Abstract
Main conclusion
This study reveals that mutations in BRIP1/2 subunits of the BAS complex disrupt root meristem development by decreasing PIN genes expression, affecting auxin transport, and downregulating essential root genes PLT.
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes play vital roles in plant development. BRAHMA-interacting proteins1 (BRIP1) and BRIP2 are subunits of BRAHMA (BRM)-associated SWI/SNF complex (BAS) in plants; however, their role and underlying regulatory mechanism in root development are still unknown. Here, we show that brip1 brip2 double mutants have a significantly shortened root meristem and an irregular arrangement in a portion of the root stem cell niche. The mutations in BRIP1 and BRIP2 cause decreased expression of the PIN-FORMED (PIN) genes, which in turn reduces the transport of auxin at the root tip, leading to the disruption of the accurate establishment of normal auxin concentration gradients in the stem cells. Chromatin immunoprecipitation (ChIP) experiments indicated that BRIP1 and BRIP2 directly bind to the PINs. Furthermore, we found a significant down-regulation in the expression of key root development genes, PLETHORA (PLT), in brip1 brip2. The brip1 brip2 plt1 plt2 quadruple mutations do not show further exacerbation in the short-root phenotype compared to plt1 plt2 double mutants. Using a dexamethasone (DEX)-inducible PLT2 transgenic line, we showed that acute overexpression of PLT2 partially rescues root meristem defects of brip1 brip2, suggesting that BRIP1 and BRIP2 act in part through the PLT1/2 pathway. Taken together, our results identify the critical role and the underlying mechanism of BRIP1/2 in maintaining the development of root meristem through the regulation of auxin output and expression of PLTs.
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Data availability
BRIP2 ChIP-seq data were downloaded from GEO under accession no. GSE142369.
Abbreviations
- SWI/SNF:
-
Switch/sucrose non-fermenting
- BRM:
-
BRAHMA
- BRIP1/2:
-
BRM-interacting protein1/2
- QC:
-
Quiescent center
- PLT:
-
PLETHORA
- PIN:
-
PIN-FORMED
- SHR:
-
SHORT-ROOT
- SCR:
-
SCARECROW
- ChIP:
-
Chromatin immunoprecipitation
- GR:
-
Glucocorticoid receptor
- DEX:
-
Dexamethasone
- DAG:
-
Day of germination
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Acknowledgements
We thank the Arabidopsis Biological Resource Center (ABRC) for seeds of T-DNA insertion lines, Songguang Yang (Guangdong Academy of Agricultural Sciences) for providing p35S:PLT2-GR, pPINs:PINs-GFP, and p35S:PLT2-GR seeds. This work was supported by the National Natural Science Foundation of China to C.L. (32070212, 32270322, and 31870289).
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CL conceived the project. XS performed most of the experiments. XS, YY, and JZ analyzed data. CL wrote the manuscript.
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Supplemental Fig. S1: a
The arrangement of QC in the WT, brip1, brip2, and brip1 brip2 root tips by PI staining at 5 DAG. The white arrow points to the position of QC. Scale bar = 50 μm. b The percentage of QC irregularly arranged in the WT, brip1, brip2, and brip1 brip2 root tips. At least 50 root tips are viewed under a microscope for each background (PPTX 410 KB)
Supplemental Fig. S2:
Root phenotype analysis in plants expressing GFP-tagged BRIP1 or BRIP2 in corresponding single/double mutant backgrounds. a The root phenotypes of the WT, brip1, brip2, brip1 brip2, pBRIP1:BRIP1-GFP brip1, pBRIP2:BRIP2-GFP brip2, pBRIP1:BRIP1-GFP brip1 brip2, and pBRIP2:BRIP2-GFP brip1 brip2 seedlings on 1/2 MS medium at 7 DAG. Scale bar = 1 cm. b Statistical result for primary root length of the WT, brip1, brip2, brip1 brip2, pBRIP1:BRIP1-GFP brip1, pBRIP2:BRIP2-GFP brip2, pBRIP1:BRIP1-GFP brip1 brip2, and pBRIP2:BRIP2-GFP brip1 brip2. The data represent mean ± SD (n = 10 plants). Lower-case letters indicate significant differences, as determined by two-way ANOVA with Tukey’s multiple comparisons test (PPTX 546 KB)
Supplemental Fig. S3:
Exogenous application of auxin fails to rescue the short-root phenotype of brip1 brip2. a The root phenotypes of the WT, brip1, brip2, and brip1 brip2 seedlings on 1/2 MS medium or 1/2 MS medium supplemented with 0.02 μM IAA, 0.05 μM IAA, 0.1 μM IAA, and 0.2 μM IAA at 5 DAG. Scale bar = 1 cm. b Statistical result for primary root length of the WT, brip1, brip2, and brip1 brip2 seedlings on 1/2 MS medium or 1/2 MS medium supplemented with 0.02 μM IAA. The data represent mean ± SD (n = 10 plants). NS, not significant as determined by Student’s t test (PPTX 599 KB)
Supplemental Fig. S4:
Exogenous application of auxin partially rescues the root meristem of brip1 brip2. a The root meristem of the WT and brip1 brip2 seedlings on 1/2 MS medium or 1/2 MS medium supplemented with 0.02 μM IAA at 5 DAG. Scale bar = 50 μm. b Statistical result for root meristem size of the WT and brip1 brip2 seedlings on 1/2 MS medium or 1/2 MS medium supplemented with 0.02 μM IAA. The data represent mean ± SD (n ≥ 10 plants). *P < 0.05; NS, not significant as determined by Student’s t test (PPTX 637 KB)
Supplemental Fig. S5:
BRIP2 does not target to PLT1 and PLT2 directly. a, b ChIP-qPCR analysis of the enrichment of BRIP2 to the different regions of PLT1and PLT2 loci in WT and pBRIP2:BRIP2-GFP Arabidopsis roots. The top of the diagram shows a schematic of the detected genes in the genome. The black thick frame, the black thin frame and the black line represent the exon, UTR, intron and promoter of genes, respectively. P/C represents the primer designed for the detected regions. *P < 0.05; NS, not significant as determined by Student’s t test. (PPTX 85 KB)
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Song, X., Yu, Y., Zhu, J. et al. BRIP1 and BRIP2 maintain root meristem by affecting auxin-mediated regulation. Planta 259, 8 (2024). https://doi.org/10.1007/s00425-023-04283-0
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DOI: https://doi.org/10.1007/s00425-023-04283-0