1
|
Hurst JP, Sato S, Ferris T, Yobi A, Zhou Y, Angelovici R, Clemente TE, Holding DR. Editing the 19 kDa alpha-zein gene family generates non-opaque2-based quality protein maize. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:946-959. [PMID: 37988568 PMCID: PMC10955486 DOI: 10.1111/pbi.14237] [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: 06/16/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
Maize grain is deficient in lysine. While the opaque2 mutation increases grain lysine, o2 is a transcription factor that regulates a wide network of genes beyond zeins, which leads to pleiotropic and often negative effects. Additionally, the drastic reduction in 19 kDa and 22 kDa alpha-zeins causes a floury kernel, unsuitable for agricultural use. Quality protein maize (QPM) overcame the undesirable kernel texture through the introgression of modifying alleles. However, QPM still lacks a functional o2 transcription factor, which has a penalty on non-lysine amino acids due to the o2 mutation. CRISPR/cas9 gives researchers the ability to directly target genes of interest. In this paper, gene editing was used to specifically target the 19 kDa alpha zein gene family. This allows for proteome rebalancing to occur without an o2 mutation and without a total alpha-zein knockout. The results showed that editing some, but not all, of the 19 kDa zeins resulted in up to 30% more lysine. An edited line displayed an increase of 30% over the wild type. While not quite the 55% lysine increase displayed by QPM, the line had little collateral impact on other amino acid levels compared to QPM. Additionally, the edited line containing a partially reduced 19 kDa showed an advantage in kernel texture that had a complete 19 kDa knockout. These results serve as proof of concept that editing the 19 kDa alpha-zein family alone can enhance lysine while retaining vitreous endosperm and a functional O2 transcription factor.
Collapse
Affiliation(s)
- J. Preston Hurst
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
| | - Shirley Sato
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Tyler Ferris
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
| | - Abou Yobi
- University of Missouri‐ColumbiaColumbiaMissouriUSA
| | - You Zhou
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | | | - Tom E. Clemente
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - David R. Holding
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraskaUSA
- Center for Plant Science InnovationLincolnNebraskaUSA
| |
Collapse
|
2
|
Abbas MA, Iqbal A, Ahmed M, Rasool G, Awan MF, Khan MKA, Rao AQ, Shahid AA, Husnain T. Transformation of Rhodococcus Pigment Production Hydroxylase (PPH) gene into Camelina sativa: an alternative marker for the detection of transgenic plants. BRAZ J BIOL 2024; 84:e254973. [DOI: 10.1590/1519-6984.254973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Production of transgenic plants with desired agronomic and horticultural traits has gained great importance to fulfill demands of the growing population. Genetic transformation is also a fundamental step to study basics of plant sciences. Different transformation protocols have been developed and used which are reliable and efficient. These protocols used antibiotic or herbicide resistance genes incorporated along with gene of interest to identify transformed plants from non-transformed ones. These marker genes may pose a threat to human and environment. Use of visual markers enables direct and easier observation of transformed plants with more precision. In current study a gene cassette with ‘pigment production hydroxylase (PPH) gene under fiber specific promoter (GhSCFP) and downstream Nos-terminator was designed. After checking the structural and functional efficiency of codon optimized gene using bioinformatics tools, the cassette was sent for chemical synthesis from commercial source. The pigment gene cassette (PPH_CEMB), cloned in pCAMBIA-1301, was transformed into Agrobacterium through electroporation. Agrobacterium-mediated floral dip method was used to transform Camelina sativa inflorescence. After seed setting a total of 600 seed were observed for change in color and out of these, 19 seeds developed a reddish-brown coloration, while the remaining 581 seeds remained yellow. The transformation efficiency calculated on basis of color change was 1.0%. PCR analysis of leaves obtained after sowing reddish seeds confirmed the transformation of pigment production gene, while no PCR amplification was observed in leaves of plants from wild type seeds. From the results it is evident that Agrobacterium-mediated transformation of C. sativa inflorescence is very efficient and environment friendly technique not only for detection of transformed plants but also to study basic cellular processes.
