakai M, Lin X, Takechi K, Takano H, Takio S. Reverse Transcriptase-Like Sequences Related to Retrotransposon in a Red Alga,Porphyra yezoensis. Biosci Biotechnol Biochem 2014; 70:1999-2003. [PMID: 16926517 DOI: 10.1271/bbb.60118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Four DNA fragments encoding a reverse transcriptase (RT)-like gene related to that of long terminal repeat (LTR) retrotransposons were isolated from the red alga Porphyra yezoensis by genomic PCR. Southern blot analysis suggested that one clone exists as a single copy per genome. Its full-length cDNA (PyRE2A) contained RT/RNase H-like sequences, which are most closely related to those of the Volvox LTR retrotransposon, although two stop codons were present within the RT region. We did not find any sequence related to LTR retrotransposons other than RT/RNase H in RyRE2A. These results indicate that PyRE2A is a single RT/RNase H-like gene and a defective progenitor of LTR retrotransposons.
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Affiliation(s)
- Wenbo Zhang
- Graduate School of Science and Technology, Kumamoto University, Japan
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Misra N, Panda PK, Parida BK. Agrigenomics for microalgal biofuel production: an overview of various bioinformatics resources and recent studies to link OMICS to bioenergy and bioeconomy. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:537-49. [PMID: 24044362 DOI: 10.1089/omi.2013.0025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other "omic" approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of "omics" in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of "omic" approaches in the metabolic pathway studies for microalgal biofuel production.
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Affiliation(s)
- Namrata Misra
- 1 Academy of Scientific and Innovative Research, CSIR-Institute of Minerals and Materials Technology , Bhubaneswar, Odisha, India
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13
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Sturm S, Engelken J, Gruber A, Vugrinec S, G Kroth P, Adamska I, Lavaud J. A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids. BMC Evol Biol 2013; 13:159. [PMID: 23899289 PMCID: PMC3750529 DOI: 10.1186/1471-2148-13-159] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/22/2013] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Light, the driving force of photosynthesis, can be harmful when present in excess; therefore, any light harvesting system requires photoprotection. Members of the extended light-harvesting complex (LHC) protein superfamily are involved in light harvesting as well as in photoprotection and are found in the red and green plant lineages, with a complex distribution pattern of subfamilies in the different algal lineages. RESULTS Here, we demonstrate that the recently discovered "red lineage chlorophyll a/b-binding-like proteins" (RedCAPs) form a monophyletic family within this protein superfamily. The occurrence of RedCAPs was found to be restricted to the red algal lineage, including red algae (with primary plastids) as well as cryptophytes, haptophytes and heterokontophytes (with secondary plastids of red algal origin). Expression of a full-length RedCAP:GFP fusion construct in the diatom Phaeodactylum tricornutum confirmed the predicted plastid localisation of RedCAPs. Furthermore, we observed that similarly to the fucoxanthin chlorophyll a/c-binding light-harvesting antenna proteins also RedCAP transcripts in diatoms were regulated in a diurnal way at standard light conditions and strongly repressed at high light intensities. CONCLUSIONS The absence of RedCAPs from the green lineage implies that RedCAPs evolved in the red lineage after separation from the the green lineage. During the evolution of secondary plastids, RedCAP genes therefore must have been transferred from the nucleus of the endocytobiotic alga to the nucleus of the host cell, a process that involved complementation with pre-sequences allowing import of the gene product into the secondary plastid bound by four membranes. Based on light-dependent transcription and on localisation data, we propose that RedCAPs might participate in the light (intensity and quality)-dependent structural or functional reorganisation of the light-harvesting antennae of the photosystems upon dark to light shifts as regularly experienced by diatoms in nature. Remarkably, in plastids of the red lineage as well as in green lineage plastids, the phycobilisome based cyanobacterial light harvesting system has been replaced by light harvesting systems that are based on members of the extended LHC protein superfamily, either for one of the photosystems (PS I of red algae) or for both (diatoms). In their proposed function, the RedCAP protein family may thus have played a role in the evolutionary structural remodelling of light-harvesting antennae in the red lineage.
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Affiliation(s)
- Sabine Sturm
- Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany
| | - Johannes Engelken
- Biochemie und Physiologie der Pflanzen, Fach 602, Universität Konstanz 78457 Konstanz, Germany
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona,Spain
| | - Ansgar Gruber
- Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany
- Present address: Department of Biochemistry & Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Sascha Vugrinec
- Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany
| | - Peter G Kroth
- Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany
| | - Iwona Adamska
- Biochemie und Physiologie der Pflanzen, Fach 602, Universität Konstanz 78457 Konstanz, Germany
| | - Johann Lavaud
- Ökophysiologie der Pflanzen, Fach 611, Universität Konstanz 78457 Konstanz, Germany
- Present address: UMR 7266 CNRS-ULR ’LIENSs’, CNRS/University of La Rochelle, Institute for Coastal and Environmental Research, La Rochelle Cedex, France
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14
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Wang L, Mao Y, Kong F, Li G, Ma F, Zhang B, Sun P, Bi G, Zhang F, Xue H, Cao M. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis. PLoS One 2013; 8:e65902. [PMID: 23734264 PMCID: PMC3667073 DOI: 10.1371/journal.pone.0065902] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Pyropia haitanensis and P. yezoensis are two economically important marine crops that are also considered to be research models to study the physiological ecology of intertidal seaweed communities, evolutionary biology of plastids, and the origins of sexual reproduction. This plastid genome information will facilitate study of breeding, population genetics and phylogenetics. PRINCIPAL FINDINGS We have fully sequenced using next-generation sequencing the circular plastid genomes of P. hatanensis (195,597 bp) and P. yezoensis (191,975 bp), the largest of all the plastid genomes of the red lineage sequenced to date. Organization and gene contents of the two plastids were similar, with 211-213 protein-coding genes (including 29-31 unknown-function ORFs), 37 tRNA genes, and 6 ribosomal RNA genes, suggesting a largest coding capacity in the red lineage. In each genome, 14 protein genes overlapped and no interrupted genes were found, indicating a high degree of genomic condensation. Pyropia maintain an ancient gene content and conserved gene clusters in their plastid genomes, containing nearly complete repertoires of the plastid genes known in photosynthetic eukaryotes. Similarity analysis based on the whole plastid genome sequences showed the distance between P. haitanensis and P. yezoensis (0.146) was much smaller than that of Porphyra purpurea and P. haitanensis (0.250), and P. yezoensis (0.251); this supports re-grouping the two species in a resurrected genus Pyropia while maintaining P. purpurea in genus Porphyra. Phylogenetic analysis supports a sister relationship between Bangiophyceae and Florideophyceae, though precise phylogenetic relationships between multicellular red alage and chromists were not fully resolved. CONCLUSIONS These results indicate that Pyropia have compact plastid genomes. Large coding capacity and long intergenic regions contribute to the size of the largest plastid genomes reported for the red lineage. Possessing the largest coding capacity and ancient gene content yet found reveal that Pyropia are more primitive multicellular red algae.
