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Brophy JAN, LaRue T, Dinneny JR. Understanding and engineering plant form. Semin Cell Dev Biol 2017; 79:68-77. [PMID: 28864344 DOI: 10.1016/j.semcdb.2017.08.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022]
Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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Zhang HD, Cui YL, Huang C, Yin QQ, Qin XM, Xu T, He XF, Zhang Y, Li ZR, Yang ZN. PPR protein PDM1/SEL1 is involved in RNA editing and splicing of plastid genes in Arabidopsis thaliana. PHOTOSYNTHESIS RESEARCH 2015; 126:311-21. [PMID: 26123918 DOI: 10.1007/s11120-015-0171-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/22/2015] [Indexed: 05/10/2023]
Abstract
After transcription, most chloroplast precursor RNAs undergo further post-transcriptional processing including cleavage, editing, and splicing. Previous investigation has shown that the cleavage of the rpoA transcript and most editing sites, including accD-1, are defective in the knockout mutant of PDM1/SEL1, a PLS-type PPR protein, and that PDM1 is associated with the rpoA transcript. In this work, we found that the splicing of group II introns in trnK and ndhA is also affected in pdm1. Co-immunoprecipitation mass spectrometry experiments were performed to identify proteins that are associated with PDM1. We obtained 126 non-redundant proteins, of which MORF9 was reported to be involved in RNA editing in chloroplast. Yeast two-hybrid assays showed that PDM1 interacts directly with MORF9, MORF2, and MORF8. RNA immunoprecipitation showed that PDM1 associates with the transcripts of trnK and ndhA, as well as accD-1, suggesting that PDM1 is involved in RNA editing and splicing. Therefore, PDM1 is an important protein for post-transcriptional regulation in chloroplast.
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Affiliation(s)
- Hong-Dao Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yong-Lan Cui
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chao Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qian-Qian Yin
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xue-Mei Qin
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Te Xu
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao-Fang He
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yi Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zi-Ran Li
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China.
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Qiao J, Li J, Chu W, Luo M. PRDA1, a novel chloroplast nucleoid protein, is required for early chloroplast development and is involved in the regulation of plastid gene expression in Arabidopsis. PLANT & CELL PHYSIOLOGY 2013; 54:2071-84. [PMID: 24132784 DOI: 10.1093/pcp/pct148] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Chloroplast development requires accurate spatio-temporal expression of plastid genes. The regulation of plastid genes mediated by plastid-encoded RNA polymerase (PEP) is rather complex, and its related mechanism remains largely unclear. Here, we report the identification of a novel protein that is essential for plant development, PEP-Related Development Arrested 1 (PRDA1). Knock-out of PRDA1 in Arabidopsis (prda1 mutant) caused a seedling-lethal, albino phenotype and arrested the development of leaf chloroplasts. Localization analysis showed that PRDA1 was specifically targeted to chloroplasts and co-localized with chloroplast nucleoids, revealing that PRDA1 is a chloroplast nucleoid-associated protein. Gene expression analyses revealed that the PEP-dependent plastid transcript levels were greatly reduced in prda1. PRDA1 was co-expressed with most of the PEP-associated proteins. Protein interaction assays showed that PRDA1 clearly interacts with MRL7 and FSD2, both of which have been verified as essential for PEP-related chloroplast development. Reactive oxygen species scavenging through dimethylthiourea markedly alleviated the cotyledon-albino phenotypes of PRDA1 and MRL7 RNA interference seedlings. These results demonstrate that PRDA1 is required for early chloroplast development and involved in the regulation of plastid gene expression.
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Affiliation(s)
- Jiangwei Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Li N, Cattolico RA. Chloroplast genome characterization in the red alga Griffithsia pacifica. ACTA ACUST UNITED AC 2006; 209:343-51. [PMID: 17191345 DOI: 10.1007/bf00329664] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
It has been suggested that cyanobacteria served as the ancestors for rhodophytic algae whose chloroplasts contain chlorophyll a and phycobilins, and that a rodophyte served as the plastid source for chromophytic plants that contain chlorophylls a and c. Although organellar DNA has been used to assess phylogenetic relatedness among terrestrial plants and green algae whose chloroplasts contain chlorophylls a and b, few data are presently available on the molecular profile of plastid DNA in chromophytes or rhodophytes. In this study the chloroplast genome of the rhodophytic, filamentous alga Griffithsia pacifica has been characterized. DNA was purified from isolated chloroplasts using protease k treatment and sodium dodecyl sulfate lysis followed by density centrifugation in Hoechst-33258 dye-CsCl gradients. Single and double restriction enzyme digests demonstrate that the DNA prepared from purified chloroplasts has a genome size of about 178 kilobase pairs (kb). A restriction map of this chloroplast genome demonstrates that it is circular and, unlike the chloroplast DNA (cpDNA) in most other plants, contains only a single ribosomal DNA operon. DNA was also purified from the mitochondria that co-isolated with chloroplasts. Mitochondrial DNA consists of molecules that range in size from 27 to 350 kb based on restriction endonuclease digestion and electron microscopic analysis.