Collapse
Affiliation(s)
- M. A. Abbas
- University of the Punjab Lahore, Pakistan; Govt. College of Science, Pakistan
| | - A. Iqbal
- University of the Punjab Lahore, Pakistan; National Research Institute, Poland
| | - M. Ahmed
- University of the Punjab Lahore, Pakistan; Govt. Boys College Sokasan, Pakistan
| | | | - M. F. Awan
- University of the Punjab Lahore, Pakistan; University of Management and Technology, Pakistan
| | | | - A. Q. Rao
- University of the Punjab Lahore, Pakistan
| | | | - T. Husnain
- University of the Punjab Lahore, Pakistan
| |
Collapse
|
3
|
Hurst JP, Yobi A, Li A, Sato S, Clemente TE, Angelovici R, Holding DR. Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment. FRONTIERS IN PLANT SCIENCE 2023; 14:1116886. [PMID: 36998682 PMCID: PMC10043997 DOI: 10.3389/fpls.2023.1116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it's grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus. METHODS A single consensus guide RNA leads to tandem deletion of multiple members of the gene family in addition to the small target site mutations in remaining genes. RNA-seq and ATAC-seq were utilized to identify changes in gene expression and chromatin accessibility in developing kernels in the absence of most alpha-kafirin expression. RESULTS Several differentially accessible chromatin regions and differentially expressed genes were identified. Additionally, several genes upregulated in the edited sorghum line were common with their syntenic orthologues differentially expressed in maize prolamin mutants. ATAC-seq showed enrichment of the binding motif for ZmOPAQUE 11, perhaps indicating the transcription factor's involvement in the kernel response to reduced prolamins. DISCUSSION Overall, this study provides a resource of genes and chromosomal regions which may be involved in sorghum's response to reduced seed storage proteins and the process of proteome rebalancing.
Collapse
Affiliation(s)
- J. Preston Hurst
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Abou Yobi
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - Aixia Li
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Shirley Sato
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| |
Collapse
|
4
|
Shen B, Schmidt MA, Collet KH, Liu ZB, Coy M, Abbitt S, Molloy L, Frank M, Everard JD, Booth R, Samadar PP, He Y, Kinney A, Herman EM. RNAi and CRISPR-Cas silencing E3-RING ubiquitin ligase AIP2 enhances soybean seed protein content. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7285-7297. [PMID: 36112496 DOI: 10.1093/jxb/erac376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
The majority of plant protein in the world's food supply is derived from soybean (Glycine max). Soybean is a key protein source for global animal feed and is incorporated into plant-based foods for people, including meat alternatives. Soybean protein content is genetically variable and is usually inversely related to seed oil content. ABI3-interacting protein 2 (AIP2) is an E3-RING ubiquitin ligase that targets the seed-specific transcription factor ABI3. Silencing both soybean AIP2 genes (AIP2a and AIP2b) by RNAi enhanced seed protein content by up to seven percentage points, with no significant decrease in seed oil content. The protein content enhancement did not alter the composition of the seed storage proteins. Inactivation of either AIP2a or AIP2b by a CRISPR-Cas9-mediated mutation increased seed protein content, and this effect was greater when both genes were inactivated. Transactivation assays in transfected soybean hypocotyl protoplasts indicated that ABI3 changes the expression of glycinin, conglycinin, 2S albumin, and oleosin genes, indicating that AIP2 depletion increased seed protein content by regulating activity of the ABI3 transcription factor protein. These results provide an example of a gene-editing prototype directed to improve global food security and protein availability in soybean that may also be applicable to other protein-source crops.
