Information report for CRL1;ARL1
Gene Details
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Functional Descriptions
- We investigated Na+ uptake and bypass flow in lateral rootless mutants (lrt1, lrt2), a crown rootless mutant (CRL1), their wild types (Oochikara, Nipponbare and Taichung 65, respectively) and in seedlings of rice cv.
- Studies on sodium bypass flow in lateral rootless mutants lrt1 and lrt2, and crown rootless mutant CRL1 of rice (Oryza sativa L.).
- ARL1 is an auxin- and ethylene-responsive gene, and the expression pattern of ARL1 in roots parallels auxin distribution.
- The CRL1 mutant showed additional auxin-related abnormal phenotypic traits in the roots, such as decreased lateral root number, auxin insensitivity in lateral root formation, and impaired root gravitropism, whereas no abnormal phenotypic traits were observed in aboveground organs.
- Expression of CRL1, which encodes a member of the plant-specific ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES protein family, was localized in tissues where crown and lateral roots are initiated and overlapped with beta-glucuronidase staining controlled by the DR5 promoter.
- We conclude that CRL1 encodes a positive regulator for crown and lateral root formation and that its expression is directly regulated by an ARF in the auxin signaling pathway.
- A putative auxin response element in the CRL5 promoter region specifically interacted with a rice ARF, demonstrating that CRL5 may be a direct target of an ARF, similar to CRL1/ADVENTITIOUS ROOTLESS1 (ARL1) that also regulates crown root initiation.
- We characterized a rice (Oryza sativa) mutant defective in crown root formation, crown rootless1 (CRL1).
- The lines with overexpression showed constitutive expression of many defense-related genes, such as PBZ1 and OsSci2, as well as early auxin-response genes, such as OsIAA4 and OsCRL1 genes.
- A CRL1 crl5 double mutant displayed an additive phenotype, indicating that these two genes function in different genetic pathways for crown root initiation.
- Exogenous auxin treatment induced CRL1 expression without de novo protein biosynthesis, and this induction required the degradation of AUXIN/INDOLE-3-ACETIC ACID proteins.
- CRL1 contains two putative auxin response elements (AuxREs) in its promoter region.
- The proximal AuxRE specifically interacted with a rice AUXIN RESPONSE FACTOR (ARF) and acted as a cis-motif for CRL1 expression.
- Our findings suggest that ARL1 is an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, and that it promotes the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem.
- The gene, designated Adventitious rootless1 (ARL1), encodes a protein with a LATERAL ORGAN BOUNDARIES (LOB) domain.
- ARL1, a LOB-domain protein required for adventitious root formation in rice.
- The results showed that shoot Na+ concentration in lrt1, lrt2 and CRL1 was lower (by 20-23%) than that of their wild types.
- In rice (Oryza sativa), auxin promotes crown root initiation via the LOB-domain transcription factor (LBD) transcription factor CROWN ROOTLESS1 (CRL1); however, the gene regulatory network downstream of CRL1 remains largely unknown.
- We tested CRL1 transcriptional activity in yeast and in planta, identified CRL1-regulated genes using an inducible gene expression system and a transcriptome analysis, and used in situ hybridization to demonstrate coexpression of a sample of CRL1-regulated genes with CRL1 in crown root primordia.
- We show that CRL1 positively regulates 277 genes, including key genes involved in meristem patterning (such as QUIESCENT-CENTER SPECIFIC HOMEOBOX; QHB), cell proliferation and hormone homeostasis.
- Here, we show that CRL1 can bind, both in vitro and in vivo, not only the LBD-box, a DNA sequence recognized by several ASL/LBD transcription factors, but also another not previously identified DNA motif that was named CRL1-box.
- Finally, we show that OsbHLH044 represses a regulatory module, uncovering how CRL1 regulates specific processes during crown root formation.
- WOX11 and CRL1 act synergistically to promote crown root development by maintaining cytokinin homeostasis in rice.
- Eletrophoretic mobility shift assays (EMSAs), transient expression and chromatin immunoprecipitation qPCR (ChIP-qPCR) suggested that WOX11 and CRL1 directly bind to OsCKX4 to regulate its expression during crown root development.
- CRL1 enhances OsCKX4 activation through direct interaction with WOX11 at root emergence and elongation stages.
- Increased expression of OsCKX4 could partially complement the crown root phenotypes of both CRL1 and wox11 mutants.
