Os03g0149100

The rice Os03g0149100 was reported as crown rootless1 (OsCrl1) and Adventitious rootless1(OsARL1) respectively in 2005 by researchers from Japan and China. (in chronological order)

Annotated Information

Figure 1. Mutant VS. WT(from reference) .

Figure 2. Mutant VS. WT(from reference) .

Function

OsCrl1 encodes an ASYMMETRIC LEAVES2 (AS2) / LATERAL ORGAN BOUNDARIES (LOB) domain transcription factor which acts as a positive regulator for crown and lateral root formation in rice . As an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, OsCrl1 can promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem.Manipulation of the regulation of this gene (and its homologs in other crops) has great potential for increasing the ability of crops to absorb water and nutrients from the soil through improvement in their root architecture, which is required for achieving high yields. OsCrl1 genes is well known as early auxin-response genes[6]

.

Mutation

1. Mutation reported by Yoshiaki Inukai et al. :

• Two-week-old OsCrl1 mutants had normal seminal root development but did not form any crown roots, whereas wild-type plants formed several crown roots at the same developmental stage(Figures 1A and 1B).
• In the wild type, crown root primordia (arrow in Figure 1C) formed on the outside, adjacent to the peripheral vascular cylinder (arrowhead in Figure 1C) of the stem. By contrast, OsCrl1 did not produce any crown root primordia(Figure 1D).
• The number of lateral roots from a seminal root in OsCrl1 also decreased to;70% of that in the wild type (Figures 1A and 1B), indicating that OsCrl1 is involved in both crown root and lateral root formation.
• At later stages of development, wild type can produce significant crown root, while the OsCrl1 only produce crown root occasionally (Figures 1E and 1F).
  
  

2. Mutation reported by Hongjia Liu et al. :

• In contrast to a normal rice plant, OsArl1 mutant seedlings lack adventitious roots (Figure 2a).
• Due to its lack of essential root structure, the homozygous OsArl1 mutant cannot grow to maturity (Figure 2b), although at the seedling stage no significant difference was observed in shoot morphology between the wild type and the mutant.
• Cross sections at the base of the stem of 5-day-old seedlings revealed that the formation of adventitious primordium is impaired in the OsArl1 mutant (Figure 2c,d).
• Adventitious root primordia were induced at the fourth node of 8-week-old wild-type plants by submergence for 24 h (Figure 1e), but were not induced in the OsArl1 mutant (Figure 2f).

Expression Pattern

• Semi-quantitative RT-PCR analysis by Yoshiaki Inukai et al. shows that OsCrl1 transcripts accumulated in unelongating basal internodes. And the localized expression of OsCrl1 in stems and roots corresponds well to the areas of crown and lateral root initiation, confirming that 'OsCrl1 is involved in the initiation of these root systems.
• The RNA in situ hybridization analysis by Hongjia Liu et al. showed that this gene is expressed at the beginning of primordium formation.
• The expression of OsCrl1 was induced within 1 h and increased dramatically until 3 h after IAA treatment, then it gradually decreased. This suggests that OsCrl1 is a member of the early auxin response family.

Figure 3. An unrooted dendogram of the AS2/LOB family proteins in Arabidopsis, maize and rice(from reference) .

Subcellular localization

• The subcellular localization analysis by Hongjia Liu et al. suggests that OsCrl1 is a nuclear protein, which is expressed in nuclei.

Evolution

Yoshiaki Inukai et al. made a BLAST search by using the AS2/LOB domain sequence of OsCrl1. They found that some AS2/LOB proteins in Arabidopsis, maize (Zea mays), and rice are more similar to OsCrl1 than to other AS2/LOB proteins (Figure 3).

Knowledge Extension

• The LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. The LOB protein encodes a conserved approximately 100-amino acid domain which contains a motif resembling a zinc finger and another similar to a leucine zipper. However, both motifs have atypical spacing and until now, the biochemical function of the LOB domain has not been defined, although proteins containing LOB domains have been assumed to be transcription factors.The discovery of OsCrl1 implies that some members of the LOB domain gene family may play an important role in organ development in plants.
• In Arabidopsis, LOB defines a subgroup of LBD genes that also includes LBD10/ASL2, LBD25/ASL3, LBD36/ASL1, and AS2/LBD6. Among this subgroup, AS2 (ASYMMETRIC LEAVES2) is the only gene with clearly defined functions. AS2 is required to prevent expression of the class I KNOX homeobox genes BREVIPEDICELLUS (BP), KNAT2, and KNAT6 in the leaf. AS2 is expressed on the adaxial side of lateral organs and misexpression leads to the formation of adaxialized leaves implicating AS2 in adaxial cell fate specification.