Collapse
Affiliation(s)
- Bo Shen
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Monica A Schmidt
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | | | - Zhan-Bin Liu
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Monique Coy
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Shane Abbitt
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Lynda Molloy
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Mary Frank
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - John D Everard
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Russ Booth
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Partha P Samadar
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | - Yonghua He
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | - Anthony Kinney
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Eliot M Herman
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
5
|
Shrestha V, Yobi A, Slaten ML, Chan YO, Holden S, Gyawali A, Flint-Garcia S, Lipka AE, Angelovici R. Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition. PLANT PHYSIOLOGY 2022; 188:111-133. [PMID: 34618082 PMCID: PMC8774818 DOI: 10.1093/plphys/kiab390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Maize (Zea mays) seeds are a good source of protein, despite being deficient in several essential amino acids. However, eliminating the highly abundant but poorly balanced seed storage proteins has revealed that the regulation of seed amino acids is complex and does not rely on only a handful of proteins. In this study, we used two complementary omics-based approaches to shed light on the genes and biological processes that underlie the regulation of seed amino acid composition. We first conducted a genome-wide association study to identify candidate genes involved in the natural variation of seed protein-bound amino acids. We then used weighted gene correlation network analysis to associate protein expression with seed amino acid composition dynamics during kernel development and maturation. We found that almost half of the proteome was significantly reduced during kernel development and maturation, including several translational machinery components such as ribosomal proteins, which strongly suggests translational reprogramming. The reduction was significantly associated with a decrease in several amino acids, including lysine and methionine, pointing to their role in shaping the seed amino acid composition. When we compared the candidate gene lists generated from both approaches, we found a nonrandom overlap of 80 genes. A functional analysis of these genes showed a tight interconnected cluster dominated by translational machinery genes, especially ribosomal proteins, further supporting the role of translation dynamics in shaping seed amino acid composition. These findings strongly suggest that seed biofortification strategies that target the translation machinery dynamics should be considered and explored further.
Collapse
Affiliation(s)
- Vivek Shrestha
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abou Yobi
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Marianne L Slaten
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Yen On Chan
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Samuel Holden
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Abiskar Gyawali
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, Columbia, Missouri 65211, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA
| | - Ruthie Angelovici
- Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211, USA
| |
Collapse
|
6
|
Schmidt MA, Mao Y, Opoku J, Mehl HL. Enzymatic degradation is an effective means to reduce aflatoxin contamination in maize. BMC Biotechnol 2021; 21:70. [PMID: 34920704 PMCID: PMC8684248 DOI: 10.1186/s12896-021-00730-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/25/2022] Open
Abstract
Background Aflatoxins are carcinogenic compounds produced by certain species of Aspergillus fungi. The consumption of crops contaminated with this toxin cause serious detrimental health effects, including death, in both livestock and humans. As a consequence, both the detection and quantification of this toxin in food/feed items is tightly regulated with crops exceeding the allowed limits eliminated from food chains. Globally, this toxin causes massive agricultural and economic losses each year. Results In this paper we investigate the feasibility of using an aflatoxin-degrading enzyme strategy to reduce/eliminate aflatoxin loads in developing maize kernels. We used an endoplasmic reticulum (ER) targeted sub-cellular compartmentalization stabilizing strategy to accumulate an aflatoxin-degrading enzyme isolated from the edible Honey mushroom Armillariella tabescens and expressed it in embryo tissue in developing maize kernels. Three transgenic maize lines that were determined to be expressing the aflatoxin-degrading enzyme both at the RNA and protein level, were challenged with the aflatoxin-producing strain Aspergillus flavus AF13 and shown to accumulate non-detectable levels of aflatoxin at 14-days post-infection and significantly reduced levels of aflatoxin at 30-days post-infection compared to nontransgenic control Aspergillus-challenged samples. Conclusions The expression of an aflatoxin-degrading enzyme in developing maize kernels was shown to be an effective means to control aflatoxin in maize in pre-harvest conditions. This aflatoxin-degradation strategy could play a significant role in the enhancement of both US and global food security and sustainability. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00730-6.
