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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet 2024; 56:1018-1031. [PMID: 38693345 PMCID: PMC11096116 DOI: 10.1038/s41588-024-01737-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Zhejiang Lab, Hanzhou, China
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum Hamburg, Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Yunnan, China
| | - Bo Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Janine M R Fürst-Jansen
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jaccoline M S Zegers
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tim P Rieseberg
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Tatyana Darienko
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Maaike J Bierenbroodspot
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture 'La Mayora', Málaga, Spain
| | - Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute/Genetics, Jena, Germany
| | - Jeffrey P Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University, Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg and Aquatic Ecophysiology and Phycology, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Xiyin Wang
- North China University of Science and Technology, Tangshan, China
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE, USA
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore, Singapore
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany.
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany.
- University of Goettingen, Goettingen Center for Molecular Biosciences, Goettingen, Germany.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JM, Dadras A, Zegers JM, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. bioRxiv 2023:2023.01.31.526407. [PMID: 36778228 PMCID: PMC9915684 DOI: 10.1101/2023.01.31.526407] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
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Affiliation(s)
- Xuehuan Feng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Jinfang Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Iker Irisarri
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Huihui Yu
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Bo Zheng
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Zahin Ali
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Sophie de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Janine M.R. Fürst-Jansen
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Jaccoline M.S. Zegers
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tim P. Rieseberg
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Maaike J. Bierenbroodspot
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Lydia Gramzow
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Romy Petroll
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (UMA-CSIC)
| | - Orestis Nousias
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Tang Li
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
| | - Elisabeth Fitzek
- Computational Biology, Department of Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - W. Scott Grayburn
- Northern Illinois University, Molecular Core Lab, Department of Biological Sciences, DeKalb, IL 60115, USA
| | - Nina Rittmeier
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Charlotte Permann
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Florian Rümpler
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - John M. Archibald
- Dalhousie University, Department of Biochemistry and Molecular Biology, 5850 College Street, Halifax NS B3H 4R2, Canada
| | - Günter Theißen
- University of Jena, Matthias Schleiden Institute / Genetics, 07743, Jena, Germany
| | - Jeffrey P. Mower
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
| | - Maike Lorenz
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Experimental Phycology and Culture Collection of Algae at Goettingen University (EPSAG), Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Henrik Buschmann
- University of Applied Sciences Mittweida, Faculty of Applied Computer Sciences and Biosciences, Section Biotechnology and Chemistry, Molecular Biotechnology, Technikumplatz 17, 09648 Mittweida, Germany
| | - Klaus von Schwartzenberg
- Universität Hamburg, Institute of Plant Science and Microbiology, Microalgae and Zygnematophyceae Collection Hamburg (MZCH) and Aquatic Ecophysiology and Phycology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Lori Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiyin Wang
- North China University of Science and Technology
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Cornell University, Plant Biology Section, Ithaca, NY, USA
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- University of Freiburg, Centre for Biological Signalling Studies (BIOSS), Freiburg, Germany
| | - Julius Ben Ari
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Noa Keren
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Assaf Mosquna
- The Hebrew University of Jerusalem, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Rehovot 7610000, Israel
| | - Andreas Holzinger
- University of Innsbruck, Department of Botany, Research Group Plant Cell Biology, Sternwartestraße 15, A-6020 Innsbruck, Austria
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP Toulouse, Castanet-Tolosan, 31326, France
| | - Chi Zhang
- University of Nebraska-Lincoln, Center for Plant Science Innovation, Lincoln, NE 68588, USA
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE 68588, USA
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jan de Vries
- University of Goettingen, Institute of Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Yanbin Yin
- University of Nebraska-Lincoln, Department of Food Science and Technology, Lincoln, NE 68588, USA
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Kirchner NJ, Hage A, Gomez J, Grayburn WS, Holbrook GP. Photosynthesis, competition, and wastewater treatment characteristics of the microalga Monoraphidium sp. Dek19 at cool temperatures. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Orton LM, Fitzek E, Feng X, Grayburn WS, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y. Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution. J Exp Bot 2020; 71:3361-3373. [PMID: 32206790 DOI: 10.1093/jxb/eraa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/19/2020] [Indexed: 05/22/2023]
Abstract
The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.