Functional Keywords
- lateral-root , ethylene , crown , crown-root , defense , adventitious-root , root , auxin , stem , seedling , shoot , cell-division , transcription-factor , meristem , homeostasis , development , crown-root-development , root-development , cytokinin
Literature and News
- The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling . DOI: 10.1111/j.1365-313X.2011.04610.x ; PMID: 21481033
- Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants . DOI: 10.1038/cr.2007.104 ; PMID: 18071364
- Studies on sodium bypass flow in lateral rootless mutants lrt1 and lrt2, and crown rootless mutant crl1 of rice (Oryza sativa L.) . DOI: 10.1111/j.1365-3040.2009.02077.x ; PMID: 19930131
- ARL1, a LOB-domain protein required for adventitious root formation in rice . DOI: 10.1111/j.1365-313X.2005.02434.x ; PMID: 15960615
- Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling . DOI: 10.1105/tpc.105.030981 ; PMID: 15829602
- Identification of CROWN ROOTLESS1-regulated genes in rice reveals specific and conserved elements of postembryonic root formation . DOI: 10.1111/nph.13196 ; PMID: 25442012
- CROWN ROOTLESS1 binds DNA with a relaxed specificity and activates OsROP and OsbHLH044 genes involved in crown root formation in rice . DOI: 10.1111/tpj.15838 ; PMID: 35596715
- WOX11 and CRL1 act synergistically to promote crown root development by maintaining cytokinin homeostasis in rice . DOI: 10.1111/nph.18522 ; PMID: 36208055
Gene Resources
- UniProt: Q5UG13
- EMBL: AB200234, AC105734, AP008209
- AlphaFoldDB: Q5UG13
- EnsemblPlants: Os03t0149100-01
- Gramene: Os03t0149100-01
- KEGG: dosa:Os03g0149100, osa:9271993
- Orthologous matrix: YHAFEHA
- InterPro: IPR004883
- PANTHER: PTHR31529, PTHR31529:SF26
- PROSITE: PS50891
- OrthoDB: Q5UG13
- SWISS-MODEL: Q5UG13
- eggNOG: ENOG502QUV3
Sequences
cDNA Sequence
- >LOC_Os03g05510.1
ATGACGGGATTTGGATCGCCGTGCGGCGCGTGCAAGTTTCTGCGGCGCAAGTGCGTGCGCGGGTGCGTGTTCGCGCCATACTTCTGCCACGAGCAAGGGGCGGCGCACTTCGCCGCCATCCACAAGGTGTTCGGCGCCAGCAACGTGTCCAAGCTGCTCGCCCACCTGCCGCTCGCCGACCGCCCCGAGGCCGCCGTCACTATCTCCTACGAGGCGCAGGCCCGCCTCCGCGACCCCATCTATGGCTGCGTCGCCCACATCTTCGCCCTCCAGCAGCAGGTGATGACGCTGCAGGCGCAGCTGGCGTCGCTCAAGGCGGCGGCGGCGCAAGGGATACACCACCAGGACGTCGGCGCCACCACCAAGGGCGGCTACATGAGCGCCGCCGCCACCGCCGCCGACGACCAATTAGGGTACGGCGGCTACAACCAGTGGTGCGGCAGCAATGGGGGCGGCGCGCCGGCGGCGTCGCAGCCGGGCGCGTATAGCAGCAATGGCGGCGCCGGCCACGGCCACGACTCCATCACCGCGCTGCTGGCGGCCGGGTCGGACTACATGCAGCACTCGCTGTACCACGCGTTCGAGCACTCGGAGGGCGCCGGCGCCGTGGACGACGGGCACGCGGCCGCCGCGGCCTTCGAGGCGGCGGCGGAGTCGTCGTCGTGCGGCATGGCGGCGTCGTTCGCCGCCGACGAGAGCGTGTGGAGGTCGTCGTCGTCGGGATACCAAGATTGCGAGGATCTCCAGAGCGTCGCCTACGCTTACCTTAACCGCTCGTAA
CDS Sequence
- >LOC_Os03g05510.1
ATGACGGGATTTGGATCGCCGTGCGGCGCGTGCAAGTTTCTGCGGCGCAAGTGCGTGCGCGGGTGCGTGTTCGCGCCATACTTCTGCCACGAGCAAGGGGCGGCGCACTTCGCCGCCATCCACAAGGTGTTCGGCGCCAGCAACGTGTCCAAGCTGCTCGCCCACCTGCCGCTCGCCGACCGCCCCGAGGCCGCCGTCACTATCTCCTACGAGGCGCAGGCCCGCCTCCGCGACCCCATCTATGGCTGCGTCGCCCACATCTTCGCCCTCCAGCAGCAGGTGATGACGCTGCAGGCGCAGCTGGCGTCGCTCAAGGCGGCGGCGGCGCAAGGGATACACCACCAGGACGTCGGCGCCACCACCAAGGGCGGCTACATGAGCGCCGCCGCCACCGCCGCCGACGACCAATTAGGGTACGGCGGCTACAACCAGTGGTGCGGCAGCAATGGGGGCGGCGCGCCGGCGGCGTCGCAGCCGGGCGCGTATAGCAGCAATGGCGGCGCCGGCCACGGCCACGACTCCATCACCGCGCTGCTGGCGGCCGGGTCGGACTACATGCAGCACTCGCTGTACCACGCGTTCGAGCACTCGGAGGGCGCCGGCGCCGTGGACGACGGGCACGCGGCCGCCGCGGCCTTCGAGGCGGCGGCGGAGTCGTCGTCGTGCGGCATGGCGGCGTCGTTCGCCGCCGACGAGAGCGTGTGGAGGTCGTCGTCGTCGGGATACCAAGATTGCGAGGATCTCCAGAGCGTCGCCTACGCTTACCTTAACCGCTCGTAA
Protein Sequence
- >LOC_Os03g05510.1
MTGFGSPCGACKFLRRKCVRGCVFAPYFCHEQGAAHFAAIHKVFGASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQAQLASLKAAAAQGIHHQDVGATTKGGYMSAAATAADDQLGYGGYNQWCGSNGGGAPAASQPGAYSSNGGAGHGHDSITALLAAGSDYMQHSLYHAFEHSEGAGAVDDGHAAAAAFEAAAESSSCGMAASFAADESVWRSSSSGYQDCEDLQSVAYAYLNRS*