101
|
Johnson EA. Monitoring foreign gene incorporation into the plastome of Chlamydomonas reinhardtii by multiplex qPCR. PHOTOSYNTHESIS RESEARCH 2013; 115:81-87. [PMID: 23649166 DOI: 10.1007/s11120-013-9835-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
The genetic material of the Chlamydomonas reinhardtii chloroplast can be easily manipulated and creation of transgenic plastomes is of interest for both photosynthetic research and for biofuel and biomass production. Because multiple copies of the chloroplast genome are present, it is important to understand whether, following the introduction of a foreign gene, the resulting transgenic plastome is homoplasmic or heteroplasmic. By quantitative PCR together with a simple DNA extraction procedure and a series of DNA oligonucleotides the following protocol will determine the extent of foreign gene incorporation into a host chloroplast plastome. This approach is used to follow the degree of heteroplasmy following biolistic transformation of several transgenic strains. The approach used is quick, simple to set up, and gives an accurate quantitation of foreign genes within of the chloroplast plastome. Possible future uses of the technique are discussed.
Collapse
Affiliation(s)
- Eric A Johnson
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218-2685, USA.
| |
Collapse
|
102
|
Yau YY, Stewart CN. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol 2013; 13:36. [PMID: 23617583 PMCID: PMC3689633 DOI: 10.1186/1472-6750-13-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
Collapse
Affiliation(s)
- Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
103
|
Sato F. Characterization of plant functions using cultured plant cells, and biotechnological applications. Biosci Biotechnol Biochem 2013; 77:1-9. [PMID: 23291765 DOI: 10.1271/bbb.120759] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant cell cultures are widely used in the micro-propagation of clonal plants, especially virus-free plants, and in the production of useful metabolites such as paclitaxel. On the other hand, the use of plant cell cultures for the more basic characterization of plant functions is rather limited due to the difficulties associated with functional differentiation in cell cultures. In this review, I overview our experience with functionally differentiated cultured plant cells and their characteristics, especially with regard to photoautotrophism and secondary metabolism. I emphasize the high potential of functionally differentiated cell cultures, as well as some of the pitfalls, in the characterization of plant functions and biotechnological applications.
Collapse
Affiliation(s)
- Fumihiko Sato
- Laboratory of Molecular and Cellular Biology of Totipotency, Department of Plant Gene and Totipotency, Graduate School of Biostudies, Kyoto University, Japan.
| |
Collapse
|
104
|
Parry MAJ, Andralojc PJ, Scales JC, Salvucci ME, Carmo-Silva AE, Alonso H, Whitney SM. Rubisco activity and regulation as targets for crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:717-30. [PMID: 23162118 DOI: 10.1093/jxb/ers336] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.
Collapse
Affiliation(s)
- Martin A J Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.
| | | | | | | | | | | | | |
Collapse
|
105
|
Hanson MR, Gray BN, Ahner BA. Chloroplast transformation for engineering of photosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:731-42. [PMID: 23162121 DOI: 10.1093/jxb/ers325] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many efforts are underway to engineer improvements in photosynthesis to meet the challenges of increasing demands for food and fuel in rapidly changing environmental conditions. Various transgenes have been introduced into either the nuclear or plastid genomes in attempts to increase photosynthetic efficiency. We examine the current knowledge of the critical features that affect levels of expression of plastid transgenes and protein accumulation in transplastomic plants, such as promoters, 5' and 3' untranslated regions, RNA-processing sites, translation signals and amino acid sequences that affect protein turnover. We review the prior attempts to manipulate the properties of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) through plastid transformation. We illustrate how plastid operons could be created for expression of the multiple genes needed to introduce new pathways or enzymes to enhance photosynthetic rates or reduce photorespiration. We describe here the past accomplishments and future prospects for manipulating plant enzymes and pathways to enhance carbon assimilation through plastid transformation.
Collapse
Affiliation(s)
- Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | | | | |
Collapse
|
106
|
Gisby MF, Mudd EA, Day A. Growth of transplastomic cells expressing D-amino acid oxidase in chloroplasts is tolerant to D-alanine and inhibited by D-valine. PLANT PHYSIOLOGY 2012; 160:2219-26. [PMID: 23085840 PMCID: PMC3510142 DOI: 10.1104/pp.112.204107] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/16/2012] [Indexed: 05/22/2023]
Abstract
Dual-conditional positive/negative selection markers are versatile genetic tools for manipulating genomes. Plastid genomes are relatively small and conserved DNA molecules that can be manipulated precisely by homologous recombination. High-yield expression of recombinant products and maternal inheritance of plastid-encoded traits make plastids attractive sites for modification. Here, we describe the cloning and expression of a dao gene encoding D-amino acid oxidase from Schizosaccharomyces pombe in tobacco (Nicotiana tabacum) plastids. The results provide genetic evidence for the uptake of D-amino acids into plastids, which contain a target that is inhibited by D-alanine. Importantly, this nonantibiotic-based selection system allows the use of cheap and widely available D-amino acids, which are relatively nontoxic to animals and microbes, to either select against (D-valine) or for (D-alanine) cells containing transgenic plastids. Positive/negative selection with d-amino acids was effective in vitro and against transplastomic seedlings grown in soil. The dual functionality of dao is highly suited to the polyploid plastid compartment, where it can be used to provide tolerance against potential D-alanine-based herbicides, control the timing of recombination events such as marker excision, influence the segregation of transgenic plastid genomes, identify loci affecting dao function in mutant screens, and develop D-valine-based methods to manage the spread of transgenic plastids tagged with dao.
