101
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Cheng DJ, Xu XJ, Yan ZY, Tettey CK, Fang L, Yang GL, Geng C, Tian YP, Li XD. The chloroplast ribosomal protein large subunit 1 interacts with viral polymerase and promotes virus infection. PLANT PHYSIOLOGY 2021; 187:174-186. [PMID: 34618134 PMCID: PMC8418413 DOI: 10.1093/plphys/kiab249] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 05/18/2023]
Abstract
Chloroplasts play an indispensable role in the arms race between plant viruses and hosts. Chloroplast proteins are often recruited by plant viruses to support viral replication and movement. However, the mechanism by which chloroplast proteins regulate potyvirus infection remains largely unknown. In this study, we observed that Nicotiana benthamiana ribosomal protein large subunit 1 (NbRPL1), a chloroplast ribosomal protein, localized to the chloroplasts via its N-terminal 61 amino acids (transit peptide), and interacted with tobacco vein banding mosaic virus (TVBMV) nuclear inclusion protein b (NIb), an RNA-dependent RNA polymerase. Upon TVBMV infection, NbRPL1 was recruited into the 6K2-induced viral replication complexes in chloroplasts. Silencing of NbRPL1 expression reduced TVBMV replication. NbRPL1 competed with NbBeclin1 to bind NIb, and reduced the NbBeclin1-mediated degradation of NIb. Therefore, our results suggest that NbRPL1 interacts with NIb in the chloroplasts, reduces NbBeclin1-mediated NIb degradation, and enhances TVBMV infection.
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Affiliation(s)
- De-Jie Cheng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiao-Jie Xu
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Carlos Kwesi Tettey
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Le Fang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Guang-Ling Yang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chao Geng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
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102
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Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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103
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Stuart D, Sandström M, Youssef HM, Zakhrabekova S, Jensen PE, Bollivar D, Hansson M. Barley Viridis-k links an evolutionarily conserved C-type ferredoxin to chlorophyll biosynthesis. THE PLANT CELL 2021; 33:2834-2849. [PMID: 34051099 PMCID: PMC8408499 DOI: 10.1093/plcell/koab150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Ferredoxins are single-electron carrier proteins involved in various cellular reactions. In chloroplasts, the most abundant ferredoxin accepts electrons from photosystem I and shuttles electrons via ferredoxin NADP+ oxidoreductase to generate NADPH or directly to ferredoxin dependent enzymes. In addition, plants contain other isoforms of ferredoxins. Two of these, named FdC1 and FdC2 in Arabidopsis thaliana, have C-terminal extensions and functions that are poorly understood. Here we identified disruption of the orthologous FdC2 gene in barley (Hordeum vulgare L.) mutants at the Viridis-k locus; these mutants are deficient in the aerobic cyclase reaction of chlorophyll biosynthesis. The magnesium-protoporphyrin IX monomethyl ester cyclase is one of the least characterized enzymes of the chlorophyll biosynthetic pathway and its electron donor has long been sought. Agroinfiltrations showed that the viridis-k phenotype could be complemented in vivo by Viridis-k but not by canonical ferredoxin. VirK could drive the cyclase reaction in vitro and analysis of cyclase mutants showed that in vivo accumulation of VirK is dependent on cyclase enzyme levels. The chlorophyll deficient phenotype of viridis-k mutants suggests that VirK plays an essential role in chlorophyll biosynthesis that cannot be replaced by other ferredoxins, thus assigning a specific function to this isoform of C-type ferredoxins.
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Affiliation(s)
- David Stuart
- Department of Biology, Lund University, Lund 22362, Sweden
| | | | - Helmy M. Youssef
- Department of Biology, Lund University, Lund 22362, Sweden
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | | | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Frederiksberg DK-1958, Denmark
| | - David Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, IL 61702-2900, USA
| | - Mats Hansson
- Department of Biology, Lund University, Lund 22362, Sweden
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104
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Anderson SA, Satyanarayan MB, Wessendorf RL, Lu Y, Fernandez DE. A homolog of GuidedEntry of Tail-anchored proteins3 functions in membrane-specific protein targeting in chloroplasts of Arabidopsis. THE PLANT CELL 2021; 33:2812-2833. [PMID: 34021351 PMCID: PMC8408437 DOI: 10.1093/plcell/koab145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/18/2021] [Indexed: 05/12/2023]
Abstract
The chloroplasts and mitochondria of photosynthetic eukaryotes contain proteins that are closely related to cytosolic Guided Entry of Tail-anchored proteins3 (Get3). Get3 is a targeting factor that efficiently escorts tail-anchored (TA) proteins to the ER. Because other components of the cytosolic-targeting pathway appear to be absent in organelles, previous investigators have asserted that organellar Get3 homologs are unlikely to act as targeting factors. However, we show here both that the Arabidopsis thaliana chloroplast homolog designated as GET3B is structurally similar to cytosolic Get3 proteins and that it selectively binds a thylakoid-localized TA protein. Based on genetic interactions between a get3b mutation and mutations affecting the chloroplast signal recognition particle-targeting pathway, as well as changes in the abundance of photosynthesis-related proteins in mutant plants, we propose that GET3B acts primarily to direct proteins to the thylakoids. Furthermore, through molecular complementation experiments, we show that function of GET3B depends on its ability to hydrolyze ATP, and this is consistent with action as a targeting factor. We propose that GET3B and related organellar Get3 homologs play a role that is analogous to that of cytosolic Get3 proteins, and that GET3B acts as a targeting factor in the chloroplast stroma to deliver TA proteins in a membrane-specific manner.
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Affiliation(s)
- Stacy A. Anderson
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Manasa B. Satyanarayan
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Ryan L. Wessendorf
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Yan Lu
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Donna E. Fernandez
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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105
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Sathasivam R, Yeo HJ, Park CH, Choi M, Kwon H, Sim JE, Park SU, Kim JK. Molecular Characterization, Expression Analysis of Carotenoid, Xanthophyll, Apocarotenoid Pathway Genes, and Carotenoid and Xanthophyll Accumulation in Chelidonium majus L. PLANTS 2021; 10:plants10081753. [PMID: 34451798 PMCID: PMC8398043 DOI: 10.3390/plants10081753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022]
Abstract
Chelidonium majus L. is a perennial herbaceous plant that has various medicinal properties. However, the genomic information about its carotenoid biosynthesis pathway (CBP), xanthophyll biosynthesis pathway (XBP), and apocarotenoid biosynthesis pathway (ABP) genes were limited. Thus, the CBP, XBP, and ABP genes of C. majus were identified and analyzed. Among the 15 carotenoid pathway genes identified, 11 full and 4 partial open reading frames were determined. Phylogenetic analysis of these gene sequences showed higher similarity with higher plants. Through 3D structural analysis and multiple alignments, several distinct conserved motifs were identified, including dinucleotide binding motif, carotene binding motif, and aspartate or glutamate residues. Quantitative RT-PCR showed that CBP, XBP, and ABP genes were expressed in a tissue-specific manner; the highest expression levels were achieved in flowers, followed by those in leaves, roots, and stems. The HPLC analysis of the different organs showed the presence of eight different carotenoids. The highest total carotenoid content was found in leaves, followed by that in flowers, stems, and roots. This study provides information on the molecular mechanisms involved in CBP, XBP, and ABP genes, which might help optimize the carotenoid production in C. majus. The results could also be a basis of further studies on the molecular genetics and functional analysis of CBP, XBP, and ABP genes.
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Affiliation(s)
- Ramaraj Sathasivam
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Hyeon Ji Yeo
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Chang Ha Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Minsol Choi
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Haejin Kwon
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
| | - Ji Eun Sim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Korea;
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (R.S.); (H.J.Y.); (C.H.P.); (M.C.); (H.K.)
- Department of Smart Agriculture Systems, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
- Correspondence: (S.U.P.); (J.K.K.); Tel.: +82-42-821-5730 (S.U.P.); +82-32-835-8241 (J.K.K.); Fax: +82-42-822-2631 (S.U.P.); +82-32-835-0763 (J.K.K.)
| | - Jae Kwang Kim
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Yeonsu-gu, Incheon 22012, Korea;
- Correspondence: (S.U.P.); (J.K.K.); Tel.: +82-42-821-5730 (S.U.P.); +82-32-835-8241 (J.K.K.); Fax: +82-42-822-2631 (S.U.P.); +82-32-835-0763 (J.K.K.)
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106
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Arabia S, Sami AA, Akhter S, Sarker RH, Islam T. Comprehensive in silico Characterization of Universal Stress Proteins in Rice ( Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:712607. [PMID: 34394169 PMCID: PMC8355530 DOI: 10.3389/fpls.2021.712607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 06/10/2023]
Abstract
In a world where climate change is real and its consequences are unprecedented, understanding of the plant adaptive capacity and native stress-responsive machinery is crucial. In recent years, universal stress proteins (USPs) have received much attention in the field of plant science due to their stress-specific transcriptional regulation. This study focuses on the extensive characterization of the USP gene family members in the monocot crop rice (Oryza sativa L. var. japonica). Here, we report a total of 44 USP genes in the rice genome. In silico characterization of these genes showed that domain architecture played a major role in the functional diversification of the USP gene family which holds for all plant USPs. On top of that, a higher conservation of OsUSP members has been exhibited with a monocot genome (Zea mays L.) as compared to a dicot genome (Arabidopsis thaliana L.). Expression profiling of the identified genes led to the discovery of multiple OsUSP genes that showed pronounced transcript alteration under various abiotic stress conditions, indicating their potential role as multi-functional stress-specific modules. Furthermore, expression validation of OsUSP genes using qRT-PCR provided a strong evidence for the utility OsUSP genes in building multi-stress tolerant plants. Altogether, this study provides leads to suitable USP candidates that could be targeted for plant breeding and genetic engineering experiments to develop stress resilient crop species.