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Affiliation(s)
- Lauren M Orton
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Elisabeth Fitzek
- Biology/Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology-CeBiTec, Bielefeld, Germany
| | - Xuehuan Feng
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - W Scott Grayburn
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Yanbin Yin
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
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Fitzek E, Orton L, Entwistle S, Grayburn WS, Ausland C, Duvall MR, Yin Y. Cell Wall Enzymes in Zygnema circumcarinatum UTEX 1559 Respond to Osmotic Stress in a Plant-Like Fashion. Front Plant Sci 2019; 10:732. [PMID: 31231410 PMCID: PMC6566377 DOI: 10.3389/fpls.2019.00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Previous analysis of charophyte green algal (CGA) genomes and transcriptomes for specific protein families revealed that numerous land plant characteristics had already evolved in CGA. In this study, we have sequenced and assembled the transcriptome of Zygnema circumcarinatum UTEX 1559, and combined its predicted protein sequences with those of 13 additional species [five embryophytes (Emb), eight charophytes (Cha), and two chlorophytes (Chl) as the outgroup] for a comprehensive comparative genomics analysis. In total 25,485 orthologous gene clusters (OGCs, equivalent to protein families) of the 14 species were classified into nine OGC groups. For example, the Cha+Emb group contains 4,174 OGCs found in both Cha and Emb but not Chl species, representing protein families that have evolved in the common ancestor of Cha and Emb. Different OGC groups were subjected to a Gene Ontology (GO) enrichment analysis with the Chl+Cha+Emb group (including 5,031 OGCs found in Chl and Cha and Emb) as the control. Interestingly, nine of the 20 top enriched GO terms in the Cha+Emb group are cell wall-related, such as biological processes involving celluloses, pectins, lignins, and xyloglucans. Furthermore, three glycosyltransferase families (GT2, 8, 43) were selected for in-depth phylogenetic analyses, which confirmed their presence in UTEX 1559. More importantly, of different CGA groups, only Zygnematophyceae has land plant cellulose synthase (CesA) orthologs, while other charophyte CesAs form a CGA-specific CesA-like (Csl) subfamily (likely also carries cellulose synthesis activity). Quantitative real-time-PCR experiments were performed on selected GT family genes in UTEX 1559. After osmotic stress treatment, significantly elevated expression was found for GT2 family genes ZcCesA, ZcCslC and ZcCslA-like (possibly mannan and xyloglucan synthases, respectively), as well as for GT8 family genes (possibly pectin synthases). All these suggest that the UTEX 1559 cell wall polysaccharide synthesis-related genes respond to osmotic stress in a manner that is similar to land plants.
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Affiliation(s)
- Elisabeth Fitzek
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld, Germany
| | - Lauren Orton
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Sarah Entwistle
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - W. Scott Grayburn
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Catherine Ausland
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Melvin R. Duvall
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL, United States
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska – Lincoln, Lincoln, NE, United States
- *Correspondence: Yanbin Yin, ;
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Zhou S, Iverson AG, Grayburn WS. Doubling the catabolic reducing power (NADH) output of Escherichia coli fermentation for production of reduced products. Biotechnol Prog 2010; 26:45-51. [PMID: 19862803 DOI: 10.1002/btpr.302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Homofermentative production of reduced products requires additional reducing power output (NADH) from glucose catabolism. Anaerobic expression of the pyruvate dehydrogenase complex (PDH, encoded by aceEF-lpd, a normal aerobic operon) is able to provide the additional NADH required for production of reduced products in Escherichia coli fermentation. The multiple promoters (pflBp(1-7)) of pyruvate formate lyase (pflB) were evaluated for anaerobic expression of the aceEF-lpd operon. Four chromosomal constructs, pflBp(1-7)-aceEF-lpd, pflBp(1-6)-aceEF-lpd, pflBp(6,7)-aceEF-lpd, and pflBp6-aceEF-lpd efficiently expressed the PDH complex in anaerobically grown cells. Doubling the reducing power output was achieved when glucose was oxidized to acetyl-CoA through glycolysis and pyruvate oxidation by the anaerobically expressed PDH complex (glucose -->2 acetyl-CoA + 4 NADH). This additional reducing power output can be used for production of reduced products in anaerobic E. coli fermentation.
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Affiliation(s)
- Shengde Zhou
- Depart. of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA.