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Affiliation(s)
- Li Wang
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Fanna Kong
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Guiyang Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Fei Ma
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Baolong Zhang
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peipei Sun
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Guiqi Bi
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fangfang Zhang
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Hongfan Xue
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Cao
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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15
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Uji T, Mizuta H, Saga N. Characterization of the sporophyte-preferential gene promoter from the red alga Porphyra yezoensis using transient gene expression. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:188-196. [PMID: 22865243 DOI: 10.1007/s10126-012-9475-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/05/2012] [Indexed: 06/01/2023]
Abstract
The life cycle of plants entails an alternation of generations, the diploid sporophyte and haploid gametophyte stages. There is little information about the characteristics of gene expression during each phase of marine macroalgae. Promoter analysis is a useful method for understanding transcriptional regulation; however, there is no report of promoter analyses in marine macroalgae. In this study, with the aim of elucidating the differences in the transcriptional regulatory mechanisms between the gametophyte and sporophyte stages in the marine red alga Porphyra yezoensis, we isolated the promoter from the sporophyte preferentially expressed gene PyKPA1, which encodes a sodium pump, and analyzed its promoter using a transient gene expression system with a synthetic β-glucuronidase (PyGUS) reporter. The deletion of -1432 to -768 relative to the transcription start site resulted in decreased GUS activity in sporophytes. In contrast, deletion from -767 to -527 increased GUS activity in gametophytes. Gain-of-function analyses showed that the -1432 to -760 region enhanced the GUS activity of a heterologous promoter in sporophytes, whereas the -767 to -510 region repressed it in gametophytes. Further mutation and gain-of-function analyses of the -767 to -510 region revealed that a 20-bp GC-rich sequence (-633 to -614) is responsible for the gametophyte-specific repressed expression. These results showed that the sporophyte-specific positive regulatory region and gametophyte-specific negative regulatory sequence play a crucial role in the preferential expression of PyKPA1 in P. yezoensis sporophytes.
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Affiliation(s)
- Toshiki Uji
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Japan
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16
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Nakamura Y, Sasaki N, Kobayashi M, Ojima N, Yasuike M, Shigenobu Y, Satomi M, Fukuma Y, Shiwaku K, Tsujimoto A, Kobayashi T, Nakayama I, Ito F, Nakajima K, Sano M, Wada T, Kuhara S, Inouye K, Gojobori T, Ikeo K. The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS One 2013; 8:e57122. [PMID: 23536760 PMCID: PMC3594237 DOI: 10.1371/journal.pone.0057122] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/09/2013] [Indexed: 11/18/2022] Open
Abstract
Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.
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Affiliation(s)
- Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
- * E-mail: (YN); (TG)
| | - Naobumi Sasaki
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahiro Kobayashi
- Seikai National Fisheries Research Institute, Fisheries Research Agency, Nagasaki-shi, Nagasaki, Japan
| | - Nobuhiko Ojima
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Yuya Shigenobu
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Masataka Satomi
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | | | - Koji Shiwaku
- Hitachi Solutions, Ltd., Shinagawa-ku, Tokyo, Japan
| | | | | | - Ichiro Nakayama
- Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | - Fuminari Ito
- National Research Institute of Aquaculture, Fisheries Research Agency, Minami-ise, Mie, Japan
| | - Kazuhiro Nakajima
- Japan Sea National Fisheries Research Institute, Fisheries Research Agency, Chuou-ku, Niigata, Japan
| | - Motohiko Sano
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Tokio Wada
- Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Satoru Kuhara
- Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | | | - Takashi Gojobori
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (YN); (TG)
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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17
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Xie C, Li B, Xu Y, Ji D, Chen C. Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers. BMC Genomics 2013; 14:107. [PMID: 23414227 PMCID: PMC3626662 DOI: 10.1186/1471-2164-14-107] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 02/02/2013] [Indexed: 01/12/2023] Open
Abstract
Background Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development. Results In this study, high-throughput sequencing was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated using an Illumina HiSeq 2000. De novo assembly with paired-end information yielded 24,575 unigenes with an average length of 645 bp. Based on sequence similarity searches with known proteins, a total of 16,377 (66.64%) genes were identified. Of these annotated unigenes, 5,471 and 9,168 unigenes were assigned to gene ontology and clusters of orthologous groups, respectively. Searching against the KEGG database indicated that 12,167 (49.51%) unigenes mapped to 124 KEGG pathways. Among the carbon fixation pathways, almost all the essential genes related to the C3- and C4-pathways for P. haitanensis were discovered. Significantly different expression levels of three key genes (Rubisco, PEPC and PEPCK) in different lifecycle stages of P. haitanensis indicated that the carbon fixation pathway in the conchocelis and thallus were different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in the unigenes. Among them, trinucleotide SSRs were the dominant repeat motif (87.17%, 2,377) and GCC/CCG motifs were the most common repeats (60.07%, 1,638). High quality primers to 824 loci were designed and 100 primer pairs were randomly evaluated in six strains of P. haitanensis. Eighty-seven primer pairs successfully yielded amplicons. Conclusion This study generated a large number of putative P. haitanensis transcript sequences, which can be used for novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.
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Affiliation(s)
- Chaotian Xie
- Fisheries College, Jimei University, Xiamen, Fujian Province 361021, People's Republic of China
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18
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Chan CX, Blouin NA, Zhuang Y, Zäuner S, Prochnik SE, Lindquist E, Lin S, Benning C, Lohr M, Yarish C, Gantt E, Grossman AR, Lu S, Müller K, W Stiller J, Brawley SH, Bhattacharya D. Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism. JOURNAL OF PHYCOLOGY 2012; 48:1328-1342. [PMID: 27009986 DOI: 10.1111/j.1529-8817.2012.01229.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 07/06/2012] [Indexed: 06/05/2023]
Abstract
The red seaweed Porphyra (Bangiophyceae) and related Bangiales have global economic importance. Here, we report the analysis of a comprehensive transcriptome comprising ca. 4.7 million expressed sequence tag (EST) reads from P. umbilicalis (L.) J. Agardh and P. purpurea (Roth) C. Agardh (ca. 980 Mbp of data generated using 454 FLX pyrosequencing). These ESTs were isolated from the haploid gametophyte (blades from both species) and diploid conchocelis stage (from P. purpurea). In a bioinformatic analysis, only 20% of the contigs were found to encode proteins of known biological function. Comparative analysis of predicted protein functions in mesophilic (including Porphyra) and extremophilic red algae suggest that the former has more putative functions related to signaling, membrane transport processes, and establishment of protein complexes. These enhanced functions may reflect general mesophilic adaptations. A near-complete repertoire of genes encoding histones and ribosomal proteins was identified, with some differentially regulated between the blade and conchocelis stage in P. purpurea. This finding may reflect specific regulatory processes associated with these distinct phases of the life history. Fatty acid desaturation patterns, in combination with gene expression profiles, demonstrate differences from seed plants with respect to the transport of fatty acid/lipid among subcellular compartments and the molecular machinery of lipid assembly. We also recovered a near-complete gene repertoire for enzymes involved in the formation of sterols and carotenoids, including candidate genes for the biosynthesis of lutein. Our findings provide key insights into the evolution, development, and biology of Porphyra, an important lineage of red algae.