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107
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Lehmann M, Vamvaka E, Torrado A, Jahns P, Dann M, Rosenhammer L, Aziba A, Leister D, Rühle T. Introduction of the Carotenoid Biosynthesis α-Branch Into Synechocystis sp. PCC 6803 for Lutein Production. FRONTIERS IN PLANT SCIENCE 2021; 12:699424. [PMID: 34295345 PMCID: PMC8291087 DOI: 10.3389/fpls.2021.699424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Lutein, made by the α-branch of the methyl-erythritol phosphate (MEP) pathway, is one of the most abundant xanthophylls in plants. It is involved in the structural stabilization of light-harvesting complexes, transfer of excitation energy to chlorophylls and photoprotection. In contrast, lutein and the α-branch of the MEP pathway are not present in cyanobacteria. In this study, we genetically engineered the cyanobacterium Synechocystis for the missing MEP α-branch resulting in lutein accumulation. A cassette comprising four Arabidopsis thaliana genes coding for two lycopene cyclases (AtLCYe and AtLCYb) and two hydroxylases (AtCYP97A and AtCYP97C) was introduced into a Synechocystis strain that lacks the endogenous, cyanobacterial lycopene cyclase cruA. The resulting synlut strain showed wild-type growth and only moderate changes in total pigment composition under mixotrophic conditions, indicating that the cruA deficiency can be complemented by Arabidopsis lycopene cyclases leaving the endogenous β-branch intact. A combination of liquid chromatography, UV-Vis detection and mass spectrometry confirmed a low but distinct synthesis of lutein at rates of 4.8 ± 1.5 nmol per liter culture at OD730 (1.03 ± 0.47 mmol mol-1 chlorophyll). In conclusion, synlut provides a suitable platform to study the α-branch of the plastidic MEP pathway and other functions related to lutein in a cyanobacterial host system.
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Affiliation(s)
- Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Evgenia Vamvaka
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alejandro Torrado
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Peter Jahns
- Plant Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marcel Dann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lea Rosenhammer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Amel Aziba
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Thilo Rühle
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Munich, Germany
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108
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Taniguchi YY, Gowik U, Kinoshita Y, Kishizaki R, Ono N, Yokota A, Westhoff P, Munekage YN. Dynamic changes of genome sizes and gradual gain of cell-specific distribution of C 4 enzymes during C 4 evolution in genus Flaveria. THE PLANT GENOME 2021; 14:e20095. [PMID: 33913619 DOI: 10.1002/tpg2.20095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
C4 plants are believed to have evolved from C3 plants through various C3 -C4 intermediate stages in which a photorespiration-dependent CO2 concentration system known as C2 photosynthesis operates. Genes involved in the C4 cycle were thought to be recruited from orthologs present in C3 species and developed cell-specific expression during C4 evolution. To understand the process of establishing C4 photosynthesis, we performed whole-genome sequencing and investigated expression and mesophyll- or bundle-sheath-cell-specific localization of phosphoenolpyruvate carboxylase (PEPC), NADP-malic enzyme (NADP-ME), pyruvate, orthophosphate dikinase (PPDK) in C3 , C3 -C4 intermediate, C4 -like, and C4 Flaveria species. While genome sizes vary greatly, the number of predicted protein-coding genes was similar among C3 , C3 -C4 intermediate, C4 -like, and C4 Flaveria species. Cell-specific localization of the PEPC, NADP-ME, and PPDK transcripts was insignificant or weak in C3 -C4 intermediate species, whereas these transcripts were expressed cell-type specific in C4 -like species. These results showed that elevation of gene expression and cell-specific control of pre-existing C4 cycle genes in C3 species was involved in C4 evolution. Gene expression was gradually enhanced during C4 evolution, whereas cell-specific control was gained independently of quantitative transcriptional activation during evolution from C3 -C4 intermediate to C4 photosynthesis in genus Flaveria.
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Affiliation(s)
- Yukimi Y Taniguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Udo Gowik
- Institute of Plant Molecular and Developmental Biology, Heinrich Heine University, Universitätsstr. 1, Dusseldorf, 40225, Germany
| | - Yuto Kinoshita
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Risa Kishizaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Naoaki Ono
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Akiho Yokota
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Peter Westhoff
- Institute of Plant Molecular and Developmental Biology, Heinrich Heine University, Universitätsstr. 1, Dusseldorf, 40225, Germany
| | - Yuri N Munekage
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
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109
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Le Moigne T, Gurrieri L, Crozet P, Marchand CH, Zaffagnini M, Sparla F, Lemaire SD, Henri J. Crystal structure of chloroplastic thioredoxin z defines a type-specific target recognition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:434-447. [PMID: 33930214 DOI: 10.1111/tpj.15300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Thioredoxins (TRXs) are ubiquitous disulfide oxidoreductases structured according to a highly conserved fold. TRXs are involved in a myriad of different processes through a common chemical mechanism. Plant TRXs evolved into seven types with diverse subcellular localization and distinct protein target selectivity. Five TRX types coexist in the chloroplast, with yet scarcely described specificities. We solved the crystal structure of a chloroplastic z-type TRX, revealing a conserved TRX fold with an original electrostatic surface potential surrounding the redox site. This recognition surface is distinct from all other known TRX types from plant and non-plant sources and is exclusively conserved in plant z-type TRXs. We show that this electronegative surface endows thioredoxin z (TRXz) with a capacity to activate the photosynthetic Calvin-Benson cycle enzyme phosphoribulokinase. The distinct electronegative surface of TRXz thereby extends the repertoire of TRX-target recognitions.
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Affiliation(s)
- Théo Le Moigne
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Faculty of Sciences, Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin, 91190, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Libero Gurrieri
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Pierre Crozet
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
- Sorbonne Université, Polytech Sorbonne, Paris, 75005, France
| | - Christophe H Marchand
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
- Plateforme de Protéomique, Institut de Biologie Physico-Chimique, FR 550, CNRS, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Francesca Sparla
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 42, Bologna, 40126, Italy
| | - Stéphane D Lemaire
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
| | - Julien Henri
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, UMR 7238, CNRS, Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR 8226, CNRS, Sorbonne Université, 13 Rue Pierre et Marie Curie, Paris, 75005, France
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Arabia S, Shah MNA, Sami AA, Ghosh A, Islam T. Identification and expression profiling of proline metabolizing genes in Arabidopsis thaliana and Oryza sativa to reveal their stress-specific transcript alteration. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1469-1485. [PMID: 34366590 PMCID: PMC8295428 DOI: 10.1007/s12298-021-01023-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 05/10/2023]
Abstract
UNLABELLED The amino acid, proline, is utilized by different organisms to offset cellular imbalances caused by environmental stresses. The wide use of proline as a stress adaptor molecule indicates that proline has a fundamental biological role in stress response. A comprehensive analysis of the transcript abundance of proline metabolizing genes is fundamental for the assessment of function and regulation of each gene. Using available microarray data and quantitative real-time RT-PCR, the expression profiles of gene encoding key proline biosynthesis and degradation enzymes i.e., OAT, P5CS, P5CR and PDH were examined. Interestingly, validation of candidate genes in rice using in-silico data provided strong evidence for their involvement in stress response. Note that, OsOAT, OsP5CS1, OsP5CS2, OsP5CR showed similar expression pattern in quantitative real-time RT-PCR results as compared to microarray data. However, OsPDH showed a different expression pattern which may be due to the genotypic variation. Furthermore, a biochemical assay measuring proline content gave us a proper indication of the accumulation of proline under stressed conditions. Identification of key proline metabolizing genes from rice and Arabidopsis provides insights on the molecular regulation of proline homeostasis, to initiate metabolic engineering to develop stress-resilient plants. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01023-0.
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Affiliation(s)
- Shatil Arabia
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000 Bangladesh
| | - Md Nur Ahad Shah
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Asif Ahmed Sami
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000 Bangladesh
| | | | - Tahmina Islam
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000 Bangladesh
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Zhang L, Ye SC, Chen WB, Han JC, Tian JJ, Zhang YB, Xu JL, Cao JY, Qin C. Screening the rate-limiting genes in the ω6 polyunsaturated fatty acid biosynthesis pathway in Nannochloropsis oceanica. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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112
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A Transcription Factor Regulates Gene Expression in Chloroplasts. Int J Mol Sci 2021; 22:ijms22136769. [PMID: 34202438 PMCID: PMC8268430 DOI: 10.3390/ijms22136769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/21/2023] Open
Abstract
The chloroplast is a semi-autonomous organelle with its own genome. The expression of chloroplast genes depends on both chloroplasts and the nucleus. Although many nucleus-encoded proteins have been shown to localize in chloroplasts and are essential for chloroplast gene expression, it is not clear whether transcription factors can regulate gene expression in chloroplasts. Here we report that the transcription factor NAC102 localizes in both chloroplasts and nucleus in Arabidopsis. Specifically, NAC102 localizes in chloroplast nucleoids. Yeast two-hybrid assay and co-immunoprecipitation assay suggested that NAC102 interacts with chloroplast RNA polymerases. Furthermore, overexpression of NAC102 in chloroplasts leads to reduced chloroplast gene expression and chlorophyll content, indicating that NAC102 functions as a repressor in chloroplasts. Our study not only revealed that transcription factors are new regulators of chloroplast gene expression, but also discovered that transcription factors can function in chloroplasts in addition to the canonical organelle nucleus.
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113
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Yunus IS, Wang Z, Sattayawat P, Muller J, Zemichael FW, Hellgardt K, Jones PR. Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803. ACS Synth Biol 2021; 10:1417-1428. [PMID: 34003632 DOI: 10.1021/acssynbio.1c00029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1-Octanol has gained interest as a chemical precursor for both high and low value commodities including fuel, solvents, surfactants, and fragrances. By harnessing the power from sunlight and CO2 as carbon source, cyanobacteria has recently been engineered for renewable production of 1-octanol. The productivity, however, remained low. In the present work, we report efforts to further improve the 1-octanol productivity. Different N-terminal truncations were evaluated on three thioesterases from different plant species, resulting in several candidate thioesterases with improved activity and selectivity toward octanoyl-ACP. The structure/function trials suggest that current knowledge and/or state-of-the art computational tools are insufficient to determine the most appropriate cleavage site for thioesterases in Synechocystis. Additionally, by tuning the inducer concentration and light intensity, we further improved the 1-octanol productivity, reaching up to 35% (w/w) carbon partitioning and a titer of 526 ± 5 mg/L 1-octanol in 12 days. Long-term cultivation experiments demonstrated that the improved strain can be stably maintained for at least 30 days and/or over ten times serial dilution. Surprisingly, the improved strain was genetically stable in contrast to earlier strains having lower productivity (and hence a reduced chance of reaching toxic product concentrations). Altogether, improved enzymes and environmental conditions (e.g., inducer concentration and light intensity) substantially increased the 1-octanol productivity. When cultured under continuous conditions, the bioproduction system reached an accumulative titer of >3.5 g/L 1-octanol over close to 180 days.