Collapse
Affiliation(s)
- Martin F. Gisby
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Elisabeth A. Mudd
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Anil Day
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| |
Collapse
|
107
|
Venkatesh J, Park SW. Plastid genetic engineering in Solanaceae. PROTOPLASMA 2012; 249:981-99. [PMID: 22395455 PMCID: PMC3459085 DOI: 10.1007/s00709-012-0391-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/21/2012] [Indexed: 05/23/2023]
Abstract
Plastid genetic engineering has come of age, becoming today an attractive alternative approach for the expression of foreign genes, as it offers several advantages over nuclear transformants. Significant progress has been made in plastid genetic engineering in tobacco and other Solanaceae plants, through the use of improved regeneration procedures and transformation vectors with efficient promoters and untranslated regions. Many genes encoding for industrially important proteins and vaccines, as well as genes conferring important agronomic traits, have been stably integrated and expressed in the plastid genome. Despite these advances, it remains a challenge to achieve marked levels of plastid transgene expression in non-green tissues. In this review, we summarize the basic requirements of plastid genetic engineering and discuss the current status, limitations, and the potential of plastid transformation for expanding future studies relating to Solanaceae plants.
Collapse
Affiliation(s)
- Jelli Venkatesh
- Department of Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701 Republic of Korea
| | - Se Won Park
- Department of Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701 Republic of Korea
| |
Collapse
|
108
|
Tungsuchat-Huang T, Maliga P. Visual marker and Agrobacterium-delivered recombinase enable the manipulation of the plastid genome in greenhouse-grown tobacco plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:717-25. [PMID: 22268515 DOI: 10.1111/j.1365-313x.2012.04918.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Successful manipulation of the plastid genome (ptDNA) has been carried out so far only in tissue-culture cells, a limitation that prevents plastid transformation being applied in major agronomic crops. Our objective is to develop a tissue-culture independent protocol that enables manipulation of plastid genomes directly in plants to yield genetically stable seed progeny. We report that in planta excision of a plastid aurea bar gene (bar(au) ) is detectable in greenhouse-grown plants by restoration of the green pigmentation in tobacco leaves. The P1 phage Cre or PhiC31 phage Int site-specific recombinase was delivered on the Agrobacterium T-DNA injected at the axillary bud site, resulting in the excision of the target-site flanked marker gene. Differentiation of new apical meristems was forced by decapitating the plants above the injection site. The new shoot apex that differentiated at the injection site contained bar(au)-free plastids in 30-40% of the injected plants, of which 7% transmitted the bar(au)-free plastids to the seed progeny. The success of obtaining seed with bar(au)-free plastids depended on repeatedly forcing shoot development from axillary buds, a process that was guided by the size and position of green sectors in the leaves. The success of in planta plastid marker excision proved that manipulation of the plastid genomes is feasible within an intact plant. Extension of the protocol to in planta plastid transformation depends on the development of new protocols for the delivery of transforming DNA encoding visual markers.
Collapse
|
109
|
Egelkrout E, Rajan V, Howard JA. Overproduction of recombinant proteins in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 184:83-101. [PMID: 22284713 DOI: 10.1016/j.plantsci.2011.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 05/21/2023]
Abstract
Recombinant protein production in microbial hosts and animal cell cultures has revolutionized the pharmaceutical and industrial enzyme industries. Plants as alternative hosts for the production of recombinant proteins are being actively pursued, taking advantage of their unique characteristics. The key to cost-efficient production in any system is the level of protein accumulation, which is inversely proportional to the cost. Levels of up to 5 g/kg biomass have been obtained in plants, making this production system competitive with microbial hosts. Increasing protein accumulation at the cellular level by varying host, germplasm, location of protein accumulation, and transformation procedure is reviewed. At the molecular level increased expression by improving transcription, translation and accumulation of the protein is critically evaluated. The greatest increases in protein accumulation will occur when various optimized parameters are more fully integrated with each other. Because of the complex nature of plants, this will take more time and effort to accomplish than has been the case for the simpler unicellular systems. However the potential for plants to become one of the major avenues for protein production appears very promising.
