In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants
Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthet...
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PeerJ Inc.
2023-07-01
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| Online Access: | https://peerj.com/articles/15696.pdf |
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| author | So Youn Won Prabhakaran Soundararajan Vadivelmurugan Irulappan Jung Sun Kim |
| author_facet | So Youn Won Prabhakaran Soundararajan Vadivelmurugan Irulappan Jung Sun Kim |
| author_sort | So Youn Won |
| collection | DOAJ |
| description | Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants. |
| first_indexed | 2024-03-09T04:09:16Z |
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| id | doaj.art-0184212b192d496ea44dee4fb6de0117 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T04:09:16Z |
| publishDate | 2023-07-01 |
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| spelling | doaj.art-0184212b192d496ea44dee4fb6de01172023-12-03T14:02:20ZengPeerJ Inc.PeerJ2167-83592023-07-0111e1569610.7717/peerj.15696In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plantsSo Youn Won0Prabhakaran Soundararajan1Vadivelmurugan Irulappan2Jung Sun Kim3Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South KoreaDepartment of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, South KoreaSingle-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in comparison with other C3, C4, and CAM model plants.https://peerj.com/articles/15696.pdfBienertia sinuspersiciCHUP1 proteinCHUP1-like proteinsSingle-Cell C4 plantsPhylogenetic analysisSubcellular compartmentalization |
| spellingShingle | So Youn Won Prabhakaran Soundararajan Vadivelmurugan Irulappan Jung Sun Kim In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants PeerJ Bienertia sinuspersici CHUP1 protein CHUP1-like proteins Single-Cell C4 plants Phylogenetic analysis Subcellular compartmentalization |
| title | In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants |
| title_full | In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants |
| title_fullStr | In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants |
| title_full_unstemmed | In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants |
| title_short | In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants |
| title_sort | in silico evolutionary and functional analysis of chup1 and its related proteins in bienertia sinuspersici a comparative study across c3 c4 cam and scc4 model plants |
| topic | Bienertia sinuspersici CHUP1 protein CHUP1-like proteins Single-Cell C4 plants Phylogenetic analysis Subcellular compartmentalization |
| url | https://peerj.com/articles/15696.pdf |
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