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Affiliation(s)
- Cheong Xin Chan
- Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Nicolas A Blouin
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Simone Zäuner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Simon E Prochnik
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, California, 94958, USA
| | - Erika Lindquist
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, California, 94958, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Martin Lohr
- Institut für Allgemeine Botanik, Johannes Gutenberg-Universität Mainz, 55099, Mainz, Germany
| | - Charles Yarish
- Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, Connecticut, 06901, USA
| | - Elisabeth Gantt
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, 20742, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, 94305, USA
| | - Shan Lu
- School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Kirsten Müller
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John W Stiller
- Department of Biology, East Carolina University, Greenville, North Carolina, 27834, USA
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, 08901, USA
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19
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de Oliveira LS, Gregoracci GB, Silva GGZ, Salgado LT, Filho GA, Alves-Ferreira M, Pereira RC, Thompson FL. Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome. BMC Genomics 2012; 13:487. [PMID: 22985125 PMCID: PMC3534612 DOI: 10.1186/1471-2164-13-487] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/31/2012] [Indexed: 11/16/2022] Open
Abstract
Background Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome. Results A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway. Conclusions This work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.
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Affiliation(s)
- Louisi Souza de Oliveira
- Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ) Av, Carlos Chagas Filho, 373-CCS - IB - BLOCO A (ANEXO) A3- 202, Rio de Janeiro, 21941-599, Brazil
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20
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Abstract
Photosynthetic diatom plastids have long been suggested to have originated by the secondary endosymbiosis of a red alga. However, recent phylogenomic studies report a high number of diatom nuclear genes phylogenetically related to green algal and green plant genes. These were interpreted as endosymbiotic gene transfers (EGT) from a cryptic green algal endosymbiosis. We reanalyzed this issue using a larger set of red algal genomic data. We show that previous studies suffer from a taxonomic sampling bias and point out that a majority of gene phylogenies are either poorly resolved or do not describe EGT events. We finally show that genes having a complete descent from cyanobacteria to diatoms through primary and secondary EGTs have been mostly transferred via a red alga. We conclude that, even if some diatom genes still support a putative green algal origin, these are not sufficient to argue for a cryptic green algal secondary endosymbiosis.
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Affiliation(s)
- Philippe Deschamps
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Univ. Paris-Sud, Orsay, France.
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21
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Li XC, Xing YZ, Jiang X, Qiao J, Tan HL, Tian Y, Zhou B. IDENTIFICATION AND CHARACTERIZATION OF THE CATALASE GENE PyCAT FROM THE RED ALGA PYROPIA YEZOENSIS (BANGIALES, RHODOPHYTA)(1). JOURNAL OF PHYCOLOGY 2012; 48:664-669. [PMID: 27011082 DOI: 10.1111/j.1529-8817.2012.01152.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Catalase is an antioxidant enzyme that plays a significant role in protection against oxidative stress by reducing hydrogen peroxide. The full-length catalase cDNA sequence as isolated from expressed sequence tags (ESTs) of Pyropia yezoensis (Ueda) M. S. Hwang et H. G. Choi (PyCAT) through rapid amplification of cDNA ends (RACE) was identified and characterized. It encoded a polypeptide of 529 amino acids, which shared 36%-44% similarity with other known catalase proteins. Phylogenetic analysis revealed that PyCAT was closer to the catalases from plants than from other organisms. The PyCAT mRNA expression was investigated using real-time PCR to determine life-cycle-specific expression and the expression pattern during desiccation. The mRNA expression level in gametophytes was significantly higher than in sporophytes, and the mRNA expression level of PyCAT was significantly up-regulated during the desiccation process. The recombinant PyCAT protein was purified and analyzed biochemically. The recombinant PyCAT protein exhibited high enzymatic activity (28,000 U·mg(-1) ) with high thermal stability and a broad pH range. All these results indicate that the PyCAT is a typical member of the plant and algal catalase family and may play a significant role in minimizing the effect of oxidative damage in P. yezoensis during desiccation.
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Affiliation(s)
- Xian C Li
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yong Z Xing
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Xue Jiang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Jing Qiao
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Hai L Tan
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yu Tian
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Bin Zhou
- College of Marine Life Science, Ocean University of China, Qingdao 266003, ChinaGuangxi Mangrove Research Center, Beihai 536000, ChinaCollege of Marine Life Science, Ocean University of China, Qingdao 266003, China
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22
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Uji T, Hirata R, Mikami K, Mizuta H, Saga N. Molecular characterization and expression analysis of sodium pump genes in the marine red alga Porphyra yezoensis. Mol Biol Rep 2012; 39:7973-80. [PMID: 22531934 DOI: 10.1007/s11033-012-1643-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 04/16/2012] [Indexed: 01/08/2023]
Abstract
Sodium pumps (EC 3.6.3.9, Na(+)-ATPase), which mediate excretion of Na(+) from the cell, play a crucial role in Na(+) homeostasis in eukaryotic cells. The objective of this study is to understand the Na(+) efflux system in a marine red alga. We identified a novel sodium pump gene, PyKPA2, from the marine red alga Porphyra yezoensis. The amino acid sequence of PyKPA2 shares 65 % identity with PyKPA1, a previously identified P. yezoensis sodium pump. Similar to PyKPA1, PyKPA2 contains conserved sequences for functions such as phosphorylation, ATP binding, and cation binding. Phylogenetic analysis revealed that the two genes cluster with sodium pumps from algae. Reverse-transcription polymerase chain reaction (RT-PCR) analysis showed that PyKPA1 is expressed preferentially in sporophytes, whereas PyKPA2 is expressed specifically in gametophytes. RT-PCR and quantitative real-time PCR analysis revealed that PyKPA1 and PyKPA2 transcripts were upregulated and downregulated, respectively, in gametophytes during exposure to alkali stress. In addition, transcription of both genes in gametophytes was also induced by cold stress. These results suggest that PyKPA1 and PyKPA2 play an important role in alkali and cold stress tolerance.
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Affiliation(s)
- Toshiki Uji
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Japan
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Edstam MM, Viitanen L, Salminen TA, Edqvist J. Evolutionary history of the non-specific lipid transfer proteins. MOLECULAR PLANT 2011; 4:947-64. [PMID: 21486996 DOI: 10.1093/mp/ssr019] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The non-specific lipid transfer proteins (nsLTPs) are small, basic proteins characterized by a tunnel-like hydrophobic cavity, capable of transferring various lipid molecules between lipid bilayers. Most nsLTPs are synthesized with an N-terminal signal peptide that localizes the protein to the apoplastic space. The nsLTPs have only been identified in seed plants, where they are encoded by large gene families. We have initiated an analysis of the evolutionary history of the nsLTP family using genomic and EST information from non-seed land plants and green algae to determine: (1) when the nsLTP family arose, (2) how often new nsLTP subfamilies have been created, and (3) how subfamilies differ in their patterns of expansion and loss in different plant lineages. In this study, we searched sequence databases and found that genes and transcripts encoding nsLTPs are abundant in liverworts, mosses, and all other investigated land plants, but not present in any algae. The tertiary structures of representative liverwort and moss nsLTPs were further studied with homology modeling. The results indicate that the nsLTP family has evolved after plants conquered land. Only two of the four major subfamilies of nsLTPs found in flowering plants are present in mosses and liverworts. The additional subfamilies have arisen later, during land plant evolution. In this report, we also introduce a modified nsLTP classification system.