Collapse
Affiliation(s)
- Erin Egelkrout
- Applied Biotechnology Institute, Cal Poly Technology Park, Building 83, San Luis Obispo, CA 93407, USA
| | | | | |
Collapse
|
110
|
Nomura Y, Takabayashi T, Kuroda H, Yukawa Y, Sattasuk K, Akita M, Nozawa A, Tozawa Y. ppGpp inhibits peptide elongation cycle of chloroplast translation system in vitro. PLANT MOLECULAR BIOLOGY 2012; 78:185-96. [PMID: 22108865 DOI: 10.1007/s11103-011-9858-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/08/2011] [Indexed: 05/08/2023]
Abstract
Chloroplasts possess common biosynthetic pathways for generating guanosine 3',5'-(bis)pyrophosphate (ppGpp) from GDP and ATP by RelA-SpoT homolog enzymes. To date, several hypothetical targets of ppGpp in chloroplasts have been suggested, but they remain largely unverified. In this study, we have investigated effects of ppGpp on translation apparatus in chloroplasts by developing in vitro protein synthesis system based on an extract of chloroplasts isolated from pea (Pisum sativum). The chloroplast extracts showed stable protein synthesis activity in vitro, and the activity was sensitive to various types of antibiotics. We have demonstrated that ppGpp inhibits the activity of chloroplast translation in dose-effective manner, as does the toxic nonhydrolyzable GTP analog guanosine 5'-(β,γ-imido)triphosphate (GDPNP). We further examined polyuridylic acid-directed polyphenylalanine synthesis as a measure of peptide elongation activity in the pea chloroplast extract. Both ppGpp and GDPNP as well as antibiotics, fusidic acid and thiostrepton, inhibited the peptide elongation cycle of the translation system, but GDP in the similar range of the tested ppGpp concentration did not affect the activity. Our results thus show that ppGpp directly affect the translation system of chloroplasts, as they do that of bacteria. We suggest that the role of the ppGpp signaling system in translation in bacteria is conserved in the translation system of chloroplasts.
Collapse
Affiliation(s)
- Yuhta Nomura
- Division of Biomolecular Engineering, Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Ehime, Japan
| | | | | | | | | | | | | | | |
Collapse
|
111
|
|
112
|
Merchant SS, Kropat J, Liu B, Shaw J, Warakanont J. TAG, you're it! Chlamydomonas as a reference organism for understanding algal triacylglycerol accumulation. Curr Opin Biotechnol 2011; 23:352-63. [PMID: 22209109 DOI: 10.1016/j.copbio.2011.12.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 12/04/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
Abstract
Photosynthetic organisms are responsible for converting sunlight into organic matter, and they are therefore seen as a resource for the renewable fuel industry. Ethanol and esterified fatty acids (biodiesel) are the most common fuel products derived from these photosynthetic organisms. The potential of algae as producers of biodiesel precursor (or triacylglycerols (TAGs)) has yet to be realized because of the limited knowledge of the underlying biochemistry, cell biology and genetics. Well-characterized pathways from fungi and land plants have been used to identify algal homologs of key enzymes in TAG synthesis, including diacylglcyerol acyltransferases, phospholipid diacylglycerol acyltransferase and phosphatidate phosphatases. Many laboratories have adopted Chlamydomonas reinhardtii as a reference organism for discovery of algal-specific adaptations of TAG metabolism. Stressed Chlamydomonas cells, grown either photoautotrophically or photoheterotrophically, accumulate TAG in plastid and cytoplasmic lipid bodies, reaching 46-65% of dry weight in starch accumulation (sta) mutants. State of the art genomic technologies including expression profiling and proteomics have identified new proteins, including key components of lipid droplets, candidate regulators and lipid/TAG degrading activities. By analogy with crop plants, it is expected that advances in algal breeding and genome engineering may facilitate realizing the potential in algae.
Collapse
Affiliation(s)
- Sabeeha S Merchant
- Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States.
| | | | | | | | | |
Collapse
|
113
|
Young HA, Lanzatella CL, Sarath G, Tobias CM. Chloroplast genome variation in upland and lowland switchgrass. PLoS One 2011; 6:e23980. [PMID: 21887356 PMCID: PMC3161095 DOI: 10.1371/journal.pone.0023980] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 08/01/2011] [Indexed: 11/25/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) exists at multiple ploidies and two phenotypically distinct ecotypes. To facilitate interploidal comparisons and to understand the extent of sequence variation within existing breeding pools, two complete switchgrass chloroplast genomes were sequenced from individuals representative of the upland and lowland ecotypes. The results demonstrated a very high degree of conservation in gene content and order with other sequenced plastid genomes. The lowland ecotype reference sequence (Kanlow Lin1) was 139,677 base pairs while the upland sequence (Summer Lin2) was 139,619 base pairs. Alignments between the lowland reference sequence and short-read sequence data from existing sequence datasets identified as either upland or lowland confirmed known polymorphisms and indicated the presence of other differences. Insertions and deletions principally occurred near stretches of homopolymer simple sequence repeats in intergenic regions while most Single Nucleotide Polymorphisms (SNPs) occurred in intergenic regions and introns within the single copy portions of the genome. The polymorphism rate between upland and lowland switchgrass ecotypes was found to be similar to rates reported between chloroplast genomes of indica and japonica subspecies of rice which were believed to have diverged 0.2–0.4 million years ago.
Collapse
Affiliation(s)
- Hugh A. Young
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - Christina L. Lanzatella
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - Gautam Sarath
- United States Department of Agriculture, Agricultural Research Service, Central-East Regional Biomass Center, Lincoln, Nebraska, United States of America
| | - Christian M. Tobias
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
- * E-mail:
| |
Collapse
|
114
|
|