Labs working on this gene

• Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
• Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188-0002, Japan
• State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029,China
• Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
• Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
• University of Agriculture Faisalabad, Sub-Campus Depalpur, Okara 38040, Pakistan
• Graduate School of Agricultural and Life Sciences,University of Tokyo, Tokyo 113-8657
• Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan

Structured Information

Gene Name	Os03g0149100
Description	Adventitious rootless1 (LOB domain protein)
Version	NM_001186339.1 GI:297721808 GeneID:9271993
Length	864 bp
Definition	Oryza sativa Japonica Group Os03g0149100, complete gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Chromosome 3
Location	Chromosome 3:2705032..2705895
Sequence Coding Region	2705032..2705532,2705617..2705895
Expression	GEO Profiles:Os03g0149100
Genome Context	<gbrowseImage1> name=NC_008396:2705032..2705895 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008396:2705032..2705895 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atgacgggatttggatcgccgtgcggcgcgtgcaagtttctgcggcgcaagtgcgtgcgcgggtgcgtgttcgcgccatacttctgccacgagcaaggggcggcgcacttcgccgccatccacaaggtgttcggcgccagcaacgtgtccaagctgctcgcccacctgccgctcgccgaccgccccgaggccgccgtcactatctcctacgaggcgcaggcccgcctccgcgaccccatctatggctgcgtcgcccacatcttcgccctccagcagcaggtgatgacgctgcaggcgcagctggcgtcgctcaaggcggcggcggcgcaagggatacaccaccaggacgtcggcgccaccaccaagggcggctacatgagcgccgccgccaccgccgccgacgaccaattagggtacggcggctacaaccagtggtgcggcagcaatgggggcggcgcgccggcggcgtcgcagccgggcgcgtatagcagcaatggcggcgccggccacggccacgactccatcaccgcgctgctggcggccgggtcggactacatgcagcactcgctgtaccacgcgttcgagcactcggagggcgccggcgccgtggacgacgggcacgcggccgccgcggccttcgaggcggcggcggagtcgtcgtcgtgcggcatggcggcgtcgttcgccgccgacgagagcgtgtggaggtcgtcgtcgtcgggataccaagattgcgaggatctccagagcgtcgcctacgcttaccttaaccgctcgtaa</cdnaseq>
Protein Sequence	<aaseq>MTGFGSPCGACKFLRRKCVRGCVFAPYFCHEQGAAHFAAIHKVF GASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQAQLA SLKAAAAQGIHHQDVGATTKGGYMSAAATAADDQLGYGGYNQWCGSNGGGAPAASQPG AYSSNGGAGHGHDSITALLAAGSDYMQHSLYHAFEHSEGAGAVDDGHAAAAAFEAAAE SSSCGMAASFAADESVWRSSSSGYQDCEDLQSVAYAYLNRS</aaseq>
Gene Sequence	<dnaseqindica>364..864#1..279#atgacgggatttggatcgccgtgcggcgcgtgcaagtttctgcggcgcaagtgcgtgcgcgggtgcgtgttcgcgccatacttctgccacgagcaaggggcggcgcacttcgccgccatccacaaggtgttcggcgccagcaacgtgtccaagctgctcgcccacctgccgctcgccgaccgccccgaggccgccgtcactatctcctacgaggcgcaggcccgcctccgcgaccccatctatggctgcgtcgcccacatcttcgccctccagcagcaggttcgtatagttcattcgatcgatgtgtcgctcgtcggcgtcgctggtttgctgatcttggtgtcgcggcgcgtgttcgaacaggtgatgacgctgcaggcgcagctggcgtcgctcaaggcggcggcggcgcaagggatacaccaccaggacgtcggcgccaccaccaagggcggctacatgagcgccgccgccaccgccgccgacgaccaattagggtacggcggctacaaccagtggtgcggcagcaatgggggcggcgcgccggcggcgtcgcagccgggcgcgtatagcagcaatggcggcgccggccacggccacgactccatcaccgcgctgctggcggccgggtcggactacatgcagcactcgctgtaccacgcgttcgagcactcggagggcgccggcgccgtggacgacgggcacgcggccgccgcggccttcgaggcggcggcggagtcgtcgtcgtgcggcatggcggcgtcgttcgccgccgacgagagcgtgtggaggtcgtcgtcgtcgggataccaagattgcgaggatctccagagcgtcgcctacgcttaccttaaccgctcgtaa</dnaseqindica>
External Link(s)	NCBI Gene:Os03g0149100, RefSeq:Os03g0149100