Genome-wide Characterization of Regulator of Chromosome Condensation 1 (RCC1) Gene Family in Artemisia Annua L. Revealed a Conservation Evolutionary Pattern

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2023 Nov 19

PMID 37980503

Authors

Jieting Chen

Wenguang Wu

Xiaoxia Ding

Danchun Zhang

Chunyan Dai

Hengyu Pan

Peiqi Shi

Chanjuan Wu

Jun Zhang

Jianmin Zhao

Baosheng Liao

Xiaohui Qiu

Zhihai Huang

Affiliations

Soon will be listed here.

Abstract

Background: Artemisia annua is the major source for artemisinin production. The artemisinin content in A. annua is affected by different types of light especially the UV light. UVR8, a member of RCC1 gene family was found to be the UV-B receptor in plants. The gene structures, evolutionary history and expression profile of UVR8 or RCC1 genes remain undiscovered in A. annua.

Results: Twenty-two RCC1 genes (AaRCC1) were identified in each haplotype genome of two diploid strains of A. annua, LQ-9 and HAN1. Varied gene structures and sequences among paralogs were observed. The divergence of most RCC1 genes occurred at 46.7 - 51 MYA which overlapped with species divergence of core Asteraceae during the Eocene, while no recent novel RCC1 members were found in A. annua genome. The number of RCC1 genes remained stable among eudicots and RCC1 genes underwent purifying selection. The expression profile of AaRCC1 is analogous to that of Arabidopsis thaliana (AtRCC1) when responding to environmental stress.

Conclusions: This study provided a comprehensive characterization of the AaRCC1 gene family and suggested that RCC1 genes were conserved in gene number, structures, constitution of amino acids and expression profiles among eudicots.

Citing Articles

LncRNA CCAT1 knockdown suppresses tongue squamous cell carcinoma progression by inhibiting the ubiquitination of PHLPP2.

Liu F, Yang H, Liu X, Ning Y, Wu Y, Yan X Mol Cell Biochem. 2024; 480(2):1063-1075.

PMID: 38763996 DOI: 10.1007/s11010-024-05004-1.

References

Ji H, Wang Y, Cloix C, Li K, Jenkins G, Wang S . The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis. PLoS Genet. 2015; 11(9):e1005471. PMC: 4579128. DOI: 10.1371/journal.pgen.1005471. View

Ji H, Wang S, Cheng C, Li R, Wang Z, Jenkins G . The RCC1 family protein SAB1 negatively regulates ABI5 through multidimensional mechanisms during postgermination in Arabidopsis. New Phytol. 2018; 222(2):907-922. DOI: 10.1111/nph.15653. View

Dunn N, Unni D, Diesh C, Munoz-Torres M, Harris N, Yao E . Apollo: Democratizing genome annotation. PLoS Comput Biol. 2019; 15(2):e1006790. PMC: 6380598. DOI: 10.1371/journal.pcbi.1006790. View

Wu M, Grahn E, Eriksson L, Strid A . Computational evidence for the role of Arabidopsis thaliana UVR8 as UV-B photoreceptor and identification of its chromophore amino acids. J Chem Inf Model. 2011; 51(6):1287-95. DOI: 10.1021/ci200017f. View

Furutani M, Hirano Y, Nishimura T, Nakamura M, Taniguchi M, Suzuki K . Polar recruitment of RLD by LAZY1-like protein during gravity signaling in root branch angle control. Nat Commun. 2020; 11(1):76. PMC: 6941992. DOI: 10.1038/s41467-019-13729-7. View

Cheong D, Tan D, Wong F, Tran T . Anti-malarial drug, artemisinin and its derivatives for the treatment of respiratory diseases. Pharmacol Res. 2020; 158:104901. PMC: 7217791. DOI: 10.1016/j.phrs.2020.104901. View

Bhattarai A, Ali A, Kachur S, Martensson A, Abbas A, Khatib R . Impact of artemisinin-based combination therapy and insecticide-treated nets on malaria burden in Zanzibar. PLoS Med. 2007; 4(11):e309. PMC: 2062481. DOI: 10.1371/journal.pmed.0040309. View

Gout J, Hao Y, Johri P, Arnaiz O, Doak T, Bhullar S . Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic Paramecium Complex. Mol Biol Evol. 2023; 40(5). PMC: 10195154. DOI: 10.1093/molbev/msad107. View

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

10.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

11.

Favory J, Stec A, Gruber H, Rizzini L, Oravecz A, Funk M . Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J. 2009; 28(5):591-601. PMC: 2657586. DOI: 10.1038/emboj.2009.4. View

12.

Ulm R, Jenkins G . Q&A: How do plants sense and respond to UV-B radiation?. BMC Biol. 2015; 13:45. PMC: 4484705. DOI: 10.1186/s12915-015-0156-y. View

13.

An X, Zhao S, Luo X, Chen C, Liu T, Li W . Genome-wide identification and expression analysis of the gene family in wheat ( L.). Front Plant Sci. 2023; 14:1124905. PMC: 9998523. DOI: 10.3389/fpls.2023.1124905. View

14.

Wang D, Zhang Y, Zhang Z, Zhu J, Yu J . KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics. 2010; 8(1):77-80. PMC: 5054116. DOI: 10.1016/S1672-0229(10)60008-3. View

15.

Frohnmeyer H, Staiger D . Ultraviolet-B radiation-mediated responses in plants. Balancing damage and protection. Plant Physiol. 2003; 133(4):1420-8. PMC: 1540342. DOI: 10.1104/pp.103.030049. View

16.

Bischoff F, Ponstingl H . Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1. Nature. 1991; 354(6348):80-2. DOI: 10.1038/354080a0. View

17.

Hurst L . The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002; 18(9):486. DOI: 10.1016/s0168-9525(02)02722-1. View

18.

Kaiserli E, Jenkins G . UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus. Plant Cell. 2007; 19(8):2662-73. PMC: 2002606. DOI: 10.1105/tpc.107.053330. View

19.

Tossi V, Regalado J, Iannicelli J, Laino L, Burrieza H, Escandon A . Beyond Arabidopsis: Differential UV-B Response Mediated by UVR8 in Diverse Species. Front Plant Sci. 2019; 10:780. PMC: 6591365. DOI: 10.3389/fpls.2019.00780. View

20.

Zhang D, Sun W, Shi Y, Wu L, Zhang T, Xiang L . Red and Blue Light Promote the Accumulation of Artemisinin in Artemisia Annua L. Molecules. 2018; 23(6). PMC: 6100300. DOI: 10.3390/molecules23061329. View