Os04g0671900

The OsARF12 gene encode a transcription activator on auxin response gene to regulate the plant developmental process.

Annotated Information

Function

"Fig. 1 Identification of OsARF mutants."

Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). OsARF12 is a transcription activator, which facilitated the transcription of the auxin response reporting gene. Auxin acts as a versatile trigger in root developmental processes, including the regulation of root growth, root patterning and root cell division and elongation. The dicotyledonous model plant Arabidopsis has a primary root (PR) and lateral roots (LRs), whereas the monocotyled- onous crop rice has fibrous roots predominantly composed of adventitious roots (ARs) and LRs. The primary root lengths (PRLs) in mutant osarf12T and osarf12 were c. 35% shorter than WT Nipponbare or Dongjin (Fig. 1a). In particular, the PRL in double mutant osarf12/25 was c. 43% of that in WT. Thus the double mutation of OsARF12 and OsARF25 increased the effect of OsARF12 loss-of-function. However, the PRLs of both mutants osarf12 and osarf12T were all greater than WT under 2,4-D treatments, indicating that these mutants were insensitive to auxin (Fig. 1b); osarf25 was sensitive to axuin, while osarf12/25 was less sensitive to it (Fig. 1b).

Longitudinal PR sections of WT, osarf12, osarf25 and osarf12/25 were examined (Fig. 2a): the elongation zones of osarf12 and osarf12/25 were distinctly shorter than the WT. Additionally, the auxin concentration in roots or leaves of osarf12 was also half that of the WT (Fig. 2b). These results suggested that decreased primary root elongation (PRE) might be caused by a shortened elongation zone of PR and reduction of auxin concentration in osarf12.

"Fig. 2 (a) Longitudinal sections of Oryza sativa primary root (PR) in wild-type (WT) plants and mutants. The thick (white) bars show the elongation zone of roots; the thinner bars are scale bars, 100 lm. (b) Contents of auxin in WT, osarf12, osarf25 and osarf12 ⁄ 25 in leaves (dark gray bars) and roots (light gray bars).."

Expression

"Fig. 3 OsARF12 expression pattern and subcellular localization."

GUS staining was mainly found in the stele and root tip (Fig. 3a and b) of PRs, ARs (same as for PRs, data no shown) and LRs (initiation to maturation) (Fig. 3f–j). In the stem, OsARF12 showed the highest expression in vascular tissue (Fig. 3c). OsARF12 expression was also observed in the stamen, ovary, glume and leaf vein (Fig. 3d,e). The transient expression of OsARF12 in onion epidermal cells confirmed that it was localized in the cell nucleus (Fig. 3l,m).

Regulation

OsARF12 expression is repressed by osa-miRNA167d in rice. Predicted by http://csrdb.ucdavis.edu/cgi-bin/rice_smrna, the 2467–2494 regions on the OsARF12 gene may be a target site of miR167d (Fig. 4a). The sqRT-PCR and qRT-PCR analyses also show that the OsARF12 expression level decreased fivefold in infected tobacco carrying 35S:OsARF12 ⁄ 35S:miR167d-1 and 35S:OsARF12 ⁄ 35S:miR167d-2 compared with 35S:OsARF12 (Fig. 4b,c)

"Fig. 4 Overexpression of osa-miR167d in Nicotiana benthamiana leaves and rice (Oryza sativa) callus."

Plant development and physiology are widely determined by polar transport of the signaling molecule auxin. This process is controlled at the cellular efflux level catalyzed by members of the PIN (pin-formed) and ATP-binding cassette protein subfamily B/P-glycoprotein family that can function either independently or in concert . The majority of OsPINs (except for OsPIN1, 1b, 1d, 2 and 8) and the majority of OsPGPs (except for OsPGP2, 3, 9, 10, 14 and 22) are significantly reduced in osarf12 (Fig. 5d–f). Experimental evidence suggests that OsARF12 may affect the expression of auxin transporter proteins and thereby modulate auxin distribution. However, it is inexplicable why the five auxin influx-like carriers (OsLAX) are all enhanced in osarf12 (Fig.5e), and OsARF12 expression was decreased by the auxin influx inhibitor NOA (Fig. 5c). These results suggests that OsARF12-regulated auxin transport has a complexity that needs to be further investigated.