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Affiliation(s)
- Monika M Edstam
- IFM Molecular Genetics, Linköping University, 581 83 Linköping, Sweden
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Shen S, Zhang G, Li Y, Wang L, Xu P, Yi L. Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH). BMC Res Notes 2011; 4:428. [PMID: 22013916 PMCID: PMC3207994 DOI: 10.1186/1756-0500-4-428] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 10/20/2011] [Indexed: 11/30/2022] Open
Abstract
Background Porphyra yezoensis Ueda is one of the most important edible seaweed, with a dimorphic life cycle which consists of gametophyte as macroscopical blade and sporophyte as microscopic filamentous. Conspicuous differences exist in the two generations, such as morphology, cell structure, biochemistry, physiology, and so on. The developmental process of Porphyra yezoensis has been studied thoroughly, but the mechanism is still ambiguous and few studies on genetic expression have been carried out. In this study, the suppression subtractive hybridization (SSH) method conducted to generate large-scale expressed sequence tags (EST) is designed to identify gene candidates related to the morphological and physiological differences between the gametophytic and sporophytic generations of Porphyra yezoensis Ueda. Findings Each 300 clones of sporophyte and gametophyte cells were dipped onto the membrane for hybridization. The result of dot-blot suggested there were 222 positive clones in gametophyte library and 236 positive clones in sporophyte library. 383 positive clones of strongest signals had been sequenced, and 191 EST sequences of gametophyte and 192 of sporophyte were obtained. A total of 196 genes were obtained, within which 104 genes were identified from the gametophyte and 92 from the sporophyte. Thirty-nine genes of the gametophyte and 62 genes of the sporophyte showed sequence similarity to those genes with known or putative functions which were classified according to their putative biological roles and molecular functions. The GO annotation showed about 58% of the cellular component of sporophyte and gametophyte cells were mainly located in cytoplasm and nucleus. The special genes were located in Golgi apparatus, and high expression in plastid, ribosome and endoplasmic reticulum. The main biological functions of gametophyte cells contributed to DNA repair/replication, carbohydrate metabolism, transport and transcription, especially in response to heat and oxidative stress. The sporophyte cell expresses more genes in transcription, transport, carbohydrate metabolism, particularly in signal transduction, DNA and protein modification, protein and nucleotide metabolism. Four genes are expressed on both gametophyte and sporophyte cells and eighteen genes have not been annotated. Conclusion According to the information of GO annotation, the gametophyte tends to growth and self- protection while the sporophyte tends to be more active in development. Interpretation of the differentially expressed genes revealed new insights into the molecular processes of the generation alternation of Porphyra yezoensis. Further investigation are needed due to insufficiency of functional genes research and indeterminancy of the functions of many sequences.
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Affiliation(s)
- Songdong Shen
- Department of Cell Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou City, Jiangsu Province, 215123, P, R, China.
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Kim E, Park HS, Jung Y, Choi DW, Jeong WJ, Park HS, Hwang MS, Park EJ, Gong YG. IDENTIFICATION OF THE HIGH-TEMPERATURE RESPONSE GENES FROM PORPHYRA SERIATA (RHODOPHYTA) EXPRESSION SEQUENCE TAGS AND ENHANCEMENT OF HEAT TOLERANCE OF CHLAMYDOMONAS (CHLOROPHYTA) BY EXPRESSION OF THE PORPHYRA HTR2 GENE(1). JOURNAL OF PHYCOLOGY 2011; 47:821-828. [PMID: 27020018 DOI: 10.1111/j.1529-8817.2011.01008.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Temperature is one of the major environmental factors that affect the distribution, growth rate, and life cycle of intertidal organisms, including red algae. In an effort to identify the genes involved in the high-temperature tolerance of Porphyra, we generated 3,979 expression sequence tags (ESTs) from gametophyte thalli of P. seriata Kjellm. under normal growth conditions and high-temperature conditions. A comparison of the ESTs from two cDNA libraries allowed us to identify the high temperature response (HTR) genes, which are induced or up-regulated as the result of high-temperature treatment. Among the HTRs, HTR2 encodes for a small polypeptide consisting of 144 amino acids, which is a noble nuclear protein. Chlamydomonas expressing the Porphyra HTR2 gene shows higher survival and growth rates than the wild-type strain after high-temperature treatment. These results suggest that HTR2 may be relevant to the tolerance of high-temperature stress conditions, and this Porphyra EST data set will provide important genetic information for studies of the molecular basis of high-temperature tolerance in marine algae, as well as in Porphyra.
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Affiliation(s)
- Euicheol Kim
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Hong-Sil Park
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Youngja Jung
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Dong-Woog Choi
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Won-Joong Jeong
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Hong-Seog Park
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Mi Sook Hwang
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Eun-Jeong Park
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
| | - Yong-Gun Gong
- Department of Biology Education, Chonnam National University, Kwagnju, 500-757, KoreaPlant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaGenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, KoreaSeaweed Research Center, National Fisheries Research and Development Institute, Mokpo, 530-931, Korea
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Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4546-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Contreras-Porcia L, Dennett G, González A, Vergara E, Medina C, Correa JA, Moenne A. Identification of copper-induced genes in the marine alga Ulva compressa (Chlorophyta). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:544-56. [PMID: 20936320 DOI: 10.1007/s10126-010-9325-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 09/23/2010] [Indexed: 05/14/2023]
Abstract
In order to identify genes/proteins involved in copper tolerance, the marine alga Ulva compressa was cultivated with 10 μM copper for 3 days. The activities of antioxidant enzymes ascorbate peroxidase (AP), peroxiredoxin (PRX), thioredoxin (TRX), and glutathione-S-transferase (GST) and the level of lipoperoxides were determined in the alga cultivated with and without copper addition. Antioxidant enzyme activities and lipoperoxides level increased in response to copper excess, indicating that the alga was under oxidative stress. A cDNA library was prepared using U. compressa cultivated with 10 μM copper for 3 days. A total of 3 × 10(4) clones were isolated and 480 clones were sequenced, resulting in 235 non-redundant ESTs, of which 104 encode proteins with known functions. Among them, we identified proteins involved in (1) antioxidant metabolism such as AP, PRX, TRX, GST, and metalothionein (MET), (2) signal transduction, such as calmodulin (CAM), (3) calcium-dependent protein kinase (CDPK) and nucleoside diphosphate kinase (NDK), (4) gene expression, (5) protein synthesis and degradation, and (6) chloroplast and mitochondria electron transport chains. Half of the identified proteins are potentially localized in organelles. The relative level of 18 genes, including those coding for AP, PRX, TRX, GST, MET, CAM, CDPK, and NDK were determined by quantitative RT-PCR in the alga cultivated with 10 μM copper for 0 to 7 days. Transcript levels increased in response to copper stress and most of them reached a maximum at days 3 and 5. Thus, the selected genes are induced by copper stress and they are probably involved in copper acclimation and tolerance.