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Lotshaw DP, Grayburn WS, Yasui LS, Gasser KW. Expression of the two‐pore domain potassium channel, TASK‐2, in rat pancreatic acinar cell zymogen granule membrane. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.938.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Li S, Myung K, Guse D, Donkin B, Proctor RH, Grayburn WS, Calvo AM. FvVE1 regulates filamentous growth, the ratio of microconidia to macroconidia and cell wall formation in Fusarium verticillioides. Mol Microbiol 2006; 62:1418-32. [PMID: 17054442 DOI: 10.1111/j.1365-2958.2006.05447.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The velvet gene, veA, co-ordinates asexual and sexual development in the homothallic fungal species Aspergillus nidulans. Studies in Aspergillus parasiticus and Aspergillus fumigatus demonstrated that veA also regulates morphological differentiation in these species. Whether veA has the same role in morphogenesis in other fungal genera has not been investigated. In this work, we studied the role of the veA homologue, FvVE1, in the heterothallic fungus Fusarium verticillioides. Deletion of FvVE1 suppressed aerial hyphal growth and reduced colony surface hydrophobicity on solid media. In submerged cultures, FvVE1 deletion caused alterations in hyphal polarity, marked activation of conidiation and yeast-like growth. The latter was promoted by shaking to increase aeration of cultures. In addition, FvVE1 deletion markedly increased the ratio of macroconidia to microconidia. Supplementation of osmotic stabilizers restored the wild-type phenotype to deletion mutants, suggesting phenotypic alterations caused by FvVE1 deletion are related to cell wall defects. This is consistent with the hypersensitivity of FvVE1 deletion mutants to SDS and with the significant reduction in the mannoprotein content of mutants compared with the wild-type strain. However, no dramatic cell wall alterations were observed when mutants were examined by transmission electron microscopy. Our data strongly suggest that FvVE1 is important for cell wall integrity, cell surface hydrophobicity, hyphal polarity and conidiation pattern.
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Affiliation(s)
- Shaojie Li
- Department of Biological Sciences, Northern Illinois University, Dekalb, IL 60115, USA
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Grayburn WS, Hudspeth DSS, Gane MK, Hudspeth MES. The mitochondrial genome of Saprolegnia ferax: organization, gene content and nucleotide sequence. Mycologia 2004; 96:981-989. [PMID: 21148919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The mitochondrial genome of the peronosporomycete water mold Saprolegnia ferax has been characterized as a 46 930 bp circle containing an 8618 bp large inverted repeat (LIR). Eighteen reading frames encode identified subunits of respiratory complexes I, III, IV and V; 16 encode polypeptides of small and large mitoribosome subunits; and one encodes a subunit of the sec-independent protein translocation pathway. Of four additional putative reading frames three are homologues of those found in the related Phytophthora infestans genome. Protein encoding loci in the tightly compacted genome typically are arranged in operon-like clusters including three abutting and two overlapping pairs of reading frames. Translational RNAs include the mitochondrial small and large subunit rRNAs and 25 tRNA species. No tRNAs are encoded to enable translation of any threonine or the arginine CGR codons. The LIR separates the molecule into 19 274 bp large and 10 420 bp small single copy regions, and it encodes intact duplicate copies of four reading frames encoding known proteins, both rRNAs, and five tRNAs. Partial 3' sequences of three additional reading frames are duplicated at single copy sequence junctions. Active recombination between LIR elements generates two distinctive gene orders and uses the duplicated 3' sequences to maintain intact copies of the partially duplicated loci.
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Affiliation(s)
- W Scott Grayburn
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115
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Grayburn WS, Hudspeth DSS, Gane MK, Hudspeth MES. The Mitochondrial Genome of Saprolegnia ferax: Organization, Gene Content and Nucleotide Sequence. Mycologia 2004. [DOI: 10.2307/3762082] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Grayburn WS, Sims TL. Anchored oligo(dT) primers for automated dye terminator DNA sequencing. Biotechniques 1998; 25:340-1, 344-6. [PMID: 9762425 DOI: 10.2144/98253bm01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- W S Grayburn
- Plant Molecular Biology Center, Northern Illinois University, DeKalb 60115, USA
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Grayburn WS, Vick BA. Transformation of sunflower (Helianthus annuus L.) following wounding with glass beads. Plant Cell Rep 1995; 14:285-289. [PMID: 24186761 DOI: 10.1007/bf00232029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/1993] [Revised: 08/26/1994] [Indexed: 06/02/2023]
Abstract
A procedure was developed for transformation of Helianthus annuus (sunflower) using Agrobacterium tumefaciens. Cotyledons were removed from young seedlings, and the remaining tissue was uniformly wounded by shaking with glass beads. The wounded tissue was then co-cultivated with a hypervirulent strain of Agrobacterium tumefaciens harboring the binary plasmid pCNL56. Minimal use of defined medium was required, and no callus was observed. The polymerase chain reaction (PCR) followed by DNA hybridization demonstrated the presence of gusA DNA from pCNL56 in total leaf DNA of 6 primary transformants and 2 progeny plants. No Agrobacterium DNA was detected in total DNA from transformed sunflower leaves that was amplified with primers specific to the miaA chromosomal gene of Agrobacterium. Foreign DNA was also detected in the next generation. β-Glucuronidase (GUS) activity was demonstrated for 5 of the T2 transgenic plants. Grafting was used to increase the number of seeds present on plants that had undergone tissue culture manipulations.