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Affiliation(s)
- N Li
- Department of Botany, University of Washington, Seattle, WA 98195, USA
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Affiliation(s)
- M W Gray
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Yamada T. Repetitive sequence-mediated rearrangements in Chlorella ellipsoidea chloroplast DNA: completion of nucleotide sequence of the large inverted repeat. Curr Genet 1991; 19:139-47. [PMID: 2065363 DOI: 10.1007/bf00326295] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A 3454 base pair (bp) sequence of the large inverted repeat (IR) of chloroplast DNA (cpDNA) from the unicellular green alga Chlorella ellipsoidea has been determined. The sequence includes: (1) the boundaries between the IR and the large single copy (LSC) and the small single copy (SSC) regions, (2) the gene for psbA and (3) an approximately 1.0 kbp region between psbA and the rRNA genes which contains a variety of short dispersed repeats. The total size of the Chlorella IR was determined to be 15243 bp. The junction between the IR and the small single copy region is located close to the putative promoter of the rRNA operon (906 bp upstream of the -35 sequence on each IR). The junction between the IR and the large single copy region is also just upstream of the putative psbA promoter, 218 bp upstream from the ATG initiation codon. A few sets of unique sequences were found repeatedly around both junctions. Some of the sequences flanking the IR-LSC junction suggest a unidirectional and serial expansion of the IR within the genome. The psbA gene is located close to the LSC-side junction and codes for a protein of 352 amino acid residues. A highly conserved C-terminal Gly is absent Unlike the psbA of Chlamydomonas species, which contains 2-4 large introns, the gene of Chlorella has no introns.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- T Yamada
- Department of Molecular Biology, Mitsubishi Kasei Institute of Life Sciences, Tokyo, Japan
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Newman SM, Cattolico RA. Ribulose bisphosphate carboxylase in algae: synthesis, enzymology and evolution. PHOTOSYNTHESIS RESEARCH 1990; 26:69-85. [PMID: 24420459 DOI: 10.1007/bf00047078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/1990] [Accepted: 06/08/1990] [Indexed: 06/03/2023]
Abstract
Studies demonstrating differences in chloroplast structure and biochemistry have been used to formulate hypotheses concerning the origin of algal plastids. Genetic and biochemical experiments indicate that significant variation occurs in ribulose-1,5-bisphosphate carboxylase (Rubisco) when supertaxa of eukaryotic algae are compared. These differences include variations in the organelle location of the genes and their arrangement, mechanism of Rubisco synthesis, polypeptide immunological reactivity and sequence, as well as efficacy of substrate (ribulose bisphosphate and CO2) binding and inhibitor (6-phosphogluconate) action. The structure-function relationships observed among chromophytic, rhodophytic, chlorophytic and prokaryotic Rubisco demonstrate that: (a) similarities among chromophytic and rhodophytic Rubisco exist in substrate/inhibitor binding and polypeptide sequence, (b) characteristic differences in enzyme kinetics and subunit polypeptide structure occur among chlorophytes, prokaryotes and chromophytes/rhodophytes, and (c) there is structural variability among chlorophytic plant small subunit polypeptides, in contrast to the conservation of this polypeptide in chromophytes and rhodophytes. Taxa-specific differences among algal Rubisco enzymes most likely reflect the evolutionary history of the plastid, the functional requirements of each polypeptide, and the consequences of encoding the large and small subunit genes in the same or different organelles.
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Affiliation(s)
- S M Newman
- Department of Botany, University of Washington, 98195, Seattle, WA, USA
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Douglas SE, Durnford DG. Sequence analysis of the plastid rDNA spacer region of the chlorophyll c-containing alga Cryptomonas phi. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1990; 1:55-62. [PMID: 2132959 DOI: 10.3109/10425179009041347] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A 0.8 kb AvaI/SmaI fragment of the plastid genome of the chlorophyll c-containing alga Cryptomonas phi encompassing the rRNA spacer region and flanking genes has been cloned and sequenced. The spacer region between the 16S and 23S rRNA genes is 275 base pairs long, one of the shortest yet reported, and it contains uninterrupted genes for tRNA(Ile) and tRNA(Ala) separated by only two base pairs. The coding regions for tRNAs and rRNAs have been compared with those from cyanobacteria, land plants and other algae and the possible evolutionary relationships discussed.