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Affiliation(s)
- Loretto Contreras-Porcia
- Departamento de Ecología, Center for Advanced Studies in Ecology and Biodiversity, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 6513677, Santiago, Chile
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Dittami SM, Michel G, Collén J, Boyen C, Tonon T. Chlorophyll-binding proteins revisited--a multigenic family of light-harvesting and stress proteins from a brown algal perspective. BMC Evol Biol 2010; 10:365. [PMID: 21110855 PMCID: PMC3008699 DOI: 10.1186/1471-2148-10-365] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 11/26/2010] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Chlorophyll-binding proteins (CBPs) constitute a large family of proteins with diverse functions in both light-harvesting and photoprotection. The evolution of CBPs has been debated, especially with respect to the origin of the LI818 subfamily, members of which function in non-photochemical quenching and have been found in chlorophyll a/c-containing algae and several organisms of the green lineage, but not in red algae so far. The recent publication of the Ectocarpus siliculosus genome represents an opportunity to expand on previous work carried out on the origin and function of CBPs. RESULTS The Ectocarpus genome codes for 53 CBPs falling into all major families except the exclusively green family of chlorophyll a/b binding proteins. Most stress-induced CBPs belong to the LI818 family. However, we highlight a few stress-induced CBPs from Phaeodactylum tricornutum and Chondrus crispus that belong to different sub-families and are promising targets for future functional studies. Three-dimensional modeling of two LI818 proteins revealed features common to all LI818 proteins that are likely to interfere with their capacity to bind chlorophyll b and lutein, but may enable binding of chlorophyll c and fucoxanthin. In the light of this finding, we examined the possibility that LI818 proteins may have originated in a chlorophyll c/fucoxanthin containing organism and compared this scenario to three alternatives: an independent evolution of LI818 proteins in different lineages, an ancient origin together with the first CBPs, before the separation of the red and the green lineage, or an origin in the green lineage and a transfer to an ancestor of haptophytes and heterokonts during a cryptic endosymbiosis event. CONCLUSIONS Our findings reinforce the idea that the LI818 family of CBPs has a role in stress response. In addition, statistical analyses of phylogenetic trees show an independent origin in different eukaryotic lineages or a green algal origin of LI818 proteins to be highly unlikely. Instead, our data favor an origin in an ancestral chlorophyll a/c-containing organism and a subsequent lateral transfer to some green algae, although an origin of LI818 proteins in a common ancestor of red and green algae cannot be ruled out.
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Affiliation(s)
- Simon M Dittami
- UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
| | - Gurvan Michel
- UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
| | - Jonas Collén
- UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
| | - Catherine Boyen
- UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
| | - Thierry Tonon
- UPMC Univ Paris 06, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680, Roscoff, France
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Su HN, Xie BB, Zhang XY, Zhou BC, Zhang YZ. The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview. PHOTOSYNTHESIS RESEARCH 2010; 106:73-87. [PMID: 20521115 DOI: 10.1007/s11120-010-9560-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 05/10/2010] [Indexed: 05/29/2023]
Abstract
Red algae are a group of eukaryotic photosynthetic organisms. Phycobilisomes (PBSs), which are composed of various types of phycobiliproteins and linker polypeptides, are the main light-harvesting antennae in red algae, as in cyanobacteria. Two morphological types of PBSs, hemispherical- and hemidiscoidal-shaped, are found in different red algae species. PBSs harvest solar energy and efficiently transfer it to photosystem II (PS II) and finally to photosystem I (PS I). The PS I of red algae uses light-harvesting complex of PS I (LHC I) as a light-harvesting antennae, which is phylogenetically related to the LHC I found in higher plants. PBSs, PS II, and PS I are all distributed throughout the entire thylakoid membrane, a pattern that is different from the one found in higher plants. Photosynthesis processes, especially those of the light reactions, are carried out by the supramolecular complexes located in/on the thylakoid membranes. Here, the supramolecular architecture, function and regulation of thylakoid membranes in red algal are reviewed.
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Affiliation(s)
- Hai-Nan Su
- The State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, People's Republic of China
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Uji T, Takahashi M, Saga N, Mikami K. Visualization of nuclear localization of transcription factors with cyan and green fluorescent proteins in the red alga Porphyra yezoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:150-9. [PMID: 19593603 DOI: 10.1007/s10126-009-9210-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 06/10/2009] [Indexed: 05/11/2023]
Abstract
Transcription factors play a central role in expression of genomic information in all organisms. The objective of our study is to analyze the function of transcription factors in red algae. One way to analyze transcription factors in eukaryotic cells is to study their nuclear localization, as reported for land plants and green algae using fluorescent proteins. There is, however, no report documenting subcellular localization of transcription factors from red algae. In the present study, using the marine red alga Porphyra yezoensis, we confirmed for the first time successful expression of humanized fluorescent proteins (ZsGFP and ZsYFP) from a reef coral Zoanthus sp. and land plant-adapted sGFP(S65T) in gametophytic cells comparable to expression of AmCFP. Following molecular cloning and characterization of transcription factors DP-E2F-like 1 (PyDEL1), transcription elongation factor 1 (PyElf1) and multiprotein bridging factor 1 (PyMBF1), we then demonstrated that ZsGFP and AmCFP can be used to visualize nuclear localization of PyElf1 and PyMBF1. This is the first report to perform visualization of subcellular localization of transcription factors as genome-encoded proteins in red algae.
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Affiliation(s)
- Toshiki Uji
- Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, 041-8611, Japan
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32
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Radakovits R, Jinkerson RE, Darzins A, Posewitz MC. Genetic engineering of algae for enhanced biofuel production. EUKARYOTIC CELL 2010; 9:486-501. [PMID: 20139239 PMCID: PMC2863401 DOI: 10.1128/ec.00364-09] [Citation(s) in RCA: 515] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
There are currently intensive global research efforts aimed at increasing and modifying the accumulation of lipids, alcohols, hydrocarbons, polysaccharides, and other energy storage compounds in photosynthetic organisms, yeast, and bacteria through genetic engineering. Many improvements have been realized, including increased lipid and carbohydrate production, improved H(2) yields, and the diversion of central metabolic intermediates into fungible biofuels. Photosynthetic microorganisms are attracting considerable interest within these efforts due to their relatively high photosynthetic conversion efficiencies, diverse metabolic capabilities, superior growth rates, and ability to store or secrete energy-rich hydrocarbons. Relative to cyanobacteria, eukaryotic microalgae possess several unique metabolic attributes of relevance to biofuel production, including the accumulation of significant quantities of triacylglycerol; the synthesis of storage starch (amylopectin and amylose), which is similar to that found in higher plants; and the ability to efficiently couple photosynthetic electron transport to H(2) production. Although the application of genetic engineering to improve energy production phenotypes in eukaryotic microalgae is in its infancy, significant advances in the development of genetic manipulation tools have recently been achieved with microalgal model systems and are being used to manipulate central carbon metabolism in these organisms. It is likely that many of these advances can be extended to industrially relevant organisms. This review is focused on potential avenues of genetic engineering that may be undertaken in order to improve microalgae as a biofuel platform for the production of biohydrogen, starch-derived alcohols, diesel fuel surrogates, and/or alkanes.
