PMID- 37076789 OWN - NLM STAT- MEDLINE DCOM- 20230421 LR - 20230422 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 23 IP - 1 DP - 2023 Apr 19 TI - RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice. PG - 202 LID - 10.1186/s12870-023-04220-z [doi] LID - 202 AB - BACKGROUND: Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown. RESULTS: In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50% were up-regulated while the other half were down-regulated. Notably, approximately 37.5% of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways. CONCLUSIONS: Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice. CI - (c) 2023. The Author(s). FAU - Purwestri, Yekti Asih AU - Purwestri YA AD - Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281. yekti@ugm.ac.id. AD - Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281. yekti@ugm.ac.id. FAU - Lee, Yang-Seok AU - Lee YS AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. FAU - Meehan, Cathal AU - Meehan C AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. FAU - Mose, Windi AU - Mose W AD - Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281. AD - Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281. AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. FAU - Susanto, Febri Adi AU - Susanto FA AD - Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281. FAU - Wijayanti, Putri AU - Wijayanti P AD - Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281. FAU - Fauzia, Anisa Nazera AU - Fauzia AN AD - Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281. FAU - Nuringtyas, Tri Rini AU - Nuringtyas TR AD - Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281. AD - Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281. FAU - Hussain, Nosheen AU - Hussain N AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. FAU - Putra, Hadi Lanang AU - Putra HL AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. FAU - Gutierrez-Marcos, Jose AU - Gutierrez-Marcos J AD - School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. j.f.gutierrez-marcos@warwick.ac.uk. LA - eng PT - Journal Article DEP - 20230419 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (Transcription Factors) RN - 0 (Arabidopsis Proteins) SB - IM MH - *Oryza/genetics/metabolism MH - Transcription Factors/genetics/metabolism MH - *Arabidopsis/genetics MH - *Arabidopsis Proteins/genetics MH - Embryonic Development MH - Gene Expression Regulation, Plant MH - Plant Somatic Embryogenesis Techniques PMC - PMC10114336 OTO - NOTNLM OT - Black rice OT - Cell reprogramming OT - Somatic embryogenesis OT - Tissue regeneration OT - Transformation COIS- J G-M is the holder of patents on "Increased Epigenetic Variation in Plants" and "Methods for Enhancing Genome Editing Efficiency" based on the use of RWP-RK transcription factors. Y.A.P., Y-S.L., C.M., W.M., F.A.S, P.W, A.N.F, T.R.N., N.H. and H.L.P declare no conflict of interest. EDAT- 2023/04/20 00:41 MHDA- 2023/04/21 06:41 PMCR- 2023/04/19 CRDT- 2023/04/19 23:52 PHST- 2023/02/03 00:00 [received] PHST- 2023/04/07 00:00 [accepted] PHST- 2023/04/21 06:41 [medline] PHST- 2023/04/20 00:41 [pubmed] PHST- 2023/04/19 23:52 [entrez] PHST- 2023/04/19 00:00 [pmc-release] AID - 10.1186/s12870-023-04220-z [pii] AID - 4220 [pii] AID - 10.1186/s12870-023-04220-z [doi] PST - epublish SO - BMC Plant Biol. 2023 Apr 19;23(1):202. doi: 10.1186/s12870-023-04220-z.