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Affiliation(s)
- W S Grayburn
- United States Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, 58105, Fargo, ND, USA
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Abstract
Nicotiana tabacum tissue was transformed with a rat stearyl-CoA desaturase gene. Gas chromatographic analysis showed an increase in monounsaturated 16 and 18 carbon fatty acids in selected transformed calli and leaves. Fractionation of lipid classes indicated that palmitoleic acid was found in the phosphatidylcholine fraction of desaturase-transformed leaves, but not in leaves transformed with vector sequences. Plant transformation was verified by polymerase chain reaction (PCR) amplification of total leaf DNA.
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Affiliation(s)
- W S Grayburn
- Department of Agronomy, University of Kentucky, Lexington 40546-0091
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Deng W, Grayburn WS, Hamilton-Kemp TR, Collins GB, Hildebrand DF. Expression of soybean-embryo lipoxygenase 2 in transgenic tobacco tissue. Planta 1992; 187:203-208. [PMID: 24178044 DOI: 10.1007/bf00201939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/30/1991] [Indexed: 06/02/2023]
Abstract
To assess the role of lipoxygenase (LOX; EC 1.13.11.12) in plants, we increased the expression of LOX in the tissues of Nicotiana tabacum L. cv. 'KY 14' by over-expression of the LOX2 gene from the soybean (Glycine max (L.) Merrill) embryo. The LOX2 cDNA was manipulated by replacing its 5'-untranslated sequence with the translational enhancer of the alfalfa mosaic virus (AMV), and subcloned into a plant expression vector, 3' to a duplicated cauliflower mosaic virus 35S promoter. The AMV-LOX2 construct was transferred into tobacco using Agrobacterium tumefaciens strain A281. The LOX2 was expressed in transgenic tobacco calli, leaves of transgenic plants, and their seed progeny at levels up to 0.1-0.2% of the total extracted protein. The introduced LOX2 affected fatty-acid oxidative metabolism as evidenced by a 50-529% increase in C6-aldehyde production. The impact on C6-aldehyde formation was greater than the effect on production of fatty-acid hydroperoxides. This is consistent with other studies indicating the greater propensity of soybean embryo LOX2 in generating C6-aldehydes than that of other well-characterized LOX isozymes.
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Affiliation(s)
- W Deng
- Department of Agronomy, University of Kentucky, 40546-0091, Lexington, KY, USA
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Liu W, Hildebrand DF, Grayburn WS, Phillips GC, Collins GB. Effects of exogenous auxins on expression of lipoxygenases in cultured soybean embryos. Plant Physiol 1991; 97:969-76. [PMID: 16668538 PMCID: PMC1081111 DOI: 10.1104/pp.97.3.969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The expression of lipoxygenases (LOXs) is known to be developmentally regulated in soybeans (Glycine max. [L.] Merr.). Hormones have been firmly established as being involved in the growth and developmental processes of a number of plant species. Correlation between the expression of LOXs and the development and germination of soybean embryos suggests that plant hormones may affect the expression of LOXs. The present studies were conducted to investigate the effects of exogenous auxins on the expression of LOX isozymes and LOX activities in cultured cotyledon tissues of immature soybean seeds. The results revealed that at least one of the more acidic nonembryo LOX isozymes was induced by either alpha-naphthaleneacetic acid or indoleacetic acid but not by 2,4-dichlorophenoxyacetic acid after 4 days' exposure. Levels of LOX-1, -2, and -3 proteins and activities were significantly decreased by 2,4-dichlorophenoxyacetic acid 10 days after explanting. S1 analysis showed that embryo LOX messenger RNAs were detectable in the tissues treated with each of the auxins. The reduced levels of the embryo LOX proteins may, therefore, be regulated at the levels of translation, posttranslational modification, or degradation. The more acidic isozymes induced by alpha-naphthaleneacetic acid showed enzymatic activity and shared the same molecular mass and isoelectric point values as the germination-associated LOX isozymes found in hypocotyls and radicles, suggesting that those LOXs are involved in germination competency of soybean embryos.