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Affiliation(s)
- Randor Radakovits
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
| | - Robert E. Jinkerson
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
| | - Al Darzins
- National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, Colorado 80401
| | - Matthew C. Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, 1500 Illinois St., Golden, Colorado 80401, and
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Lapidot M, Shrestha RP, Weinstein Y, Arad S. Red Microalgae: From Basic Know-How to Biotechnology. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Bangiophytes: From one Class to Six; Where Do We Go from Here? CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Porphyra: Complex Life Histories in a Harsh Environment: P. umbilicalis, an Intertidal Red Alga for Genomic Analysis. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3795-4_7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Ammonium induced expression of the red algal chloroplast gene Ycf18, a putative homolog of the cyanobacterial NblA gene involved in nitrogen deficiency-induced phycobilisome degradation. Biosci Biotechnol Biochem 2009; 73:740-3. [PMID: 19270416 DOI: 10.1271/bbb.80662] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In cyanobacteria, nutrient deficiency-induced phycobilisome degradation is controlled by the NblA gene. Red algae also have an NblA-related gene, Ycf18, in their chloroplast genomes. To elucidate the role of Ycf18, the expression pattern of Ycf18 in a red alga, Porphyra yezoensis, was investigated. Ycf18 expression was low in nitrate medium, but was greatly promoted in ammonium medium. Nitrogen starvation caused bleaching, but did not affect the expression of Ycf18. The responses of Ycf18 to nitrogen-starvation and the supply of ammonium were distinct from those of NblA, suggesting that Ycf18 has a role other than the regulation of phycobilisome degradation.
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Roberts E, Roberts AW. A CELLULOSE SYNTHASE (CESA) GENE FROM THE RED ALGA PORPHYRA YEZOENSIS (RHODOPHYTA)(1). JOURNAL OF PHYCOLOGY 2009; 45:203-12. [PMID: 27033658 DOI: 10.1111/j.1529-8817.2008.00626.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The cell walls of Porphyra species, like those of land plants, contain cellulose microfibrils that are synthesized by clusters of cellulose synthase enzymes ("terminal complexes"), which move in the plasma membrane. However, the morphologies of the Porphyra terminal complexes and the cellulose microfibrils they produce differ from those of land plants. To characterize the genetic basis for these differences, we have identified, cloned, and sequenced a cellulose synthase (CESA) gene from Porphyra yezoensis Ueda strain TU-1. A partial cDNA sequence was identified in the P. yezoensis expressed sequence tag (EST) index using a land plant CESA sequence as a query. High-efficiency thermal asymmetric interlaced PCR was used to amplify sequences upstream of the cDNA sequence from P. yezoensis genomic DNA. Using the resulting genomic sequences as queries, we identified additional EST sequences and a full-length cDNA clone, which we named PyCESA1. The conceptual translation of PyCESA1 includes the four catalytic domains and the N- and C-terminal transmembrane domains that characterize CESA proteins. Genomic PCR demonstrated that PyCESA1 contains no introns. Southern blot analysis indicated that P. yezoensis has at least three genomic sequences with high similarity to the cloned gene; two of these are pseudogenes based on analysis of amplified genomic sequences. The P. yezoensis CESA peptide sequence is most similar to cellulose synthase sequences from the oomycete Phytophthora infestans and from cyanobacteria. Comparing the CESA genes of P. yezoensis and land plants may facilitate identification of sequences that control terminal complex and cellulose microfibril morphology.
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Affiliation(s)
- Eric Roberts
- Department of Biology, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, USADepartment of Biological Sciences, Ranger Hall, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Alison W Roberts
- Department of Biology, Rhode Island College, 600 Mount Pleasant Avenue, Providence, Rhode Island 02908, USADepartment of Biological Sciences, Ranger Hall, University of Rhode Island, Kingston, Rhode Island 02881, USA
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Abstract
Sequencing of cDNA libraries is an efficient and inexpensive approach to analyze the protein-coding portion of a genome. It is frequently used for surveying the genomes of poorly studied eukaryotes, and is particularly useful for species that are not easily amenable to genome sequencing, because they are nonaxenic and/or difficult to cultivate. In this chapter, we describe protocols that have been applied successfully to construct and normalize a variety of cDNA libraries from many different species of free-living protists and fungi, and that require only small quantities of cell material.
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Grossman AR. In the Grip of Algal Genomics. TRANSGENIC MICROALGAE AS GREEN CELL FACTORIES 2008; 616:54-76. [DOI: 10.1007/978-0-387-75532-8_6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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40
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Peddigari S, Zhang W, Takechi K, Takano H, Takio S. Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis. Gene 2008; 424:153-8. [PMID: 18708130 DOI: 10.1016/j.gene.2008.07.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 07/16/2008] [Accepted: 07/21/2008] [Indexed: 12/11/2022]
Abstract
A copia-like retrotransposon referred to as PyRE1G1 was isolated from the genome of the red alga Porphyra yezoensis. PyRE1G1 is 4807 bp in length, with 204 bp long terminal repeats (LTRs) at both ends. PyRE1G1 has an open reading frame of 1401 residues encoding gag, protease, integrase, reverse transcriptase (RT), and RNase H. From the order of gene arrangement of proteins, PyRE1G1 appears to be a copia-like retrotransposon. Genomic Southern blot analysis suggests that PyRE1G1 consists of a small gene family. From the phylogenetic tree of RT sequences, PyRE1G1 is grouped in the clade of usual copia elements and distinct from the previously isolated red algal copia-like gene PyRE10G in that the latter is closely related to a new clade of aquatic animal-specific copia-like retrotransposons.
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Affiliation(s)
- Suresh Peddigari
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555, Japan
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Structural features and gene-expression profiles of actin homologs in Porphyra yezoensis (Rhodophyta). Gene 2008; 423:79-84. [PMID: 18678234 DOI: 10.1016/j.gene.2008.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/09/2008] [Accepted: 07/09/2008] [Indexed: 11/23/2022]
Abstract
The marine red alga Porphyra yezoensis contains an actin gene family consisting of at least four isoforms (PyACT1, 2, 3 and 4). The amino acid identity between isoforms exceeds 83%, and each contains a putative nuclear export signal (NES). We scanned the sequences for amino acids in regions homologous to the intermonomeric interface of actin filaments. Few residues expected to engage in cross-linking were conserved between the four isoforms. The results of the sequence analyses suggest that PyACT2 probably functions in the nucleus as a monomer (G-actin) or in other unconventional forms. In addition, the distribution and position of the introns were different from those in florideophycean actin genes. The expression level of PyACT3 in matured gametophytes was significantly higher than in those in a vegetative state, although the mRNA was detected at similar levels in both apical and basal parts of thalli. The expression levels of PyACT2 and 4, on the other hand, did not change significantly between the matured and vegetative gametophytes. The PyACT3 may serve as a molecular marker for monitoring thallus maturation in this species.
