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
IntroductionSorghum 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...
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1116886/full |
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| author | J. Preston Hurst J. Preston Hurst Abou Yobi Aixia Li Aixia Li Shirley Sato Shirley Sato Thomas E. Clemente Thomas E. Clemente Ruthie Angelovici David R. Holding David R. Holding |
| author_facet | J. Preston Hurst J. Preston Hurst Abou Yobi Aixia Li Aixia Li Shirley Sato Shirley Sato Thomas E. Clemente Thomas E. Clemente Ruthie Angelovici David R. Holding David R. Holding |
| author_sort | J. Preston Hurst |
| collection | DOAJ |
| description | IntroductionSorghum 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.MethodsA 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. ResultsSeveral 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.DiscussionOverall, 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. |
| first_indexed | 2024-04-10T00:37:19Z |
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| id | doaj.art-4abdb4a1ca2f4f78a896be002ac9c790 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T00:37:19Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-4abdb4a1ca2f4f78a896be002ac9c7902023-03-14T12:41:28ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-03-011410.3389/fpls.2023.11168861116886Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichmentJ. Preston Hurst0J. Preston Hurst1Abou Yobi2Aixia Li3Aixia Li4Shirley Sato5Shirley Sato6Thomas E. Clemente7Thomas E. Clemente8Ruthie Angelovici9David R. Holding10David R. Holding11Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United StatesDepartment of Biological Sciences, University of Missouri, Columbia, MO, United StatesSchool of Life Sciences, Ministry of Education, Shandong University, Jinan, ChinaDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United StatesDepartment of Biological Sciences, University of Missouri, Columbia, MO, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United StatesDepartment of Biological Sciences, University of Missouri, Columbia, MO, United StatesDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United StatesDepartment of Biological Sciences, University of Missouri, Columbia, MO, United StatesSchool of Life Sciences, Ministry of Education, Shandong University, Jinan, ChinaDepartment of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United StatesDepartment of Biological Sciences, University of Missouri, Columbia, MO, United StatesIntroductionSorghum 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.MethodsA 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. ResultsSeveral 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.DiscussionOverall, 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1116886/fullCRISPR/Cas9sorghumATACseqRNAseqseed proteingrain quality |
| spellingShingle | J. Preston Hurst J. Preston Hurst Abou Yobi Aixia Li Aixia Li Shirley Sato Shirley Sato Thomas E. Clemente Thomas E. Clemente Ruthie Angelovici David R. Holding David R. Holding 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 CRISPR/Cas9 sorghum ATACseq RNAseq seed protein grain quality |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | CRISPR/Cas9 sorghum ATACseq RNAseq seed protein grain quality |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1116886/full |
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