Collapse
Affiliation(s)
- Monica A Schmidt
- BIO5 Institute, University of Arizona, 1657 E. Helen St, Tucson, AZ, 85718, USA.
| | - Yizhou Mao
- BIO5 Institute, University of Arizona, 1657 E. Helen St, Tucson, AZ, 85718, USA
| | - Joseph Opoku
- Arid Land Agricultural Research Center, USDA Agricultural Research Service, 416 W Congress St, Tucson, AZ, 85701, USA
| | - Hillary L Mehl
- Arid Land Agricultural Research Center, USDA Agricultural Research Service, 416 W Congress St, Tucson, AZ, 85701, USA
| |
Collapse
|
7
|
Lyzenga WJ, Harrington M, Bekkaoui D, Wigness M, Hegedus DD, Rozwadowski KL. CRISPR/Cas9 editing of three CRUCIFERIN C homoeologues alters the seed protein profile in Camelina sativa. BMC PLANT BIOLOGY 2019; 19:292. [PMID: 31272394 PMCID: PMC6611024 DOI: 10.1186/s12870-019-1873-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/05/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The oilseed Camelina sativa is grown for a range of applications, including for biofuel, biolubricants, and as a source of omega-3 fatty acids for the aquaculture feed industry. The seed meal co-product is used as a source of protein for animal feed; however, the low value of the meal hinders profitability and more widespread application of camelina. The nutritional quality of the seed meal is largely determined by the abundance of specific seed storage proteins and their amino acid composition. Manipulation of seed storage proteins has been shown to be an effective means for either adjustment of nutritional content of seeds or for enhancing accumulation of high-value recombinant proteins in seeds. RESULTS CRISPR/Cas9 gene editing technology was used to generate deletions in the first exon of the three homoeologous genes encoding the seed storage protein CRUCIFERIN C (CsCRUC), creating an identical premature stop-codon in each and resulting in a CsCRUC knockout line. The mutant alleles were detected by applying a droplet digital PCR drop-off assay. The quantitative nature of this technique is particularly valuable when applied to polyploid species because it can accurately determine the number of mutated alleles in a gene family. Loss of CRUC protein did not alter total seed protein content; however, the abundance of other cruciferin isoforms and other seed storage proteins was altered. Consequently, seed amino acid content was significantly changed with an increase in the proportion of alanine, cysteine and proline, and decrease of isoleucine, tyrosine and valine. CsCRUC knockout seeds did not have changed total oil content, but the fatty acid profile was significantly altered with increased relative abundance of all saturated fatty acids. CONCLUSIONS This study demonstrates the plasticity of the camelina seed proteome and establishes a CRUC-devoid line, providing a framework for modifying camelina seed protein composition. The results also illustrate a possible link between the composition of the seed proteome and fatty acid profile.
Collapse
Affiliation(s)
- Wendy J. Lyzenga
- Present address: Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Myrtle Harrington
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Diana Bekkaoui
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Merek Wigness
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Dwayne D. Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Kevin L. Rozwadowski
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| |
Collapse
|
8
|
Schmidt MA, Herman EM. Characterization and functional biology of the soybean aleurone layer. BMC PLANT BIOLOGY 2018; 18:354. [PMID: 30545296 PMCID: PMC6293662 DOI: 10.1186/s12870-018-1579-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Soybean is a globally important oil seed crop. Both the high protein and oil content of soybean seeds make this crop a lucrative commodity. As in higher eukaryotic species with available genomes, the functional annotation of most of soybean's genes still remains to be investigated. A major hurdle in the functional genomics of soybean is a rapid method to test gene constructs before embarking on stable transformation experiments. RESULTS In this paper we describe the morphology and composition of the persistent single-cell aleurone layer that derives from the endosperm of developing soybean seeds. Its composition compared to cotyledonary tissue indicates the aleurone layer plays a role in both abiotic and biotic stress. The potential utility as the aleurone layer as a transient expression system in soybean was shown. As a near transparent single-cell layer it can be used as a transient expression system to study transgene expression and inter- and intra-cellular targeting as it is amenable to microscopic techniques. CONCLUSION The transparent single cell aleurone layer was shown to be compositionally comparable to cotyledonary tissue in soybean with an enrichment in oxidative response proteins and shown to be a potential transient expression platform.
Collapse
Affiliation(s)
- Monica A. Schmidt
- School of Plant Sciences/BIO5 Institute/University of Arizona, 1657 E. Helen St, Tucson, AZ 85721 USA
| | - Eliot M. Herman
- School of Plant Sciences/BIO5 Institute/University of Arizona, 1657 E. Helen St, Tucson, AZ 85721 USA
| |
Collapse
|