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Kitade Y, Asamizu E, Fukuda S, Nakajima M, Ootsuka S, Endo H, Tabata S, Saga N. IDENTIFICATION OF GENES PREFERENTIALLY EXPRESSED DURING ASEXUAL SPORULATION IN PORPHYRA YEZOENSIS GAMETOPHYTES (BANGIALES, RHODOPHYTA)(1). JOURNAL OF PHYCOLOGY 2008; 44:113-123. [PMID: 27041048 DOI: 10.1111/j.1529-8817.2007.00456.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Asexual reproduction via archeospores in Porphyra yezoensis Ueda gametophytes is a very valuable character to nori farming; however, there is little information available on the molecular basis of the developmental process. To identify genes involved in the Porphyra asexual sporulation, we compared the gene expression profiles derived from four developmental stages of the life cycle (three from gametophytes; one from sporophytes) using cDNA macroarray, which includes 4,896 nonredundant expressed sequence tag (EST) groups. Candidate genes were screened by two different macroarray data analyses combined with reverse transcription-PCR (RT-PCR) analysis or Northern analysis. RT-PCR analysis revealed that nine genes (one: similarity to 5'-3' exoribonuclease; the other eight: no sequence similarity to known proteins) were expressed with a gametophyte (G)-specific manner, and two genes (named ASPO2608, ASPO1527) were expressed only in gametophytes that formed archeospores. The deduced amino acid sequences for the latter two genes are predicted to contain signal peptides for secretion at their N-termini. Northern analysis revealed that expression levels of Calvin cycle genes in the gametophytic stage that formed archeospores (G-A stage) were higher than those of the gametophyte blade with no archeospores (G-NA stage). In the macroarray analysis based on the rank data of G-preferentially expressed genes, which were detected in the previous P. yezoensis EST analysis, one gene encoding the cyclase associated protein (CAP) exhibited a change upwardly in the G-A stage >1,000 ranks to the G-NA stage. We propose that ASPO2608 and CAP may function in a signaling pathway of asexual sporulation.
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Affiliation(s)
- Yukihiro Kitade
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Erika Asamizu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Satoru Fukuda
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Maiko Nakajima
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Shuuji Ootsuka
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Hirotoshi Endo
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Satoshi Tabata
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Naotsune Saga
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanGraduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, JapanKazusa DNA Research Institute, Kisarazu, Chiba 292-0812, JapanFaculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
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A Copia-like Retrotransposon Gene Encoding Gypsy-like Integrase in a Red Alga, Porphyra yezoensis. J Mol Evol 2007; 66:72-9. [DOI: 10.1007/s00239-007-9057-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 11/07/2007] [Indexed: 11/26/2022]
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Wunder T, Martin R, Löffelhardt W, Schleiff E, Steiner JM. The invariant phenylalanine of precursor proteins discloses the importance of Omp85 for protein translocation into cyanelles. BMC Evol Biol 2007; 7:236. [PMID: 18045484 PMCID: PMC2222254 DOI: 10.1186/1471-2148-7-236] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 11/28/2007] [Indexed: 11/10/2022] Open
Abstract
Background Today it is widely accepted that plastids are of cyanobacterial origin. During their evolutionary integration into the metabolic and regulatory networks of the host cell the engulfed cyanobacteria lost their independency. This process was paralleled by a massive gene transfer from symbiont to the host nucleus challenging the development of a retrograde protein translocation system to ensure plastid functionality. Such a system includes specific targeting signals of the proteins needed for the function of the plastid and membrane-bound machineries performing the transfer of these proteins across the envelope membranes. At present, most information on protein translocation is obtained by the analysis of land plants. However, the analysis of protein import into the primitive plastids of glaucocystophyte algae, revealed distinct features placing this system as a tool to understand the evolutionary development of translocation systems. Here, bacterial outer membrane proteins of the Omp85 family have recently been discussed as evolutionary seeds for the development of translocation systems. Results To further explore the initial mode of protein translocation, the observed phenylalanine dependence for protein translocation into glaucophyte plastids was pursued in detail. We document that indeed the phenylalanine has an impact on both, lipid binding and binding to proteoliposomes hosting an Omp85 homologue. Comparison to established import experiments, however, unveiled a major importance of the phenylalanine for recognition by Omp85. This finding is placed into the context of the evolutionary development of the plastid translocon. Conclusion The phenylalanine in the N-terminal domain signs as a prerequisite for protein translocation across the outer membrane assisted by a "primitive" translocon. This amino acid appears to be optimized for specifically targeting the Omp85 protein without enforcing aggregation on the membrane surface. The phenylalanine has subsequently been lost in the transit sequence, but can be found at the C-terminal position of the translocating pore. Thereby, the current hypothesis of Omp85 being the prokaryotic contribution to the ancestral Toc translocon can be supported.
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Affiliation(s)
- Tobias Wunder
- Ludwig-Maximilians-Universität Munich, Department of Biology I, VW-Research Group, Menzinger Str, 67, 80638 Munich, Germany.
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Fujiwara S, Hirokawa Y, Takatsuka Y, Suda K, Asamizu E, Takayanagi T, Shibata D, Tabata S, Tsuzuki M. Gene expression profiling of coccolith-bearing cells and naked cells in haptophyte Pleurochrysis haptonemofera with a cDNA macroarray system. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:550-60. [PMID: 17659451 DOI: 10.1007/s10126-007-9039-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 03/05/2007] [Indexed: 05/16/2023]
Abstract
Pleurochrysis haptonemofera is a unicellular marine coccolithophorid that has calcified scales, coccoliths, on the cell surface. Some coccolithophorids including P. haptonemofera have a coccolith-bearing stage and a naked stage in their life cycles. To characterize genes involved in the coccolithogenesis, we generated a total of 9550 expressed sequence tags (EST) from a normalized cDNA library that was prepared using both coccolith-bearing cells (C-cells) and naked cells (N-cells), constructed a cDNA macroarray using the EST clones, and then analyzed the gene expression specificity in C-cells and N-cells. When cDNA clones whose expression ratio exceeded 3-fold were selected, as many as 180 clones were identified as C-cell-specific ones, while only 12 were found to be N-cell-specific ones. These clones were sequenced, assembled, and homology-searched against a public nonredundant protein database. As a result, they were grouped into 54 C-cell-specific and 6 N-cell-specific genes, and 59% and 50% of these genes exhibited significant similarity to those of other known proteins, respectively. To assess mRNA expression further, Northern hybridization was performed for 12 of the C-cell-specific genes and one of the N-cell-specific ones. These clones, together with the new cDNA macroarray, will provide a powerful tool for the future genome-wide functional analysis of uncharacterized genes related to the regulation of the calcification and life cycle of coccolithophorids.