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Affiliation(s)
- Ian Sofian Yunus
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Zhixuan Wang
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Pachara Sattayawat
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jonathan Muller
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Fessehaye W. Zemichael
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Klaus Hellgardt
- Department of Chemical Engineering, Imperial College London, SW7 2AZ London, United Kingdom
| | - Patrik R. Jones
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
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Evolution of an assembly factor-based subunit contributed to a novel NDH-PSI supercomplex formation in chloroplasts. Nat Commun 2021; 12:3685. [PMID: 34140516 PMCID: PMC8211685 DOI: 10.1038/s41467-021-24065-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2021] [Indexed: 11/09/2022] Open
Abstract
Chloroplast NADH dehydrogenase-like (NDH) complex is structurally related to mitochondrial Complex I and forms a supercomplex with two copies of Photosystem I (the NDH-PSI supercomplex) via linker proteins Lhca5 and Lhca6. The latter was acquired relatively recently in a common ancestor of angiosperms. Here we show that NDH-dependent Cyclic Electron Flow 5 (NDF5) is an NDH assembly factor in Arabidopsis. NDF5 initiates the assembly of NDH subunits (PnsB2 and PnsB3) and Lhca6, suggesting that they form a contact site with Lhca6. Our analysis of the NDF5 ortholog in Physcomitrella and angiosperm genomes reveals the subunit PnsB2 to be newly acquired via tandem gene duplication of NDF5 at some point in the evolution of angiosperms. Another Lhca6 contact subunit, PnsB3, has evolved from a protein unrelated to NDH. The structure of the largest photosynthetic electron transport chain complex has become more complicated by acquiring novel subunits and supercomplex formation with PSI. The chloroplast NDH complex interacts with Photosystem I to form the NDH-PSI supercomplex. Here the authors show that Arabidopsis NDF5 shares a common ancestor with the NDH subunit PnsB2 and acts as an NDH assembly factor initiating the assembly of PnsB2 and the evolutionarily distinct PnsB3.
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Li M, Ruwe H, Melzer M, Junker A, Hensel G, Tschiersch H, Schwenkert S, Chamas S, Schmitz-Linneweber C, Börner T, Stein N. The Arabidopsis AAC Proteins CIL and CIA2 Are Sub-functionalized Paralogs Involved in Chloroplast Development. FRONTIERS IN PLANT SCIENCE 2021; 12:681375. [PMID: 34163512 PMCID: PMC8215611 DOI: 10.3389/fpls.2021.681375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/06/2021] [Indexed: 05/22/2023]
Abstract
The Arabidopsis gene Chloroplast Import Apparatus 2 (CIA2) encodes a transcription factor that positively affects the activity of nuclear genes for chloroplast ribosomal proteins and chloroplast protein import machineries. CIA2-like (CIL) is the paralogous gene of CIA2. We generated a cil mutant by site-directed mutagenesis and compared it with cia2 and cia2cil double mutant. Phenotype of the cil mutant did not differ from the wild type under our growth conditions, except faster growth and earlier time to flowering. Compared to cia2, the cia2cil mutant showed more impaired chloroplast functions and reduced amounts of plastid ribosomal RNAs. In silico analyses predict for CIA2 and CIL a C-terminal CCT domain and an N-terminal chloroplast transit peptide (cTP). Chloroplast (and potentially nuclear) localization was previously shown for HvCMF3 and HvCMF7, the homologs of CIA2 and CIL in barley. We observed nuclear localization of CIL after transient expression in Arabidopsis protoplasts. Surprisingly, transformation of cia2 with HvCMF3, HvCMF7, or with a truncated CIA2 lacking the predicted cTP could partially rescue the pale-green phenotype of cia2. These data are discussed with respect to potentially overlapping functions between CIA2, CIL, and their barley homologs and to the function of the putative cTPs of CIA2 and CIL.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Rhoda Erdmann Haus, Berlin, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, IPK, Gatersleben, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | - Henning Tschiersch
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, IPK, Gatersleben, Germany
| | - Serena Schwenkert
- Department of Biology I, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Sindy Chamas
- Plant Reproductive Biology, Department of Physiology and Cell Biology, IPK, Gatersleben, Germany
| | | | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Rhoda Erdmann Haus, Berlin, Germany
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research (CiBreed), Georg-August-Universität Göttingen, Göttingen, Germany
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Ding XT, Fan Y, Jiang EY, Shi XY, Krautter E, Hu GR, Li FL. Expression of the Vitreoscilla hemoglobin gene in Nannochloropsis oceanica regulates intracellular oxygen balance under high-light. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 221:112237. [PMID: 34116318 DOI: 10.1016/j.jphotobiol.2021.112237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
Nannochloropsis oceanica is widely used as a model photosynthetic chassis to produce fatty acids and carotenoid pigments. However, intense light typically causes excessive generation of reactive oxygen species (ROS) and photorespiration in microalgal cells, which results in decreased cell growth rate and unsaturated fatty acid content. In this study, the Vitreoscilla hemoglobin gene (vgb) was introduced into N. oceanica cells and expressed by using the light-harvesting complex promoter and its signal peptide. Compared with wild type (WT), the growth rate of transformants increased by 7.4%-18.5%, and the eicosapentaenoic acid content in an optimal transformant increased by 21.0%. Correspondingly, the intracellular ROS levels decreased by 56.9%-70.0%, and the catalase content in transformants was about 1.8 times that of WT. The photorespiration level of transformants was reduced by the measurement and calculation of the dissolved oxygen concentration under the condition of light-dark transition. The expression level of the key genes related to the photorespiration pathway in transformants was more than 80% lower than that in WT. These results indicated that Vitreoscilla hemoglobin could improve microalgal growth by reducing ROS damage and modulating photorespiration under stress conditions.
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Affiliation(s)
- Xiao-Ting Ding
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Yong Fan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Er-Ying Jiang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Yi Shi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | | | - Guang-Rong Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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Anami S, Yamashino T, Suzuki R, Nakai K, Sato K, Wu B, Ryo M, Sugita M, Aoki S. Red light-regulated interaction of Per-Arnt-Sim histidine kinases with partner histidine-containing phosphotransfer proteins in Physcomitrium patens. Genes Cells 2021; 26:698-713. [PMID: 34086383 DOI: 10.1111/gtc.12878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022]
Abstract
Multi-step phosphorelay (MSP) is a broadly distributed signaling system in organisms. In MSP, histidine kinases (HKs) receive various environmental signals and transmit them by autophosphorylation followed by phosphotransfer to partner histidine-containing phosphotransfer proteins (HPts). Previously, we reported that Per-Arnt-Sim (PAS) domain-containing HK1 (PHK1) and PHK2 of the moss Physcomitrium (Physcomitrella) patens repressed red light-induced protonema branching, a critical step in the moss life cycle. In plants, PHK homolog-encoding genes are conserved only in early-diverging lineages such as bryophytes and lycophytes. PHKs-mediated signaling machineries attract attention especially from an evolutionary viewpoint, but they remain uninvestigated. Here, we studied the P. patens PHKs focusing on their subcellular patterns of localization and interaction with HPts. Yeast two-hybrid analysis, a localization assay with a green fluorescent protein, and a bimolecular fluorescence complementation analysis together showed that PHKs are localized and interact with partner HPts mostly in the nucleus, as unprecedented features for plant HKs. Additionally, red light triggered the interactions between PHKs and HPts in the cytoplasm, and light co-repressed the expression of PHK1 and PHK2 as well as genes encoding their partner HPts. Our results emphasize the uniqueness of PHKs-mediated signaling machineries, and functional implications of this uniqueness are discussed.
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Affiliation(s)
- Shu Anami
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | | | - Ryo Suzuki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kota Nakai
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Kensuke Sato
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Bowen Wu
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Masashi Ryo
- Graduate School of Information Science, Nagoya University, Nagoya, Japan
| | - Mamoru Sugita
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
| | - Setsuyuki Aoki
- Graduate School of Informatics, Nagoya University, Nagoya, Japan
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118
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Myo T, Wei F, Zhang H, Hao J, Zhang B, Liu Z, Cao G, Tian B, Shi G. Genome-wide identification of the BASS gene family in four Gossypium species and functional characterization of GhBASSs against salt stress. Sci Rep 2021; 11:11342. [PMID: 34059742 PMCID: PMC8166867 DOI: 10.1038/s41598-021-90740-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
Bile acid sodium symporter (BASS) family proteins encode a class of sodium/solute symporters. Even though the sodium transporting property of BASSs in mammals was well studied, their sodium transportability and functional roles in plant salt tolerance remained largely unknown. Here, BASS family members from 4 cotton species, as well as 30 other species were identified. Then, they were designated as members of BASS1 to BASS5 subfamilies according to their sequence similarity and phylogenetic relationships. There were 8, 11, 16 and 18 putative BASS genes in four cotton species. While whole-genome duplications (WGD) and segmental duplications rendered the expansion of the BASS gene family in cotton, BASS gene losses occurred in the tetraploid cotton during the evolution from diploids to allotetraploids. Concerning functional characterizations, the transcript profiling of GhBASSs revealed that they not only preferred tissue-specific expression but also were differently induced by various stressors and phytohormones. Gene silencing and overexpression experiments showed that GhBASS1 and GhBASS3 positively regulated, whereas GhBASS2, GhBASS4 and GhBASS5 negatively regulated plant salt tolerance. Taken together, BASS family genes have evolved before the divergence from the common ancestor of prokaryotes and eukaryotes, and GhBASSs are plastidial sodium-dependent metabolite co-transporters that can influence plant salt tolerance.
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Affiliation(s)
- Thwin Myo
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Fang Wei
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Honghao Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jianfeng Hao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Bin Zhang
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Zhixian Liu
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gangqiang Cao
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Baoming Tian
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Gongyao Shi
- grid.207374.50000 0001 2189 3846Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
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Ceusters N, Ceusters J, Hurtado-Castano N, Dever LV, Boxall SF, Kneřová J, Waller JL, Rodick R, Van den Ende W, Hartwell J, Borland AM. Phosphorolytic degradation of leaf starch via plastidic α-glucan phosphorylase leads to optimized plant growth and water use efficiency over the diel phases of Crassulacean acid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4419-4434. [PMID: 33754643 PMCID: PMC8266541 DOI: 10.1093/jxb/erab132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/19/2021] [Indexed: 05/27/2023]
Abstract
In plants with Crassulacean acid metabolism (CAM), it has been proposed that the requirement for nocturnal provision of phosphoenolpyruvate as a substrate for CO2 uptake has resulted in a re-routing of chloroplastic starch degradation from the amylolytic route to the phosphorolytic route. To test this hypothesis, we generated and characterized four independent RNAi lines of the obligate CAM species Kalanchoë fedtschenkoi with a >10-fold reduction in transcript abundance of plastidic α-glucan phosphorylase (PHS1). The rPHS1 lines showed diminished nocturnal starch degradation, reduced dark CO2 uptake, a reduction in diel water use efficiency (WUE), and an overall reduction in growth. A re-routing of starch degradation via the hydrolytic/amylolytic pathway was indicated by hyperaccumulation of maltose in all rPHS1 lines. Further examination indicated that whilst operation of the core circadian clock was not compromised, plasticity in modulating net dark CO2 uptake in response to changing photoperiods was curtailed. The data show that phosphorolytic starch degradation is critical for efficient operation of the CAM cycle and for optimizing WUE. This finding has clear relevance for ongoing efforts to engineer CAM into non-CAM species as a means of boosting crop WUE for a warmer, drier future.