"Fig. 5 OsARF12 may affect the expression of auxin transporter proteins and thereby modulate auxin distribution."

OsSCR2 and OsMIR are up-regulated in osarf12 and osarf12/25. The knockout mutant of OsMIR accumulates more Fe than does the WT. Conversely, short postembryonic root1 (OsSPR1) was inhibited in osarf12 or osarf12/25. The knockdown mutant of osspr1 accumulates less Fe compared with the WT. This all indicated that both mitochondrial proteins, OsMIR and OsSPR1, involved in root development and Fe homeostasis may be negatively/positively regulated by OsARF12. The Fe concentrations in leaves and roots of osarf12 and osarf12/25 are distinctly lower than WT while the concentration in seed was slightly lower than WT (Fig. 7a–c). The results suggested that the knockout of OsARF12 might impair Fe accumulation.

"Fig. 6 Fe concentrations in Oryza sativa wild-type (WT), osarf12, osarf25 and osarf12 ⁄ 25, and expression of genes related to Fe uptake and transport in WT and osarf12. The five biological repeats in each line were used in measurement of Fe concentrations (lg g)1) of leaves (a), roots (b) and seeds (c)."

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Labs working on this gene

• State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
• State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 359 Tiyuchang Road, Hangzhou 310006, China

Structured Information

Gene Name	Os04g0671900
Description	Similar to P-167-1_1 (Fragment)
Version	NM_001060757.1 GI:115461243 GeneID:4337363
Length	7369 bp
Definition	Oryza sativa Japonica Group Os04g0671900, 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 4
Location	Chromosome 4:34677017..34684385
Sequence Coding Region	34677814..34677910,34678831..34679021,34679125..34680113,34680723..34680870,34681083..34681158 ,34681475..34681597,34681680..34681844,34681930..34682020,34682803..34682887 ,34682990..34683145,34683264..34683320,34683447..34683545,34683661..34683770 ,34683873..34683942
Expression	GEO Profiles:Os04g0671900
Genome Context	<gbrowseImage1> name=NC_008397:34677017..34684385 source=RiceChromosome04 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008397:34677017..34684385 source=RiceChromosome04 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atgagctcgtcgtcggcggccagcatcgggccgccgcagccgccgccgccccccgcgccgcccgaggaagagaagaagtgcctcaactcggagctatggcacgcctgcgccggcccgctcgtctgcctccccaccgtcggcacgcgcgtcgtctacttcccgcaaggccacagcgagcaggtggcggcgtcgacgaacaaggaggtggagggtcacatcccgaactaccccaacctgccggcgcagctgatctgccagctccacgatgtcacaatgcatgcggatgtggagactgacgaggtgtacgcgcagatgacgctccagccactgaacccacaggagcagaacgatgcgtaccttcccgcggagatggggataatgagcaagcagccgacgaattacttctgcaagacattgacggcgagcgacaccagcacgcacggggggttctccgtgccccgccgtgctgctgagcgcgtcttccctcctttggatttcacacagcagcctccagcccaggagctaattgcacgggatattcatgacatcgagtggaagttcaggcacatctttcgaggccaacccaaacgacacctgctaaccactggctggagcgtttttgtcagtgctaagagacttgttgctggagattctgtgcttttcatatggaacgagaaaaaccagcttttacttggaataagacgtgccagtcggccacagactgtgatgccttcctctgttctttcaagcgatagcatgcacataggtctccttgcagcagcagctcatgctgctgctacaaacagccgtttcactattttctacaacccccgggcaagtccatcagaatttgtcataccactgtcaaaatacatcaaggctgtttttcacacccggatatcggttgggatgcggttcaggatgttgtttgagactgaggaatcaagcgttcgcaggtatatggggactataactgaagttagtgatgcagacccagtccgttggcctagttcctattggagatctgtgaaggttggttgggatgaatcaactgcaggggaaagaccaccaagagtttctttatgggaaattgaaccattgacaacctttccaatgtatccatctctgttcccactgagagttaagcatccttggtattcaggagttgcttccctgcatgatgacagcaatgctttaatgtggctgagaggagttgctggtgagggaggttttcagtctctgaactttcagtcacctggtattggctcctggggacaacagaggctccatccatccttactgagcagcgatcacgatcagtaccaagcagtagttgctgctgctgctgcttcccaatctggtggttacttaaaacagcaattcttgcaccttcagcaacctatgcagtcccctcaagaacactgcaacctcaacccattattgcagcaacaaattctgcagcaagcaagccagcaacagataattaatcctgatgcccaaaatatccaaacgatgttgagcccaagtgctatacaacagcaactccagcaactacagcaaatgcagcaagttcagaatgatcagaagcagaagattcaaccagatcaaagctaccaagttcctacaagtgcagttctcccaagtccaacatcattaccgagtcatttgcgagaaaaatttggcttctctgatcctaatgcgaattcttcaagcttcatcacctctagcagtagtgataacatgttggattcgagcttccttcagggaagttcgaaagctgtggacttatctcgatttaatcagcctgtagctagtgagcagcagcagcagcagcaacaggcatggaagcagaagtttatgggttcacagtcagtgtcttttgggggctcggttttgcataactcacccacaagcaaagatggttctgttgaaaacaaaattggtcgtgatgtgcaaaaccagtccctttttagtccacaagttgactcttcatccctcctgtacaacatggttcctaatctgacttcgaatgtttcggatggcaacttatcaacgatcccttctggatcaacttatctgcagaatgcaatgtatggttgcttggacgactcttctggtttattgcaaaatacaggagagaacgatccagcaaccagaacatttgtgaaggtttacaagtcaggttcggttgggaggtcgttggacataacccggttctctaattatgctgaacttcgagaagaactgggtcagatgttcggcattaagggtcaattggacgaccctgatagatcaggctggcagcttgtattcgtcgacagggagaatgatgtgcttctccttggagacgacccttgggagtcctttgtgaatagtgtatggtacatcaagatactttcacctgaggatgtgcataagatgggaaagcaaggaaatgatccacggtatctgtcctga</cdnaseq>
Protein Sequence	<aaseq>MSSSSAASIGPPQPPPPPAPPEEEKKCLNSELWHACAGPLVCLP TVGTRVVYFPQGHSEQVAASTNKEVEGHIPNYPNLPAQLICQLHDVTMHADVETDEVY AQMTLQPLNPQEQNDAYLPAEMGIMSKQPTNYFCKTLTASDTSTHGGFSVPRRAAERV FPPLDFTQQPPAQELIARDIHDIEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDS VLFIWNEKNQLLLGIRRASRPQTVMPSSVLSSDSMHIGLLAAAAHAAATNSRFTIFYN PRASPSEFVIPLSKYIKAVFHTRISVGMRFRMLFETEESSVRRYMGTITEVSDADPVR WPSSYWRSVKVGWDESTAGERPPRVSLWEIEPLTTFPMYPSLFPLRVKHPWYSGVASL HDDSNALMWLRGVAGEGGFQSLNFQSPGIGSWGQQRLHPSLLSSDHDQYQAVVAAAAA SQSGGYLKQQFLHLQQPMQSPQEHCNLNPLLQQQILQQASQQQIINPDAQNIQTMLSP SAIQQQLQQLQQMQQVQNDQKQKIQPDQSYQVPTSAVLPSPTSLPSHLREKFGFSDPN ANSSSFITSSSSDNMLDSSFLQGSSKAVDLSRFNQPVASEQQQQQQQAWKQKFMGSQS VSFGGSVLHNSPTSKDGSVENKIGRDVQNQSLFSPQVDSSSLLYNMVPNLTSNVSDGN LSTIPSGSTYLQNAMYGCLDDSSGLLQNTGENDPATRTFVKVYKSGSVGRSLDITRFS NYAELREELGQMFGIKGQLDDPDRSGWQLVFVDRENDVLLLGDDPWESFVNSVWYIKI LSPEDVHKMGKQGNDPRYLS</aaseq>