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Affiliation(s)
- S E Douglas
- Atlantic Research Laboratory, National Research Council, Halifax, Nova Scotia, Canada
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Abstract
Analysis of organellar genomes strongly supports the idea that chloroplasts and mitochondria originated in evolution as eubacteria-like endosymbionts, whose closest contemporaries are cyanobacteria and purple photosynthetic bacteria, respectively. However, there is still much debate about whether a single endosymbiotic event or multiple ones gave rise to each organelle in different eukaryotes, and considerable uncertainty about what has happened to the genomes of chloroplasts and mitochondria since their appearance in the eukaryotic cell.
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Abstract
Eukaryotic algae are traditionally separated into three broad divisions: the rhodophytes, the chromophytes and the chlorophytes. The evolutionary relationships between these groups, their links with other eukaryotes and with other photosynthetic groups, such as euglenophytes and cryptophytes, have been the subject of much debate and speculation. Here we analyse partial sequences of the large (28S) cytoplasmic ribosomal RNA from ten new species of protists belonging to various groups of unicellular algae. By combining them with the homologous sequences from 14 other unicellular and multicellular eukaryotes, we show that rhodophytes, chromophytes and chlorophytes emerge as three distinct groups late among eukaryotes, that is, close to the metazoa-metaphytes radiation. This implies a relatively late occurrence of eukaryotic photosynthetic symbiosis. We also provide details of intra- and inter-phyla relationships.
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Affiliation(s)
- R Perasso
- Laboratoire de Biologie Cellulaire 4 (URA 25 CNRS), Université Paris Sud, Orsay, France
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Delaney TP, Cattolico RA. Chloroplast ribosomal DNA organization in the chromophytic alga Olisthodiscus luteus. Curr Genet 1989; 15:221-9. [PMID: 2766384 DOI: 10.1007/bf00435509] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There are almost no data describing chloroplast genome organization in chromophytic (chlorophyll a/c) plants. In this study chloroplast ribosomal operon placement and gene organization has been determined for the golden-brown alga Olisthodiscus luteus. Ribosomal RNA genes are located on the chloroplast DNA inverted repeat structure. Nucleotide sequence analysis, demonstrated that in contrast to the larger spacer regions in land plants, the 16S-23S rDNA spacer of O. luteus is only 265 bp in length. This spacer contains tRNA(Ile) and tRNA(Ala) genes which lack introns and are separated by only 3 bp. The sequences of the tRNA genes and 16S and 23S rDNA termini flanking the spacer were examined to determine homology between O. luteus, chlorophytic plant chloroplast DNA, and prokaryotes.
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Affiliation(s)
- T P Delaney
- University of Washington, Department of Botany, Seattle 98195
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Physical mapping of the plastid genome from the chlorophyll c-containing alga, Cryptomonas ? Curr Genet 1988. [DOI: 10.1007/bf00434085] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Newman S, Cattolico RA. Synthesis of active Olisthodiscus luteus ribulose-1,5-bisphosphate carboxylase in Escherichia coli. PLANT MOLECULAR BIOLOGY 1988; 11:821-831. [PMID: 24272632 DOI: 10.1007/bf00019522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/1988] [Accepted: 09/21/1988] [Indexed: 06/02/2023]
Abstract
The ribulose-1,5-bisphosphate carboxylase (Rubisco) large- and small-subunit genes are encoded on the chloroplast genome of the eukaryotic chromophytic alga Olisthodiscus luteus. Northern blot experiments indicate that both genes are co-transcribed into a single (>6 kb) mRNA molecule. Clones from the O. luteus rbc gene region were constructed with deleted 5' non-coding regions and placed under control of the lac promoter, resulting in the expression of high levels of O. luteus Rubisco large and small subunits in Escherichia coli. Sucrose gradient centrifugation of soluble extracts fractionated a minute amount of carboxylase activity that cosedimented with native hexadecameric O. luteus Rubisco. Most of the large subunit synthesized in E. coli appeared insoluble or formed an aggregate with the small subunit possessing an altered charge: mass ratio compared to the native holoenzyme. The presence in O. luteus of a polypeptide that has an identical molecular mass and cross reacts with antiserum generated against pea large-subunit binding protein may indicate that a protein of similar function is required for Rubisco assembly in O. luteus.
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Affiliation(s)
- S Newman
- Department of Botany KB-15, University of Washington, 98195, Seattle, WA, USA
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