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Affiliation(s)
- Nathalie Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, 2440 Geel, Belgium
| | - Johan Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, 2440 Geel, Belgium
- UHasselt, Centre for Environmental Sciences, Environmental Biology, Campus Diepenbeek, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Natalia Hurtado-Castano
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Louisa V Dever
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Susanna F Boxall
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jana Kneřová
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jade L Waller
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Rebecca Rodick
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Wim Van den Ende
- Faculty of Science, Department of Biology, Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Heverlee, Belgium
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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Chin-Fatt A, Menassa R. A V HH-Fc Fusion Targeted to the Chloroplast Thylakoid Lumen Assembles and Neutralizes Enterohemorrhagic E. coli O157:H7. FRONTIERS IN PLANT SCIENCE 2021; 12:686421. [PMID: 34122494 PMCID: PMC8193579 DOI: 10.3389/fpls.2021.686421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Chimeric fusion proteins comprising a single domain antibody (VHH) fused to a crystallizable fragment (Fc) of an immunoglobulin are modular glycoproteins that are becoming increasingly in demand because of their value as diagnostics, research reagents and passive immunization therapeutics. Because ER-associated degradation and misfolding may potentially be limiting factors in the oxidative folding of VHH-Fc fusion proteins in the ER, we sought to explore oxidative folding in an alternative sub-compartment, the chloroplast thylakoid lumen, and determine its viability in a molecular farming context. We developed a set of in-house expression vectors for transient transformation of Nicotiana benthamiana leaves that target a VHH-Fc to the thylakoid lumen via either secretory (Sec) or twin-arginine translocation (Tat) import pathways. Compared to stromal [6.63 ± 3.41 mg/kg fresh weight (FW)], cytoplasmic (undetectable) and Tat-import pathways (5.43 ± 2.41 mg/kg FW), the Sec-targeted VHH-Fc showed superior accumulation (30.56 ± 5.19 mg/kg FW), but was less than that of the ER (51.16 ± 9.11 mg/kg FW). Additionally, the introduction of a rationally designed de novo disulfide bond enhances in planta accumulation when introduced into the Sec-targeted Fc fusion protein from 50.24 ± 4.08 mg/kg FW to 110.90 ± 6.46 mg/kg FW. In vitro immunofluorescent labeling assays on VHH-Fc purified from Sec, Tat, and stromal pathways demonstrate that the antibody still retains VHH functionality in binding Escherichia coli O157:H7 and neutralizing its intimate adherence to human epithelial type 2 cells. These results overall provide a proof of concept that the oxidative folding environment of the thylakoid lumen may be a viable compartment for stably folding disulfide-containing recombinant VHH-Fc proteins.
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Affiliation(s)
- Adam Chin-Fatt
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Rima Menassa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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Kleiner FH, Vesteg M, Steiner JM. An ancient glaucophyte c6-like cytochrome related to higher plant cytochrome c6A is imported into muroplasts. J Cell Sci 2021; 134:261815. [DOI: 10.1242/jcs.255901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
Abstract
Cytochrome c6 is a redox carrier in the thylakoid lumen of cyanobacteria and some eukaryotic algae. Although the isofunctional plastocyanin is present in land plants and the green alga Chlamydomonas reinhardtii, these organisms also possess a cytochrome c6-like protein designated as cytochrome c6A. Two other cytochrome c6-like groups, c6B and c6C, have been identified in cyanobacteria. In this study, we have identified a novel c6-like cytochrome called PetJ2, which is encoded in the nuclear genome of Cyanophora paradoxa, a member of the glaucophytes – the basal branch of the Archaeplastida. We propose that glaucophyte PetJ2 protein is related to cyanobacterial c6B and c6C cytochromes, and that cryptic green algal and land plant cytochromes c6A evolved from an ancestral archaeplastidial PetJ2 protein. In vitro import experiments with isolated muroplasts revealed that PetJ2 is imported into plastids. Although it harbors a twin-arginine motif in its thylakoid-targeting peptide, which is generally indicative of thylakoid import via the Tat import pathway, our import experiments with isolated muroplasts and the heterologous pea thylakoid import system revealed that PetJ2 uses the Sec pathway instead of the Tat import pathway.
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Affiliation(s)
- Friedrich Hans Kleiner
- Institute of Biology – Plant Physiology, Martin Luther University Halle-Wittenberg, Halle/Saale 06099, Germany
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
- School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Jürgen Michael Steiner
- Institute of Biology – Plant Physiology, Martin Luther University Halle-Wittenberg, Halle/Saale 06099, Germany
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
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High-throughput insertional mutagenesis reveals novel targets for enhancing lipid accumulation in Nannochloropsis oceanica. Metab Eng 2021; 66:239-258. [PMID: 33971293 DOI: 10.1016/j.ymben.2021.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022]
Abstract
The microalga Nannochloropsis oceanica is considered a promising platform for the sustainable production of high-value lipids and biofuel feedstocks. However, current lipid yields of N. oceanica are too low for economic feasibility. Gaining fundamental insights into the lipid metabolism of N. oceanica could open up various possibilities for the optimization of this species through genetic engineering. Therefore, the aim of this study was to discover novel genes associated with an elevated neutral lipid content. We constructed an insertional mutagenesis library of N. oceanica, selected high lipid mutants by five rounds of fluorescence-activated cell sorting, and identified disrupted genes using a novel implementation of a rapid genotyping procedure. One particularly promising mutant (HLM23) was disrupted in a putative APETALA2-like transcription factor gene. HLM23 showed a 40%-increased neutral lipid content, increased photosynthetic performance, and no growth impairment. Furthermore, transcriptome analysis revealed an upregulation of genes related to plastidial fatty acid biosynthesis, glycolysis and the Calvin-Benson-Bassham cycle in HLM23. Insights gained in this work can be used in future genetic engineering strategies for increased lipid productivity of Nannochloropsis.
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Furubayashi M, Kubo A, Takemura M, Otani Y, Maoka T, Terada Y, Yaoi K, Ohdan K, Misawa N, Mitani Y. Capsanthin Production in Escherichia coli by Overexpression of Capsanthin/Capsorubin Synthase from Capsicum annuum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5076-5085. [PMID: 33890772 DOI: 10.1021/acs.jafc.1c00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Capsanthin, a characteristic red carotenoid found in the fruits of red pepper (Capsicum annuum), is widely consumed as a food and a functional coloring additive. An enzyme catalyzing capsanthin synthesis was identified as capsanthin/capsorubin synthase (CCS) in the 1990s, but no microbial production of capsanthin has been reported. We report here the first successful attempt to biosynthesize capsanthin in Escherichia coli by carotenoid-pathway engineering. Our initial attempt to coexpress eight enzyme genes required for capsanthin biosynthesis did not detect the desired product. The dual activity of CCS as a lycopene β-cyclase as well as a capsanthin/capsorubin synthase likely complicated the task. We demonstrated that a particularly high expression level of the CCS gene and the minimization of byproducts by regulating the seven upstream carotenogenic genes were crucial for capsanthin formation in E. coli. Our results provide a platform for further study of CCS activity and capsanthin production in microorganisms.
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Affiliation(s)
- Maiko Furubayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan
| | - Akiko Kubo
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka 555-8502, Japan
| | - Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yuko Otani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan
| | - Takashi Maoka
- Division of Food Function and Chemistry, Research Institute for Production Development, Kyoto 606-0805, Japan
| | - Yoshinobu Terada
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka 555-8502, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Kohji Ohdan
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka 555-8502, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan
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Guardini Z, Dall’Osto L, Barera S, Jaberi M, Cazzaniga S, Vitulo N, Bassi R. High Carotenoid Mutants of Chlorella vulgaris Show Enhanced Biomass Yield under High Irradiance. PLANTS 2021; 10:plants10050911. [PMID: 34062906 PMCID: PMC8147269 DOI: 10.3390/plants10050911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/30/2022]
Abstract
Microalgae represent a carbon-neutral source of bulk biomass, for extraction of high-value compounds and production of renewable fuels. Due to their high metabolic activity and reproduction rates, species of the genus Chlorella are highly productive when cultivated in photobioreactors. However, wild-type strains show biological limitations making algal bioproducts expensive compared to those extracted from other feedstocks. Such constraints include inhomogeneous light distribution due to high optical density of the culture, and photoinhibition of the surface-exposed cells. Thus, the domestication of algal strains for industry makes it increasingly important to select traits aimed at enhancing light-use efficiency while withstanding excess light stress. Carotenoids have a crucial role in protecting against photooxidative damage and, thus, represent a promising target for algal domestication. We applied chemical mutagenesis to Chlorella vulgaris and selected for enhanced tolerance to the carotenoid biosynthesis inhibitor norflurazon. The NFR (norflurazon-resistant) strains showed an increased carotenoid pool size and enhanced tolerance towards photooxidative stress. Growth under excess light revealed an improved carbon assimilation rate of NFR strains with respect to WT. We conclude that domestication of Chlorella vulgaris, by optimizing both carotenoid/chlorophyll ratio and resistance to photooxidative stress, boosted light-to-biomass conversion efficiency under high light conditions typical of photobioreactors. Comparison with strains previously reported for enhanced tolerance to singlet oxygen, reveals that ROS resistance in Chlorella is promoted by at least two independent mechanisms, only one of which is carotenoid-dependent.
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Li M, Guo G, Pidon H, Melzer M, Prina AR, Börner T, Stein N. ATP-Dependent Clp Protease Subunit C1, HvClpC1, Is a Strong Candidate Gene for Barley Variegation Mutant luteostrians as Revealed by Genetic Mapping and Genomic Re-sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:664085. [PMID: 33936155 PMCID: PMC8086601 DOI: 10.3389/fpls.2021.664085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Implementation of next-generation sequencing in forward genetic screens greatly accelerated gene discovery in species with larger genomes, including many crop plants. In barley, extensive mutant collections are available, however, the causative mutations for many of the genes remains largely unknown. Here we demonstrate how a combination of low-resolution genetic mapping, whole-genome resequencing and comparative functional analyses provides a promising path toward candidate identification of genes involved in plastid biology and/or photosynthesis, even if genes are located in recombination poor regions of the genome. As a proof of concept, we simulated the prediction of a candidate gene for the recently cloned variegation mutant albostrians (HvAST/HvCMF7) and adopted the approach for suggesting HvClpC1 as candidate gene for the yellow-green variegation mutant luteostrians.