Gene Sequence	<dnaseqindica>6476..6572#5365..5555#4273..5261#3516..3663#3228..3303#2789..2911#2542..2706#2366..2456#1499..1583#1241..1396#1066..1122#841..939#616..725#444..513#cgctactgtacggccccctgcgctgcgccccccctcgtcgcgcacacgcacacacgcactcgcactactcgaaccacgcgaacccctctctttctctctctctctctctctcgcttaaatgccacaaacctaatcatttccacccctcttgcgctctctctctctctctccaaccccaccctttctccccaccatggtggcgatctccgagctcgggtgagcggaagagaaaggttggttggtcccttgccggcggggtgggggttggattgattttgctttgctttgctctgtggtttgttgatgcttgttgttggtgttggtgttggtggtggtggtgcagaatgcggccgatttgaggagggggatggggttttcgggtggatttgtgaggggatagattaagagtttgtgcttctctggtttggtcggaggaggaggagatgagctcgtcgtcggcggccagcatcgggccgccgcagccgccgccgccccccgcgccgcccgaggaaggtgggtggctaggtttgtttccgccgcttcgcttcgcggttcgctttacttcccttctcgtttggttgatgactcgatctgctgctgctgctgctgctgcagagaagaagtgcctcaactcggagctatggcacgcctgcgccggcccgctcgtctgcctccccaccgtcggcacgcgcgtcgtctacttcccgcaaggccacagcgagcaggtgaggctgagctcacctcctcagccgtctcgtgggcgcgcttgctttgcttctctctctctatctctgctggtttctcttgtttctgacgcgggtgagctttgcatacgtgaaggtggcggcgtcgacgaacaaggaggtggagggtcacatcccgaactaccccaacctgccggcgcagctgatctgccagctccacgatgtcacaatgcatgtacgtggttccttgccctaatttctcggggcatttctcagatcgatgcggcgtcacctccactccactcctccggtttatctccatggctgtcggtgctgacttgggctggcaatttttttgcaggcggatgtggagactgacgaggtgtacgcgcagatgacgctccagccactgaacccagtaaggcgcctggggtttttgcatgatgtttgcagtgctgaggttttgatggtttgaaggcgtgaaatattctaagcggttaatttgatggtttttttggatgtgttcattcgtgcagcaggagcagaacgatgcgtaccttcccgcggagatggggataatgagcaagcagccgacgaattacttctgcaagacattgacggcgagcgacaccagcacgcacggggggttctccgtgccccgccgtgctgctgagcgcgtcttccctcctttggtgtgatgagtggtgtaatttggggctgtgctcctttcttgtacttcttgggtggttgggttttgctgttgccaataacaggtggtatagtgtggtttgtaggatttcacacagcagcctccagcccaggagctaattgcacgggatattcatgacatcgagtggaagttcaggcacatctttcgaggtaacttcttaaaaatctgtagagcttatggcagtcttgaattcttcataacggtgaattatgatattcttaaagggaatttcctaataatcatctctgccccttttccattcgataagttcaccctttgtaatcatggcttaaaaccttcctaataaaaacgttttcaagtgttctgagaaaaacttcaaccattctcacacaatgtgatgtaagcgtctttttcacttaaaaatcagttggtgtgaatggagcaagagatacttgattgaattagggttatgcatagaaatgaagttacgagatcattaattggataagcacataaaaaatatcaaattttaatatgttaggatagttagcagtggatcaagttacaattgacatatgaatacatgatactttcagaggcgtactgaaatatttactagagttcgcaggtcttacaaaattgcacaatgagcaatcactgtactggacagtataattctcggtgtaggcttctttttgtatgccttgaattcccatctttctgcagggttgaacttattgttagtgtgttttctgacacagaatgtactttgtattgatcacaataactaaaaaaatgttgtcttaacataaatgttgatagtacatatgcttgaggtacttgtgctgtattgattatgaaatgggatctgctcaacactaatgatgttgttagtaattgtgtttagtagttttatatttttgaacatgccatgttactatcttttgtagtaatatgctgtttttgacaggccaacccaaacgacacctgctaaccactggctggagcgtttttgtcagtgctaagagacttgttgctggagattctgtgcttttcatatggtttgttttccatctctcttgcatttgtgattttcttttttacctgtgctaatgagtagggcgcattgttgattctctgactcaggaacgagaaaaaccagcttttacttggaataagacgtgccagtcggccacagactgtgatgccttcctctgttctttcaagcgatagcatgcacataggtctccttgcagcagcagctcatgctgctgctacaaacagccgtttcactattttctacaacccccggtaagttggacttttaaattagtatatatgcattgttgtttttcctccccatgtacaccgttaatagaaagagtgtttgtagggcaagtccatcagaatttgtcataccactgtcaaaatacatcaaggctgtttttcacacccggatatcggttgggatgcggttcaggatgttgtttgagactgaggaatcaagcgttcgcaggtgacctagcaaatgtcaatgctcagtccttattctataatctaggccaaatatataaatgatggtactttttttagataatacttggttacctagcaccaggagatcctatacatgtttgtaggatgtatgtgactatgccagtggctgaaattgccattatctgtactttttatgctttcacgcgttgatgttcttgaaaaatctgcgcatctgtcaggacatcaccccattatttatgggaattttataattgggcctctataaaaatccataatatactaatgcgcccaatgcacactttaatgaaacacaggtatatggggactataactgaagttagtgatgcagacccagtccgttggcctagttcctattggagatctgtgaaggtaatttttatattacttgaggttgttctaaagagctgtgggggtttaaacgtgatttgtgttgtctttcctgattatcttcatcttctttagttgcattttcttatgatctgtacctctggttttcattataacaatcatggaactgccttcagatgttattgcactagtgcttgcttccacagttccactaactagtgtgatattttcaggttggttgggatgaatcaactgcaggggaaagaccaccaagagtttctttatgggaaattgaaccattgacaacctttccaatgtatccatctctgttcccactgagagttaagcatccttggtattcaggagttgcttccctgcatggtacgcttaagattcttgttactgtgtgtcaggcataaactagttttgaagctattttgctgtatgcttgctatgtgtgtgcgcctatcatgtggaagtttatttggtgcatttacatagtgttttagccatcacactcaaattactgaagccacagccttaataaatttctgaacctgccacatcaaccagctgatgattctaactaaaataacctgaagttgagattgtggtgcaagagcaagaggctatagttcaagtcagtgttctctactgtgaacaatatgcctcaaatgatggttctggatacagagattgatcagggaactttataaaatgctcatataggctaaaagtaaaacaagttatggtgtaagtgaaaagttgatctcttccttccatttcttaagcacccaaggtggatcaatgttatttgataaggctcttccgtagcaaatgtaacgttctataatatgcattctttttattcattgtctttctgtgcattcttgttatggagaatgcattgatctgcctgacataattccattttctagtatctctcattcatatttctgttcttttattaactgctgtatcacacttaagatgacagcaatgctttaatgtggctgagaggagttgctggtgagggaggttttcagtctctgaactttcagtcacctggtattggctcctggggacaacagaggctccatccatccttactgagcagcgatcacgatcagtaccaagcagtagttgctgctgctgctgcttcccaatctggtggttacttaaaacagcaattcttgcaccttcagcaacctatgcagtcccctcaagaacactgcaacctcaacccattattgcagcaacaaattctgcagcaagcaagccagcaacagataattaatcctgatgcccaaaatatccaaacgatgttgagcccaagtgctatacaacagcaactccagcaactacagcaaatgcagcaagttcagaatgatcagaagcagaagattcaaccagatcaaagctaccaagttcctacaagtgcagttctcccaagtccaacatcattaccgagtcatttgcgagaaaaatttggcttctctgatcctaatgcgaattcttcaagcttcatcacctctagcagtagtgataacatgttggattcgagcttccttcagggaagttcgaaagctgtggacttatctcgatttaatcagcctgtagctagtgagcagcagcagcagcagcaacaggcatggaagcagaagtttatgggttcacagtcagtgtcttttgggggctcggttttgcataactcacccacaagcaaagatggttctgttgaaaacaaaattggtcgtgatgtgcaaaaccagtccctttttagtccacaagttgactcttcatccctcctgtacaacatggttcctaatctgacttcgaatgtttcggatggcaacttatcaacgatcccttctggatcaacttatctgcagaatgcaatgtatggttgcttggacgactcttctggtttattgcaaaatacaggagagaacgatccagcaaccagaacatttgtgaaggtaactagtataatttgcattgttgctaggtcaaatatgagctcctctttttcctccaaaaaatatatattcttcttttcatggaaccattgtaaaattgcaggtttacaagtcaggttcggttgggaggtcgttggacataacccggttctctaattatgctgaacttcgagaagaactgggtcagatgttcggcattaagggtcaattggacgaccctgatagatcaggctggcagcttgtattcgtcgacagggagaatgatgtgcttctccttggagacgacccttgggagtaagaaatattctcagaattctgatttatttattagttttagtaatcaatatccatgcatgcgcactacaaattcaagttttagtaagcaatataaatttaagtttcatcttaccgttctatgatttggttgcaaaaaaatctgcttaaattttagtactacacttggcataccctgtccatgtgtgcacactacaaactgaatctcttaattgatgttggcctcaaaacggccaagttaacatgctaagtaaaaatttcaaatctacatcaggcattgtaacttcattgtatatctaaataatttaaagatattaaacgtgcctaagatcaacaaaatttggcttgactagcaagtgcaaaagtggctgtcttatacttcctccgtttcataatgtaagactttctagcattgcccacattcatatagatgttaatgaatctagaaatatatgtgtgtctagattcattaacatctatatgaatgtgagcaatgctaaaaagtcttacattatgaaacggagggagtacaatactttggtttcctggtttccacaactaatagcttatcgaggaaaggtatgtacaatgtgaatggatatcccttcttcattcactgaaagacatgttgacagctcatggacagtatctaatgaatatgtttaaaagtactagtgttatatggagtatatttttgcaatgttcggtgcctaattgtgatctcaaacagaattcatgtgcattcagtcatacatctttaatgtgtattaatatgttaaatttttttactagactgttcttccttcaataatatgtgttggtcagtcactatatgttgatgctcagttacccaagacccttcgtgagagtaaacatcagacatgattcttcttgaaactgaccttcctcatatgatgtaggtcctttgtgaatagtgtatggtacatcaagatactttcacctgaggatgtgcataagatgggaaagcaaggaaatgatccacggtatctgtcctgaagtgagagaacatggtgccatttctggtaagatgtcataattatatttattgtaacgattaccaaatcccacactaatccttaaaaacctatgactggatagagatgttcttttctgagtaaatctgttatcatgttgtgtacttcgatagttgttgacatattggcatcatgtgttttttgtcccttattgaatgtaaaatggtctcattgtgcgggttgaagaatgtctgtttgctctaatttttattgctcggaataactcacatcttaattgacgactcaaatttaatttagagtctttttatgcatattcatctctgcatactaacatgtcctggtatactatcacagggcttccaggaggattctgcagtgcatggtggcactcttgctctcgacaatgcacgtcgtcagaagtcccaaatttgtatcttgcatgtacgccgtacatgtttccagaactctctgttacctattcggtgcaggccaccggaaccacgaaacctgatattttgtaggttccacttaggaatcagtatcggtttaactcttatcctagatgatttgtaactcgcacggcagtccactgttttcatgtttcatcgagtcttcctagacattaaacttagttgatattgtatcaggatttatgtgtattgagattcctctacatgctttcaaccaaaaaaaactgcaataatcgaagcgcacgaggattgtttcaattcgtgttgtaggatctggattttcaccgattgtccggttatgtcagtttcgagaggagctgtcaatctg</dnaseqindica>
External Link(s)	NCBI Gene:Os04g0671900, RefSeq:Os04g0671900