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Affiliation(s)
- W Liu
- Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546
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Grayburn WS, Schneider GR, Hamilton-Kemp TR, Bookjans G, Ali K, Hildebrand DF. Soybean leaves contain multiple lipoxygenases. Plant Physiol 1991; 95:1214-8. [PMID: 16668114 PMCID: PMC1077675 DOI: 10.1104/pp.95.4.1214] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Chromatofocusing of soybean (Glycine max L.) leaf lipoxygenases revealed three distinct peaks of activity. Based on their isoelectric points (pls), pH optima, and mutant analysis it appears that the leaf isozymes are different from those described from mature soybean seed. At least one leaf lipoxygenase appears to differ from those found in hypocotyls. The pls of the main bands of the three leaf lipoxygenase peaks are 6.67, 5.91, and 5.67. The pH optima curves of three active fractions exhibit peaks at pH 6.2, 5.5, and 8.5, respectively. One of the fractions has two polypeptides with slightly different molecular weights, both of which react to soybean seed lipoxygenase antibodies. The other two fractions contain a polypeptide of unit molecular weight reacting with the lipoxygenase antibodies.
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Affiliation(s)
- W S Grayburn
- Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546
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Abstract
5S rRNA genes of Neurospora crassa are generally dispersed in the genome and are unmethylated. The xi-eta region of Oak Ridge strains represents an informative exception. Most of the cytosines in this region, which consists of a diverged tandem duplication of a 0.8-kilobase-pair segment including a 5S rRNA gene, appear to be methylated (E. U. Selker and J. N. Stevens, Proc. Natl. Acad. Sci. USA 82:8114-8118, 1985). Previous work demonstrated that the xi-eta region functions as a portable signal for de novo DNA methylation (E. U. Selker and J. N. Stevens, Mol. Cell. Biol. 7:1032-1038, 1987; E. U. Selker, B. C. Jensen, and G. A. Richardson, Science 238:48-53, 1987). To identify the structural basis of this property, we have isolated and characterized an unmethylated allele of the xi-eta region from N. crassa Abbott 4. The Abbott 4 allele includes a single 5S rRNA gene, theta, which is different from all previously identified Neurospora 5S rRNA genes. Sequence analysis suggests that the xi-eta region arose from the theta region by duplication of a 794-base-pair segment followed by 267 G.C to A.T mutations in the duplicated DNA. The distribution of these mutations is not random. We propose that the RIP process of N. crassa (E. U. Selker, E. B. Cambareri, B. C. Jensen, and K. R. Haack, Cell 51:741-752, 1987; E. U. Selker, and P. W. Garrett, Proc. Natl. Acad. Sci. USA 85:6870-6874, 1988; E. B. Cambareri, B. C. Jensen, E. Schabtach, and E. U. Selker, Science 244:1571-1575, 1989) is responsible for the numerous transition mutations and DNA methylation in the xi-eta region. A long homopurine-homopyrimidine stretch immediately following the duplicated segment is 9 base pairs longer in the Oak Ridge allele than in the Abbott 4 allele. Triplex DNA, known to occur in homopurine-homopyrimidine sequences, may have mediated the tandem duplication.
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Affiliation(s)
- W S Grayburn
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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Abstract
The relative abundance of a cloned 4.5 kilobase (kb) pair mitochondrial DNA sequence in two suspension cultures of tobacco (Nicotiana tabacum cv Turkish samsun and Nicotiana tabacum NT-1) has been examined. This sequence is 70-fold reduced in NT-1 relative to Turkish samsun; the reduction is correlated with an increase in supercoiled mitochondrial DNA. This sequence does not hybridize with mitochondrial DNA from watermelon, maize, or Saccharomyces cerevisiae, nor with several cloned mitochondrial genes and is thus probably not a gene. It may represent most of the plant mitochondrial genome thought to be non-essential for mitochondrial function. The sequence complexity of supercoiled mitochondrial DNA from NT-1 cells is about one-third that found for the entire mitochondrial genome and does not include the cytochrome oxidase subunit II gene.
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Affiliation(s)
- W S Grayburn
- Department of Botany, University of Washington, Seattle
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Abstract
A portion of the surface of detached Graptopetalum paraquayense E. Walther leaves can be used to assay small amounts of reagents in lanolin for their ability to induce shoots only at the site of application. The cytokinins benzyladenine, kinetin, and 6-(gamma,gamma-dimethylallylamino)purine (DMAAP) were tested, and DMAAP was most effective in bud induction at concentrations below 1%. The higher the hormone concentration, the sooner the appearance of leaf primordia and the higher the ultimate yield of buds. Leaves treated with DMAAP for 2 days developed buds as rapidly as those with longer treatments.
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Affiliation(s)
- W S Grayburn
- Department of Biological Sciences, Stanford University, Stanford, California 94305
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