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Affiliation(s)
- Mingjiu Li
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Alberto R. Prina
- Institute of Genetics ‘Ewald A. Favret’ (IGEAF), INTA CICVyA/Argentina, Hurlingham, Buenos Aires, Argentina
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
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126
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Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida. Antioxidants (Basel) 2021; 10:antiox10040597. [PMID: 33924520 PMCID: PMC8069737 DOI: 10.3390/antiox10040597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 11/17/2022] Open
Abstract
Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization.
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127
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Jonckheere V, Van Damme P. N-Terminal Acetyltransferase Naa40p Whereabouts Put into N-Terminal Proteoform Perspective. Int J Mol Sci 2021; 22:ijms22073690. [PMID: 33916271 PMCID: PMC8037211 DOI: 10.3390/ijms22073690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/21/2022] Open
Abstract
The evolutionary conserved N-alpha acetyltransferase Naa40p is among the most selective N-terminal acetyltransferases (NATs) identified to date. Here we identified a conserved N-terminally truncated Naa40p proteoform named Naa40p25 or short Naa40p (Naa40S). Intriguingly, although upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40p (Naa40L), but expressing Naa40S. Interestingly, human Naa40L and Naa40S displayed differential expression and subcellular localization patterns by exhibiting a principal nuclear and cytoplasmic localization, respectively. Furthermore, Naa40L was shown to be N-terminally myristoylated and to interact with N-myristoyltransferase 1 (NMT1), implicating NMT1 in steering Naa40L nuclear import. Differential interactomics data obtained by biotin-dependent proximity labeling (BioID) further hints to context-dependent roles of Naa40p proteoforms. More specifically, with Naa40S representing the main co-translationally acting actor, the interactome of Naa40L was enriched for nucleolar proteins implicated in ribosome biogenesis and the assembly of ribonucleoprotein particles, overall indicating a proteoform-specific segregation of previously reported Naa40p activities. Finally, the yeast histone variant H2A.Z and the transcriptionally regulatory protein Lge1 were identified as novel Naa40p substrates, expanding the restricted substrate repertoire of Naa40p with two additional members and further confirming Lge1 as being the first redundant yNatA and yNatD substrate identified to date.
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128
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Wang R, Ren Y, Yan H, Teng X, Zhu X, Wang Y, Zhang X, Guo X, Lin Q, Cheng Z, Lei C, Wang J, Jiang L, Wang Y, Wan J. ENLARGED STARCH GRAIN1 affects amyloplast development and starch biosynthesis in rice endosperm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110831. [PMID: 33691965 DOI: 10.1016/j.plantsci.2021.110831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
Cereal crops accumulate large amounts of starch which is synthesized and stored in amyloplasts in the form of starch grains (SGs). Despite significant progress in deciphering starch biosynthesis, our understanding of amyloplast development in rice (Oryza sativa) endosperm remains largely unknown. Here, we report a novel rice floury mutant named enlarged starch grain1 (esg1). The mutant has decreased starch content, altered starch physicochemical properties, slower grain-filling rate and reduced 1000-grain weight. A distinctive feature in esg1 endosperm is that SGs are much larger, mainly due to an increased number of starch granules per SG. Spherical and loosely assembled granules, together with those weakly stained SGs may account for decreased starch content in esg1. Map-based cloning revealed that ESG1 encodes a putative permease subunit of a bacterial-type ABC (ATP-binding cassette) lipid transporter. ESG1 is constitutively expressed in various tissues. It encodes a protein localized to the chloroplast and amyloplast membranes. Mutation of ESG1 causes defective galactolipid synthesis. The overall study indicates that ESG1 is a newly identified protein affecting SG development and subsequent starch biosynthesis, which provides novel insights into amyloplast development in rice.
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Affiliation(s)
- Rongqi Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaopin Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Jeon S, Koh HG, Cho JM, Kang NK, Chang YK. Enhancement of lipid production in Nannochloropsis salina by overexpression of endogenous NADP-dependent malic enzyme. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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130
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Li M, Xu J, Lyu F, Khomenko I, Biasioli F, Villani M, Baldan B, Varotto C. Evolution of isoprene emission in Arecaceae (palms). Evol Appl 2021; 14:902-914. [PMID: 33897811 PMCID: PMC8061277 DOI: 10.1111/eva.13169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 01/05/2023] Open
Abstract
Isoprene synthase (IspS) is the sole enzyme in plants responsible for the yearly emission in the atmosphere of thousands of tonnes of the natural hydrocarbon isoprene worldwide. Species of the monocotyledonous family Arecaceae (palms) are among the highest plant emitters, but to date no IspS gene from this family has been identified. Here, we screened with PTR-ToF-MS 18 genera of the Arecaceae for isoprene emission and found that the majority of the sampled species emits isoprene. Putative IspS genes from six different genera were sequenced and three of them were functionally characterized by heterologous overexpression in Arabidopsis thaliana, demonstrating that they encode functional IspS genes. Site-directed mutagenesis and expression in Arabidopsis demonstrated the functional relevance of a novel IspS diagnostic tetrad from Arecaceae, whose most variable amino acids could not preserve catalytic function when substituted by a putatively dicotyledonous-specific tetrad. In particular, mutation of threonine 479 likely impairs the open-closed transition of the enzyme by altering the network of hydrogen bonds between helices H1α, H, and I. These results shed new light on the evolution of IspS in monocots, suggesting that isoprene emission is an ancestral trait within the Arecaceae family. The identification of IspS from Arecaceae provides promising novel enzymes for the production of isoprene in heterologous systems and allows the screening and selection of commercially relevant palm varieties with lower environmental impact.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Jia Xu
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Fuling Lyu
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
- Experimental Center of Forestry in North ChinaChinese Academy of ForestryBeijingChina
| | - Iuliia Khomenko
- Department of Food Quality and Nutrition, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Franco Biasioli
- Department of Food Quality and Nutrition, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | | | - Barbara Baldan
- Botanical Garden of PadovaUniversity of PadovaPadovaItaly
- Department of BiologyUniversity of PadovaPadovaItaly
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
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131
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Shao H, Huang W, Avilan L, Receveur-Bréchot V, Puppo C, Puppo R, Lebrun R, Gontero B, Launay H. A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana. Cell Commun Signal 2021; 19:38. [PMID: 33761918 PMCID: PMC7992989 DOI: 10.1186/s12964-021-00718-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. Methods A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. Results Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. Conclusions These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. ![]()
Video Abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-021-00718-x.
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Affiliation(s)
- Hui Shao
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Wenmin Huang
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Luisana Avilan
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | | | - Carine Puppo
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France
| | - Rémy Puppo
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Régine Lebrun
- CNRS FR 3479, Plate-Forme Protéomique de L'Institut de Microbiologie de La Méditerranée (IMM), Aix Marseille Univ, 13009, Marseille, France
| | - Brigitte Gontero
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
| | - Hélène Launay
- CNRS, BIP UMR 7281, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20, France.
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132
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Pyrih J, Žárský V, Fellows JD, Grosche C, Wloga D, Striepen B, Maier UG, Tachezy J. The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista. BMC Ecol Evol 2021; 21:46. [PMID: 33740894 PMCID: PMC7980591 DOI: 10.1186/s12862-021-01777-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/08/2021] [Indexed: 11/22/2022] Open
Abstract
Background Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions. Results We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either α-proteobacterial or cyanobacterial endosymbionts. Conclusion Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans). Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01777-x.
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Affiliation(s)
- Jan Pyrih
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Justin D Fellows
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Christopher Grosche
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA.,Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 380 South University Avenue, Philadelphia, PA, 19104, USA
| | - Uwe G Maier
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic.
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133
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Kildegaard KR, Arnesen JA, Adiego-Pérez B, Rago D, Kristensen M, Klitgaard AK, Hansen EH, Hansen J, Borodina I. Tailored biosynthesis of gibberellin plant hormones in yeast. Metab Eng 2021; 66:1-11. [PMID: 33746070 PMCID: PMC8205117 DOI: 10.1016/j.ymben.2021.03.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/02/2021] [Accepted: 03/13/2021] [Indexed: 11/25/2022]
Abstract
The application of small amounts of natural plant growth hormones, such as gibberellins (GAs), can increase the productivity and quality of many vegetable and fruit crops. However, gibberellin growth hormones usage is limited by the high cost of their production, which is currently based on fermentation of a natural fungal producer Fusarium fujikuroi that produces a mix of several GAs. We explored the potential of the oleaginous yeast Yarrowia lipolytica to produce specific profiles of GAs. Firstly, the production of the GA-precursor ent-kaurenoic acid (KA) at 3.75 mg/L was achieved by expression of biosynthetic enzymes from the plant Arabidopsis thaliana and upregulation of the mevalonate (MVA) pathway. We then built a GA4-producing strain by extending the GA-biosynthetic pathway and upregulating the MVA-pathway further, resulting in 17.29 mg/L GA4. Additional expression of the F. fujikoroi GA-biosynthetic enzymes resulted in the production of GA7 (trace amounts) and GA3 (2.93 mg/L). Lastly, through protein engineering and the expression of additional KA-biosynthetic genes, we increased the GA3-production 4.4-fold resulting in 12.81 mg/L. The developed system presents a promising resource for the recombinant production of specific gibberellins, identifying bottlenecks in GA biosynthesis, and discovering new GA biosynthetic genes. Classification Biological Sciences, Applied Biological Sciences. A complete biosynthetic pathway towards gibberellins was reconstructed in a microbial host The pathway towards ent-kaurenoic acid consisted of Arabidopsis thaliana enzymes The pathway from ent-kaurenoic acid to gibberellins GA3, GA4 and GA7 consisted of Fusarium fujikuroi enzymes Y. lipolytica expressed 14 heterologous genes for gibberellins biosynthesis and had 5 genome edits for improved mevalonate flux The strains produced up to 12 mg/L of GA3 and up to 17 mg/L GA4 in small-scale cultivations
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Affiliation(s)
- Kanchana R Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Jonathan A Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Belén Adiego-Pérez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Andreas K Klitgaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Esben H Hansen
- River Stone Biotech ApS, Fruebjergvej 3, 2100, København Ø, Denmark
| | - Jørgen Hansen
- River Stone Biotech ApS, Fruebjergvej 3, 2100, København Ø, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark.
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134
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Tzelepis G, Dölfors F, Holmquist L, Dixelius C. Plant mitochondria and chloroplasts are targeted by the Rhizoctonia solani RsCRP1 effector. Biochem Biophys Res Commun 2021; 544:86-90. [PMID: 33550013 DOI: 10.1016/j.bbrc.2021.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 01/10/2023]
Abstract
The fungal species Rhizoctonia solani belongs to the Basidiomycota division and is a ubiquitous soil-borne pathogen. It is the main agent of the damping-off disease in seedlings and causes the root and crown rot disease in sugar beets. Plant pathogens deploy small secreted proteins, called effectors, to manipulate plant immunity in order to infect the host. Here, a gene (RsCRP1) encoded a putative effector cysteine-rich protein was cloned, expressed in Cercospora beticola and used for virulence assays. The RsCRP1 gene was highly induced upon the early-infection stage of sugar beet seedlings and disease was promoted. Confocal microscopy demonstrated localization to the chloroplasts and mitochondria upon transient expression of RsCRP1 in leaves of Nicotiana benthamiana. Further, this effector was unable to induce necrosis or to suppress hypersensitive response induced by the Avr4/Cf4 complex in N. benthamiana. Overall, these data indicate that RsCRP1 is a novel effector targeting distinct plant cell organelles in order to facilitate a successful infection at the early stages of the disease development.
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Affiliation(s)
- Georgios Tzelepis
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala Biocenter, Box 7026, SE-750 07, Uppsala, Sweden.
| | - Fredrik Dölfors
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Louise Holmquist
- MariboHilleshög Research AB, Säbyholmsvägen 24, S-26191, Landskrona, Sweden
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
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135
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A molecular switch in sulfur metabolism to reduce arsenic and enrich selenium in rice grain. Nat Commun 2021; 12:1392. [PMID: 33654102 PMCID: PMC7925690 DOI: 10.1038/s41467-021-21282-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
Rice grains typically contain high levels of toxic arsenic but low levels of the essential micronutrient selenium. Anthropogenic arsenic contamination of paddy soils exacerbates arsenic toxicity in rice crops resulting in substantial yield losses. Here, we report the identification of the gain-of-function arsenite tolerant 1 (astol1) mutant of rice that benefits from enhanced sulfur and selenium assimilation, arsenic tolerance, and decreased arsenic accumulation in grains. The astol1 mutation promotes the physical interaction of the chloroplast-localized O-acetylserine (thiol) lyase protein with its interaction partner serine-acetyltransferase in the cysteine synthase complex. Activation of the serine-acetyltransferase in this complex promotes the uptake of sulfate and selenium and enhances the production of cysteine, glutathione, and phytochelatins, resulting in increased tolerance and decreased translocation of arsenic to grains. Our findings uncover the pivotal sensing-function of the cysteine synthase complex in plastids for optimizing stress resilience and grain quality by regulating a fundamental macronutrient assimilation pathway. Contamination of paddy soils can lead to toxic arsenic accumulation in rice grains and low levels of the micronutrient selenium. Here the authors show that a gain of function mutant affecting an O-acetylserine (thiol) lyase enhances sulfur and selenium assimilation while reducing arsenic accumulation in grains.
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136
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Hall CJ, Lee M, Boarder MP, Mangion AM, Gendall AR, Panjikar S, Perugini MA, Soares da Costa TP. Differential lysine-mediated allosteric regulation of plant dihydrodipicolinate synthase isoforms. FEBS J 2021; 288:4973-4986. [PMID: 33586321 DOI: 10.1111/febs.15766] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/16/2021] [Accepted: 02/12/2021] [Indexed: 12/31/2022]
Abstract
Lysine biosynthesis in plants occurs via the diaminopimelate pathway. The first committed and rate-limiting step of this pathway is catalysed by dihydrodipicolinate synthase (DHDPS), which is allosterically regulated by the end product, l-lysine (lysine). Given that lysine is a common nutritionally limiting amino acid in cereal crops, there has been much interest in probing the regulation of DHDPS. Interestingly, knockouts in Arabidopsis thaliana of each isoform (AtDHDPS1 and AtDHDPS2) result in different phenotypes, despite the enzymes sharing > 85% protein sequence identity. Accordingly, in this study, we compared the catalytic activity, lysine-mediated inhibition and structures of both A. thaliana DHDPS isoforms. We found that although the recombinantly produced enzymes have similar kinetic properties, AtDHDPS1 is 10-fold more sensitive to lysine. We subsequently used X-ray crystallography to probe for structural differences between the apo- and lysine-bound isoforms that could account for the differential allosteric inhibition. Despite no significant changes in the overall structures of the active or allosteric sites, we noted differences in the rotamer conformation of a key allosteric site residue (Trp116) and proposed that this could result in differences in lysine dissociation. Microscale thermophoresis studies supported our hypothesis, with AtDHDPS1 having a ~ 6-fold tighter lysine dissociation constant compared to AtDHDPS2, which agrees with the lower half minimal inhibitory concentration for lysine observed. Thus, we highlight that subtle differences in protein structures, which could not have been predicted from the primary sequences, can have profound effects on the allostery of a key enzyme involved in lysine biosynthesis in plants. DATABASES: Structures described are available in the Protein Data Bank under the accession numbers 6VVH and 6VVI.
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Affiliation(s)
- Cody J Hall
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Mihwa Lee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Matthew P Boarder
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Alexandra M Mangion
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Anthony R Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, Australia.,Australian Research Council Research Hub for Medicinal Agriculture, AgriBio, La Trobe University, Bundoora, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, Australia.,Department of Molecular Biology and Biochemistry, Monash University, Melbourne, Australia
| | - Matthew A Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
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137
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Ma LT, Wang CH, Hon CY, Lee YR, Chu FH. Discovery and characterization of diterpene synthases in Chamaecyparis formosensis Matsum. which participated in an unprecedented diterpenoid biosynthesis route in conifer. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110790. [PMID: 33568294 DOI: 10.1016/j.plantsci.2020.110790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/24/2020] [Accepted: 12/06/2020] [Indexed: 05/20/2023]
Abstract
Chamaecyparis formosensis Matsum. is an endemic and precious coniferous species of Taiwan, and is known for a high abundance of specialized metabolites, which contributes to the excellent timber durability. Several terpenoids were identified and isolated from C. formosensis wood and needles, and exhibit anti-fungal and anti-bacterial bioactivities, which may participate in plant defense against pathogens. In various identified compounds, not only cadinene and ferruginol, were identified in C. formosensis extracts but also unique diterpenoids, which include pisferal, totarol, and derivates of isoabienol. To understand the biosynthesis of these specific diterpenoids, we conducted a series of functional characterization of the C. formosensis diterpene synthases (CfdiTPSs), which participate in skeleton formation and differentiation of diterpenes. In this study, we identified eight diTPSs from C. formosensis transcriptome, and they all contain either class I or class II motif, which indicates they are all monofunctional enzymes. These candidates consist of three class II diTPSs and five class I diTPSs, and after conducting in vivo and in vitro assays, class II diTPS CfCPS1 was characterized as a (+)-copalyl diphosphate synthase ((+)-CPS), and class I diTPSs CfKSL1 could further convert (+)-copalyl diphosphate ((+)-CPP) to levopimaradiene. Meanwhile, CfKSL1 also accepted labda-13-en-8-ol diphosphate (LPP) as substrate and formed monoyl oxide. Another class I diTPS, CfKSL4, exhibits a strong enzymatic ability of isoabienol synthase, which is firstly reported in conifer. This finding provides potential participants in the biosynthesis of unique diterpenoids, and with this knowledge, we can further expand our understanding of diterpenoid metabolism in Cupressaceae and their potential role in plant defense.
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Affiliation(s)
- Li-Ting Ma
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chang-Hsin Wang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chong-Yao Hon
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Ru Lee
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan.
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138
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Shrestha K, Pant S, Huang Y. Genome-wide identification and classification of Lipoxygenase gene family and their roles in sorghum-aphid interaction. PLANT MOLECULAR BIOLOGY 2021; 105:527-541. [PMID: 33387173 DOI: 10.1007/s11103-020-01107-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/10/2020] [Indexed: 05/29/2023]
Abstract
This report shows detailed characterization of LOX gene family in sorghum and provides new insight of sorghum LOX genes in genetic structure and their roles in plant response to infestation by sugarcane aphids. Lipoxygenases (LOXs) are monomeric, nonheme iron-containing dioxygenases that initiate the fatty acid oxidation pathway creating oxylipins and plant hormone jasmonate both have a key role in plant development and defense. To date, a comprehensive and systematic analysis of sorghum LOXs is still deficient. Thus, we performed a genome-wide analysis of the sorghum LOXs genome and identified nine LOXs genes. Detailed examination of protein sequences and phylogenetic analysis categorized the sorghum LOXs into two subclasses, 9-LOXs (SbLOX1, SbLOX3, SbLOX4, SbLOXm, and SbLOXo), 13-LOXs (SbLOX9, SbLOX5, and SbLOX2), and the unclassified SbLOX8. This classification was further supported by sequence similarity/identity matrix and subcellular localization analysis. The lipoxygenase domains, motifs, and vital amino acids were highly conserved in all sorghum LOX genes. In silico analysis of the promoter region of SbLOXs identified different hormones responsive cis-elements. Furthermore, to explore the roles of sorghum LOXs during sugarcane aphid feeding and exogenous MeJA application, expression analysis was conducted for all the eight LOXs in resistant (Tx2783) and susceptible (Tx7000) sorghum lines, respectively. As detailed in this report, the data generated from both genome-wide identification and expression analysis of lipoxygenase genes suggest the putative functions of two 13-LOXs (SbLOX9 and SbLOX5) and three 9-LOXs (SbLOX1, SbLOX3, and SbLOXo) in biosynthesis of jasmonic acid, green leaf volatiles and death acids, and all of them are involved in defense-related functions in plants. Furthermore, this report represents the first genome-wide analysis of the LOX gene family in sorghum, which will facilitate future studies to characterize the roles of each individual LOXs gene in aphid resistance and defense responses to other stresses.
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Affiliation(s)
- Kumar Shrestha
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Shankar Pant
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Laboratory, USDA-ARS), Stillwater, OK, 74075, USA
| | - Yinghua Huang
- Department of Plant Biology, Ecology and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA.
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Laboratory, USDA-ARS), Stillwater, OK, 74075, USA.