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Affiliation(s)
- Shoko Fujiwara
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, Japan.
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Wong TKM, Ho CL, Lee WW, Rahim RA, Phang SM. ANALYSES OF EXPRESSED SEQUENCE TAGS FROM SARGASSUM BINDERI(PHAEOPHYTA). JOURNAL OF PHYCOLOGY 2007; 43:528-534. [DOI: 10.1111/j.1529-8817.2007.00349.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Collén J, Guisle-Marsollier I, Léger JJ, Boyen C. Response of the transcriptome of the intertidal red seaweed Chondrus crispus to controlled and natural stresses. THE NEW PHYTOLOGIST 2007; 176:45-55. [PMID: 17803640 DOI: 10.1111/j.1469-8137.2007.02152.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Intertidal seaweeds inhabit an inherently stressful environment with rapidly changing physical conditions with the turning tides. Many macroalgae are therefore very resistant to abiotic stress; however, the bases for this tolerance and the relative importance of different stressors are largely unknown. Here, the effects of stress on the transcriptome of the red seaweed Chondrus crispus were investigated using cDNA microarrays. The responses were studied after exposure to high light, high temperature, and hypo- and hyperosmotic conditions in the laboratory and compared with gene expression in nature at different stress loads: at high and low tide at solar noon, and during a cloudy and a sunny day, respectively. The study identifies key stress genes and marker genes for specific stressors. The data also provide an insight into the physiological effects of stress; for example, high light stress and high natural stress caused an increase in antioxidative proteins, suggesting an increased oxidative stress. Clustering analysis suggested that osmotic stress modulated the gene expression in nature under high-stress conditions and was thus the most significant natural stressor. The potential cross-talk between stress reactions and methyl jasmonate-induced responses was also investigated and is tentatively suggested to be mediated by reactive oxygen species.
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Affiliation(s)
- Jonas Collén
- Centre National de la Recherche Scientifique, Université Pierre et Marie Curie-Paris 6, Laboratoire International Associé-Dispersal and Adaptation in Marine Species, Unité Mixte de Recherche 7139, Station Biologique, BP 74, 29682 Roscoff cedex, France
| | | | - Jean J Léger
- INSERM U533, Institut du Thorax, BP 53508, 44035 Nantes cedex 1, France
| | - Catherine Boyen
- Centre National de la Recherche Scientifique, Université Pierre et Marie Curie-Paris 6, Laboratoire International Associé-Dispersal and Adaptation in Marine Species, Unité Mixte de Recherche 7139, Station Biologique, BP 74, 29682 Roscoff cedex, France
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O'Brien EA, Koski LB, Zhang Y, Yang L, Wang E, Gray MW, Burger G, Lang BF. TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res 2007; 35:D445-51. [PMID: 17202165 PMCID: PMC1899108 DOI: 10.1093/nar/gkl770] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 09/11/2006] [Accepted: 10/01/2006] [Indexed: 11/29/2022] Open
Abstract
The TBestDB database contains approximately 370,000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/.
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Affiliation(s)
- Emmet A O'Brien
- Département de Biochimie, Canadian Institute for Advanced Research, Robert-Cedergren Centre for Research in Bioinformatics and Genomics, Université de Montréal, 2900 Edouard-Montpetit, Montréal, QC, Canada H3T 1J4.
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Glanz S, Bunse A, Wimbert A, Balczun C, Kück U. A nucleosome assembly protein-like polypeptide binds to chloroplast group II intron RNA in Chlamydomonas reinhardtii. Nucleic Acids Res 2006; 34:5337-51. [PMID: 17012281 PMCID: PMC1636423 DOI: 10.1093/nar/gkl611] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In the unicellular green alga Chlamydomonas reinhardtii, the chloroplast-encoded tscA RNA is part of a tripartite group IIB intron, which is involved in trans-splicing of precursor mRNAs. We have used the yeast three-hybrid system to identify chloroplast group II intron RNA-binding proteins, capable of interacting with the tscA RNA. Of 14 candidate cDNAs, 13 encode identical polypeptides with significant homology to members of the nuclear nucleosome assembly protein (NAP) family. The RNA-binding property of the identified polypeptide was demonstrated by electrophoretic mobility shift assays using different domains of the tripartite group II intron as well as further chloroplast transcripts. Because of its binding to chloroplast RNA it was designated as NAP-like (cNAPL). In silico analysis revealed that the derived polypeptide carries a 46 amino acid chloroplast leader peptide, in contrast to nuclear NAPs. The chloroplast localization of cNAPL was demonstrated by laser scanning confocal fluorescence microscopy using different chimeric cGFP fusion proteins. Phylogenetic analysis shows that no homologues of cNAPL and its related nuclear counterparts are present in prokaryotic genomes. These data indicate that the chloroplast protein described here is a novel member of the NAP family and most probably has not been acquired from a prokaryotic endosymbiont.
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Affiliation(s)
| | | | | | | | - Ulrich Kück
- To whom correspondence should be addressed. Tel: +49 234 3226212; Fax: +49 234 3214184;
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Hervé C, Tonon T, Collén J, Corre E, Boyen C. NADPH oxidases in Eukaryotes: red algae provide new hints! Curr Genet 2005; 49:190-204. [PMID: 16344959 DOI: 10.1007/s00294-005-0044-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 10/19/2005] [Accepted: 10/31/2005] [Indexed: 11/30/2022]
Abstract
The red macro-alga Chondrus crispus is known to produce superoxide radicals in response to cell-free extracts of its green algal pathogenic endophyte Acrochaete operculata. So far, no enzymes involved in this metabolism have been isolated from red algae. We report here the isolation of a gene encoding a homologue of the respiratory burst oxidase gp91(phox) in C. crispus, named Ccrboh. This single copy gene encodes a polypeptide of 825 amino acids. Search performed in available genome and EST algal databases identified sequences showing common features of NADPH oxidases in other algae such as the red unicellular Cyanidioschyzon merolae, the economically valuable red macro-alga Porphyra yezoensis and the two diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Domain organization and phylogenetic relationships with plant, animal, fungal and algal NADPH oxidase homologues were analyzed. Transcription analysis of the C. crispus gene revealed that it was over-transcribed during infection of C. crispus gametophyte by the endophyte A. operculata, and after incubation in presence of atrazine, methyl jasmonate and hydroxyperoxides derived from C20 polyunsaturated fatty acids (PUFAs). These results also illustrate the interest of exploring the red algal lineage for gaining insight into the deep evolution of NADPH oxidases in Eukaryotes.
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Affiliation(s)
- Cécile Hervé
- UMR7139 (CNRS-UPMC-LIA DIAMS), Station Biologique, F-29682, Roscoff Cedex, France
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