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139
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Colon R, Rein KS. Essential components of the xanthophyll cycle differ in high and low toxin Karenia brevis. HARMFUL ALGAE 2021; 103:102006. [PMID: 33980446 PMCID: PMC10246377 DOI: 10.1016/j.hal.2021.102006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 06/09/2023]
Abstract
The dinoflagellate Karenia brevis, blooms annually in the Gulf of Mexico, producing a suite of neurotoxins known as the brevetoxins. The cellular toxin content of K. brevis, however, is highly variable between or even within strains. Herein, we investigate physiological differences between high (KbHT) and low (KbLT) toxin producing cultures both derived from the Wilson strain, related to energy-dependent quenching (qE) by photosystem II, and reduced thiol content of the proteome. We demonstrate that gene and protein expression of the xanthophyll cycle enzyme diadinoxanthin de-epoxidase (Dde) and monogalactosyldiacylglycerol (MGDG) synthase are not significantly different in the two cultures. Using redox proteomics, we report a significantly higher reduced cysteine content in the low toxin proteome, including plastid localized thioredoxin reductase (Trx) which can result in inactivation of Dde and activation of MGDG synthase. We also report significant differences in the lipidomes of KbHT and KbLT with respect to MGDG, which facilitates the xanthophyll cycle.
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Affiliation(s)
- Ricardo Colon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, United States.
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140
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Hasan MS, Singh V, Islam S, Islam MS, Ahsan R, Kaundal A, Islam T, Ghosh A. Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L. PLoS One 2021; 16:e0247170. [PMID: 33606812 PMCID: PMC7894904 DOI: 10.1371/journal.pone.0247170] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/02/2021] [Indexed: 12/21/2022] Open
Abstract
Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants-Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1-chloro-2,4-dinitrobenzene (CDNB) with the lowest binding energy of-5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.
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Affiliation(s)
- Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Vishal Singh
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, Utah, United States of America
| | - Shiful Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md. Sifatul Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Raju Ahsan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Amita Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, Utah, United States of America
| | - Tahmina Islam
- Department of Botany, University of Dhaka, Dhaka, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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141
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Luu Trinh MD, Miyazaki D, Ono S, Nomata J, Kono M, Mino H, Niwa T, Okegawa Y, Motohashi K, Taguchi H, Hisabori T, Masuda S. The evolutionary conserved iron-sulfur protein TCR controls P700 oxidation in photosystem I. iScience 2021; 24:102059. [PMID: 33554065 PMCID: PMC7848650 DOI: 10.1016/j.isci.2021.102059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
In natural habitats, plants have developed sophisticated regulatory mechanisms to optimize the photosynthetic electron transfer rate at the maximum efficiency and cope with the changing environments. Maintaining proper P700 oxidation at photosystem I (PSI) is the common denominator for most regulatory processes of photosynthetic electron transfers. However, the molecular complexes and cofactors involved in these processes and their function(s) have not been fully clarified. Here, we identified a redox-active chloroplast protein, the triplet-cysteine repeat protein (TCR). TCR shared similar expression profiles with known photosynthetic regulators and contained two triplet-cysteine motifs (CxxxCxxxC). Biochemical analysis indicated that TCR localizes in chloroplasts and has a [3Fe-4S] cluster. Loss of TCR limited the electron sink downstream of PSI during dark-to-light transition. Arabidopsis pgr5-tcr double mutant reduced growth significantly and showed unusual oxidation and reduction of plastoquinone pool. These results indicated that TCR is involved in electron flow(s) downstream of PSI, contributing to P700 oxidation. P700 oxidation at photosystem I is important for regulation of photosynthesis TCR is a redox active chloroplast protein harboring a 3Fe-4S iron-sulfur cluster TCR controls electron flow around photosystem I, contributing to P700 oxidation
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Affiliation(s)
- Mai Duy Luu Trinh
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Daichi Miyazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Sumire Ono
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Jiro Nomata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masaru Kono
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Mino
- Division of Materials Science (Physics), Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yuki Okegawa
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
- Corresponding author
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142
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Murai R, Okegawa Y, Sato N, Motohashi K. Evaluation of CBSX Proteins as Regulators of the Chloroplast Thioredoxin System. FRONTIERS IN PLANT SCIENCE 2021; 12:530376. [PMID: 33664754 PMCID: PMC7921703 DOI: 10.3389/fpls.2021.530376] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The chloroplast-localized cystathionine β-synthase X (CBSX) proteins CBSX1 and CBSX2 have been proposed as modulators of thioredoxins (Trxs). In this study, the contribution of CBSX proteins to the redox regulation of thiol enzymes in the chloroplast Trx system was evaluated both in vitro and in vivo. The in vitro biochemical studies evaluated whether CBSX proteins alter the specificities of classical chloroplastic Trx f and Trx m for their target proteins. However, addition of CBSX proteins did not alter the specificities of Trx f and Trx m for disulfide bond reduction of the photosynthesis-related major thiol enzymes, FBPase, SBPase, and NADP-MDH. In vivo analysis showed that CBSX-deficient mutants grew similarly to wild type plants under continuous normal light conditions and that CBSX deficiency did not affect photo-reduction of photosynthesis-related thiol enzymes by Trx system at several light intensities. Although CBSX proteins have been suggested as modulators in the chloroplast Trx system, our results did not support this model, at least in the cases of FBPase, SBPase, and NADP-MDH in leaves. However, fresh weights of the cbsx2 mutants were decreased under short day. Since Trxs regulate many proteins participating in various metabolic reactions in the chloroplast, CBSX proteins may function to regulate other chloroplast Trx target proteins, or serve as modulators in non-photosynthetic plastids of flowers. As a next stage, further investigations are required to understand the modulation of Trx-dependent redox regulation by plastidal CBSX proteins.
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Affiliation(s)
- Ryota Murai
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yuki Okegawa
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Nozomi Sato
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Ken Motohashi
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
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143
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Mathur V, Kwong WK, Husnik F, Irwin NAT, Kristmundsson Á, Gestal C, Freeman M, Keeling PJ. Phylogenomics Identifies a New Major Subgroup of Apicomplexans, Marosporida class nov., with Extreme Apicoplast Genome Reduction. Genome Biol Evol 2021; 13:evaa244. [PMID: 33566096 PMCID: PMC7875001 DOI: 10.1093/gbe/evaa244] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of nonphotosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicomplexan parasites evolved from free-living ancestors and can provide insights into reductive organelle evolution. Here, we sequenced the transcriptomes and apicoplast genomes of three deep-branching apicomplexans, Margolisiella islandica, Aggregata octopiana, and Merocystis kathae. Phylogenomic analyses show that these taxa, together with Rhytidocystis, form a new lineage of apicomplexans that is sister to the Coccidia and Hematozoa (the lineages including most medically significant taxa). Members of this clade retain plastid genomes and the canonical apicomplexan plastid metabolism. However, the apicoplast genomes of Margolisiella and Rhytidocystis are the most reduced of any apicoplast, are extremely GC-poor, and have even lost genes for the canonical plastidial RNA polymerase. This new lineage of apicomplexans, for which we propose the class Marosporida class nov., occupies a key intermediate position in the apicomplexan phylogeny, and adds a new complexity to the models of stepwise reductive evolution of genome structure and organelle function in these parasites.
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Affiliation(s)
- Varsha Mathur
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Waldan K Kwong
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Árni Kristmundsson
- Fish Disease Laboratory, Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland
| | - Camino Gestal
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Mark Freeman
- Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis, West Indies
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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144
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De La Peña R, Sattely ES. Rerouting plant terpene biosynthesis enables momilactone pathway elucidation. Nat Chem Biol 2021; 17:205-212. [PMID: 33106662 PMCID: PMC7990393 DOI: 10.1038/s41589-020-00669-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022]
Abstract
Momilactones from rice have allelopathic activity, the ability to inhibit growth of competing plants. Transferring momilactone production to other crops is a potential approach to combat weeds, yet a complete momilactone biosynthetic pathway remains elusive. Here, we address this challenge through rapid gene screening in Nicotiana benthamiana, a heterologous plant host. This required us to solve a central problem: diminishing intermediate and product yields remain a bottleneck for multistep diterpene pathways. We increased intermediate and product titers by rerouting diterpene biosynthesis from the chloroplast to the cytosolic, high-flux mevalonate pathway. This enabled the discovery and reconstitution of a complete route to momilactones (>10-fold yield improvement in production versus rice). Pure momilactone B isolated from N. benthamiana inhibited germination and root growth in Arabidopsis thaliana, validating allelopathic activity. We demonstrated the broad utility of this approach by applying it to forskolin, a Hedgehog inhibitor, and taxadiene, an intermediate in taxol biosynthesis (~10-fold improvement in production versus chloroplast expression).
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Affiliation(s)
- Ricardo De La Peña
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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145
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Westrich LD, Gotsmann VL, Herkt C, Ries F, Kazek T, Trösch R, Armbruster L, Mühlenbeck JS, Ramundo S, Nickelsen J, Finkemeier I, Wirtz M, Storchová Z, Räschle M, Willmund F. The versatile interactome of chloroplast ribosomes revealed by affinity purification mass spectrometry. Nucleic Acids Res 2021; 49:400-415. [PMID: 33330923 PMCID: PMC7797057 DOI: 10.1093/nar/gkaa1192] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
In plant cells, chloroplast gene expression is predominantly controlled through post-transcriptional regulation. Such fine-tuning is vital for precisely orchestrating protein complex assembly as for the photosynthesis machinery and for quickly responding to environmental changes. While regulation of chloroplast protein synthesis is of central importance, little is known about the degree and nature of the regulatory network, mainly due to challenges associated with the specific isolation of transient ribosome interactors. Here, we established a ribosome affinity purification method, which enabled us to broadly uncover putative ribosome-associated proteins in chloroplasts. Endogenously tagging of a protein of the large or small subunit revealed not only interactors of the holo complex, but also preferential interactors of the two subunits. This includes known canonical regulatory proteins as well as several new proteins belonging to the categories of protein and RNA regulation, photosystem biogenesis, redox control and metabolism. The sensitivity of the here applied screen was validated for various transiently interacting proteins. We further provided evidence for the existence of a ribosome-associated Nα-acetyltransferase in chloroplasts and its ability to acetylate substrate proteins at their N-terminus. The broad set of ribosome interactors underscores the potential to regulate chloroplast gene expression on the level of protein synthesis.
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Affiliation(s)
- Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Tanja Kazek
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Jens Stephan Mühlenbeck
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, 600 16th St, N316, San Francisco, CA 94143, USA
| | - Jörg Nickelsen
- Department of Molecular Plant Science, University of Munich, Grosshaderner-Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, 48149 Münster, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Paul-Ehrlich-Str. 24, 67663 Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Str. 23, 67663 Kaiserslautern, Germany
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146
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Ferrarini MG, Nisimura LM, Girard RMBM, Alencar MB, Fragoso MSI, Araújo-Silva CA, Veiga ADA, Abud APR, Nardelli SC, Vommaro RC, Silber AM, France-Sagot M, Ávila AR. Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis. mSphere 2021; 6:e01002-20. [PMID: 33408226 PMCID: PMC7845590 DOI: 10.1128/msphere.01002-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022] Open
Abstract
Toxoplasmosis, a protozoan infection caused by Toxoplasma gondii, is estimated to affect around 2.5 billion people worldwide. Nevertheless, the side effects of drugs combined with the long period of therapy usually result in discontinuation of the treatment. New therapies should be developed by exploring peculiarities of the parasite's metabolic pathways, similarly to what has been well described in cancer cell metabolism. An example is the switch in the metabolism of cancer that blocks the conversion of pyruvate into acetyl coenzyme A in mitochondria. In this context, dichloroacetate (DCA) is an anticancer drug that reverts the tumor proliferation by inhibiting the enzymes responsible for this switch: the pyruvate dehydrogenase kinases (PDKs). DCA has also been used in the treatment of certain symptoms of malaria; however, there is no evidence of how this drug affects apicomplexan species. In this paper, we studied the metabolism of T. gondii and demonstrate that DCA also inhibits T. gondii's in vitro infection with no toxic effects on host cells. DCA caused an increase in the activity of pyruvate dehydrogenase followed by an unbalanced mitochondrial activity. We also observed morphological alterations frequently in mitochondria and in a few apicoplasts, essential organelles for parasite survival. To date, the kinases that potentially regulate the activity of pyruvate metabolism in both organelles have never been described. Here, we confirmed the presence in the genome of two putative kinases (T. gondii PDK [TgPDK] and T. gondii branched-chain α-keto acid dehydrogenase kinase [TgBCKDK]), verified their cellular localization in the mitochondrion, and provided in silico data suggesting that they are potential targets of DCA.IMPORTANCE Currently, the drugs used for toxoplasmosis have severe toxicity to human cells, and the treatment still lacks effective and safer alternatives. The search for novel drug targets is timely. We report here that the treatment of T. gondii with an anticancer drug, dichloroacetate (DCA), was effective in decreasing in vitro infection without toxicity to human cells. It is known that PDK is the main target of DCA in mammals, and this inactivation increases the conversion of pyruvate into acetyl coenzyme A and reverts the proliferation of tumor cells. Moreover, we verified the mitochondrial localization of two kinases that possibly regulate the activity of pyruvate metabolism in T. gondii, which has never been studied. DCA increased pyruvate dehydrogenase (PDH) activity in T. gondii, followed by an unbalanced mitochondrial activity, in a manner similar to what was previously observed in cancer cells. Thus, we propose the conserved kinases as potential regulators of pyruvate metabolism and interesting targets for new therapies.
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Affiliation(s)
- Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon 1, Villeurbanne, France
| | - Lindice Mitie Nisimura
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
| | - Richard Marcel Bruno Moreira Girard
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Mayke Bezerra Alencar
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Carlla Assis Araújo-Silva
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alan de Almeida Veiga
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
| | | | | | - Rossiane C Vommaro
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ariel Mariano Silber
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Marie France-Sagot
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon 1, Villeurbanne, France
- INRIA Grenoble Rhône-Alpes, Montbonnot-Saint-Martin, France
| | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz, Paraná, Brazil
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147
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Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. FRONTIERS IN PLANT SCIENCE 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
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148
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Li M, Hensel G, Melzer M, Junker A, Tschiersch H, Ruwe H, Arend D, Kumlehn J, Börner T, Stein N. Mutation of the ALBOSTRIANS Ohnologous Gene HvCMF3 Impairs Chloroplast Development and Thylakoid Architecture in Barley. FRONTIERS IN PLANT SCIENCE 2021; 12:732608. [PMID: 34659298 PMCID: PMC8517540 DOI: 10.3389/fpls.2021.732608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/10/2021] [Indexed: 05/12/2023]
Abstract
Gene pairs resulting from whole genome duplication (WGD), so-called ohnologous genes, are retained if at least one member of the pair undergoes neo- or sub-functionalization. Phylogenetic analyses of the ohnologous genes ALBOSTRIANS (HvAST/HvCMF7) and ALBOSTRIANS-LIKE (HvASL/HvCMF3) of barley (Hordeum vulgare) revealed them as members of a subfamily of genes coding for CCT motif (CONSTANS, CONSTANS-LIKE and TIMING OF CAB1) proteins characterized by a single CCT domain and a putative N-terminal chloroplast transit peptide. Recently, we showed that HvCMF7 is needed for chloroplast ribosome biogenesis. Here we demonstrate that mutations in HvCMF3 lead to seedlings delayed in development. They exhibit a yellowish/light green - xantha - phenotype and successively develop pale green leaves. Compared to wild type, plastids of mutant seedlings show a decreased PSII efficiency, impaired processing and reduced amounts of ribosomal RNAs; they contain less thylakoids and grana with a higher number of more loosely stacked thylakoid membranes. Site-directed mutagenesis of HvCMF3 identified a previously unknown functional domain, which is highly conserved within this subfamily of CCT domain containing proteins. HvCMF3:GFP fusion constructs were localized to plastids and nucleus. Hvcmf3Hvcmf7 double mutants exhibited a xantha-albino or albino phenotype depending on the strength of molecular lesion of the HvCMF7 allele. The chloroplast ribosome deficiency is discussed as the primary observed defect of the Hvcmf3 mutants. Based on our observations, the genes HvCMF3 and HvCMF7 have similar but not identical functions in chloroplast development of barley supporting our hypothesis of neo-/sub-functionalization between both ohnologous genes.
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Affiliation(s)
- Mingjiu Li
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Structural Cell Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Astrid Junker
- Acclimation Dynamics and Phenotyping, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Henning Tschiersch
- Heterosis Research Group, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Daniel Arend
- Research Group Bioinformatics and Information Technology, Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Jochen Kumlehn
- Plant Reproductive Biology, Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
- *Correspondence: Thomas Börner,
| | - Nils Stein
- Genomics of Genetic Resources, Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
- Nils Stein,
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149
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Protochlorophyllide synthesis by recombinant cyclases from eukaryotic oxygenic phototrophs and the dependence on Ycf54. Biochem J 2020; 477:2313-2325. [PMID: 32469391 PMCID: PMC7319587 DOI: 10.1042/bcj20200221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022]
Abstract
The unique isocyclic E ring of chlorophylls contributes to their role as light-absorbing pigments in photosynthesis. The formation of the E ring is catalyzed by the Mg-protoporphyrin IX monomethyl ester cyclase, and the O2-dependent cyclase in prokaryotes consists of a diiron protein AcsF, augmented in cyanobacteria by an auxiliary subunit Ycf54. Here, we establish the composition of plant and algal cyclases, by demonstrating the in vivo heterologous activity of O2-dependent cyclases from the green alga Chlamydomonas reinhardtii and the model plant Arabidopsis thaliana in the anoxygenic photosynthetic bacterium Rubrivivax gelatinosus and in the non-photosynthetic bacterium Escherichia coli. In each case, an AcsF homolog is the core catalytic subunit, but there is an absolute requirement for an algal/plant counterpart of Ycf54, so the necessity for an auxiliary subunit is ubiquitous among oxygenic phototrophs. A C-terminal ∼40 aa extension, which is present specifically in green algal and plant Ycf54 proteins, may play an important role in the normal function of the protein as a cyclase subunit.
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Ramundo S, Asakura Y, Salomé PA, Strenkert D, Boone M, Mackinder LCM, Takafuji K, Dinc E, Rahire M, Crèvecoeur M, Magneschi L, Schaad O, Hippler M, Jonikas MC, Merchant S, Nakai M, Rochaix JD, Walter P. Coexpressed subunits of dual genetic origin define a conserved supercomplex mediating essential protein import into chloroplasts. Proc Natl Acad Sci U S A 2020; 117:32739-32749. [PMID: 33273113 PMCID: PMC7768757 DOI: 10.1073/pnas.2014294117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In photosynthetic eukaryotes, thousands of proteins are translated in the cytosol and imported into the chloroplast through the concerted action of two translocons-termed TOC and TIC-located in the outer and inner membranes of the chloroplast envelope, respectively. The degree to which the molecular composition of the TOC and TIC complexes is conserved over phylogenetic distances has remained controversial. Here, we combine transcriptomic, biochemical, and genetic tools in the green alga Chlamydomonas (Chlamydomonas reinhardtii) to demonstrate that, despite a lack of evident sequence conservation for some of its components, the algal TIC complex mirrors the molecular composition of a TIC complex from Arabidopsis thaliana. The Chlamydomonas TIC complex contains three nuclear-encoded subunits, Tic20, Tic56, and Tic100, and one chloroplast-encoded subunit, Tic214, and interacts with the TOC complex, as well as with several uncharacterized proteins to form a stable supercomplex (TIC-TOC), indicating that protein import across both envelope membranes is mechanistically coupled. Expression of the nuclear and chloroplast genes encoding both known and uncharacterized TIC-TOC components is highly coordinated, suggesting that a mechanism for regulating its biogenesis across compartmental boundaries must exist. Conditional repression of Tic214, the only chloroplast-encoded subunit in the TIC-TOC complex, impairs the import of chloroplast proteins with essential roles in chloroplast ribosome biogenesis and protein folding and induces a pleiotropic stress response, including several proteins involved in the chloroplast unfolded protein response. These findings underscore the functional importance of the TIC-TOC supercomplex in maintaining chloroplast proteostasis.
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Affiliation(s)
- Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Yukari Asakura
- Laboratory of Organelle Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Morgane Boone
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Luke C M Mackinder
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Kazuaki Takafuji
- Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Emine Dinc
- Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Michèle Rahire
- Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Michèle Crèvecoeur
- Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Leonardo Magneschi
- Institute of Plant Biology and Biotechnology, University of Münster, Münster 48143, Germany
| | - Olivier Schaad
- Department of Biochemistry, University of Geneva, Geneva CH-1211, Switzerland
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, Münster 48143, Germany
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Sabeeha Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Masato Nakai
- Laboratory of Organelle Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan;
| | - Jean-David Rochaix
- Department of Molecular Biology, University of Geneva, Geneva CH-1211, Switzerland;
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Peter Walter
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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