ABI Genomic sequences

Minimum number of tobacco ABI3-VP1 genes: 76

Count of tobacco ABI3-VP1 sequences: 94

Pfam accession: B3


SHOULD possess a B3 domain but SHOULD NOT possess AP2 Auxin_resp domains

Suzuki et al. (1997) showed that when expressed and purified as a separate peptide, the B3 domain has a highly cooperative DNA binding activity that is specific for the Sph sequence. They found that the properties of this activity are in compelling agreement with the functional analyses of VP1 and regulatory sequences in the C7 promoter. These results identify a new class of DNA binding proteins, which thus far are known only in the plant kingdom, that have critical functions in development .

ABI3/VP1 proteins are members of a large group of transcription factors which act as intermediaries in regulating abscisic acid (ABA)-responsive genes during seed development. Lesions in the genes affect the later stages of seed development and have adverse effects on many important processes such as reserve deposition, dormancy imposition and the acquisition of a tolerance of seed tissues to desiccation. ABI3 does not act in isolation to control gene expression central to seed maturation programmes, but rather acts in concert with various other transcription factors such as LEC1, LEC2 and FUS3; these interactions prevent the precocious activation of genes associated with germination and growth . Maize (Zea mays) Viviparous1 (VP1) and Arabidopsis ABI3 are orthologous transcription factors.

ABI3/VP1 is a multidomain transcription factor that functions as both an activator and a repressor depending on the promoter context . Three basic protein domains, B1, B2, and B3, are highly conserved among ABI3/VP1 factors from various plant species. The C-terminal B3 domain of VP1 binds specifically to the Sph DNA element in the maize C1 promoter, whereas the N-terminal B1 and B2 domains are implicated in nuclear localization and interactions with other proteins. The N-terminal co-activation repression domain is necessary and sufficient for ABA-dependent co-activation functions and repressor activities of VP1/ABI3, whereas the C-terminal B3 is required for a discrete subset of gene activation functions. Recent genetic analysis of abi3 alleles has revealed further complexity of the role of ABI3 in ABA signaling, suggesting that multiple ABA-signaling pathways are perceived through ABI3. Moreover, modification of chromatin structure by PvALF, the Phaseolus sp. ABI3 ortholog, has been shown, suggesting that VP1/ABI3 has a potential to recruit additional DNA-binding proteins to promoters

Papers

Nag, R; Maity, MK; Dasgupta, M. Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin. Plant Mol. Biol. 2005. 59(5):821-38 PMID: 16270233

Suzuki, M; Kao, CY; McCarty, DR. The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell 1997. 9(5):799-807 PMID: 9165754

Lazarova G, Zeng Y, Kermode AR. Cloning and expression of an ABSCISIC ACID-INSENSITIVE 3 (ABI3) gene homologue of yellow-cedar. J Exp Bot. 2002 May;53(371):1219-21. PMID: 11971933

Suzuki M, Ketterling MG, Li QB, McCarty DR. Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling. Plant Physiol. 2003 Jul;132(3):1664-77. PMID: 12857845



Number of contigs: 66

Number of singlets: 30

Number of N terminal – 1

Number of C terminal – 17

Number of genes with missing N terminal part – 17

Number of genes with missing C terminal part – 2

Number of middle bits – 14

Number of full – 40

Total minimum number – 76




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
ABI_1 [comment=missing C terminal part of B3 domain] ET049720
ABI_2 [comment=full of B3 domain ] ET046761
ABI_3 [comment=full of B3 domain] ET051804
ABI_4 [comment=missing N terminal part of B3 domain] ET049616
ABI_5 [comment=missing N terminal part of B3 domain] ET044744
ET046198
ABI_6 [comment=missing N terminal part of B3 domain] ET049577
ET042834
ABI_7 [comment=full B3 domain (ARF)] ET045502
ET043479
ABI_9 [comment=missing N terminal part of B3 domain] ET042854
ET042072
ABI_11 [comment=middle bit of B3 domain (FUSCA)] ET049820
ET042122
ABI_12 [comment=missing N terminal part of B3 domain] ET043445
ET044351
ABI_13 [comment=full B3 domain (ARF)] ET045384
ET043977
ABI_14 [comment=full B3 domain (ARF)] ET048698
ET043921
ABI_15 [comment=middle bit of B3 domain] ET049819
ET046288
ABI_16 [comment=missing N terminal from B3 domain] ET049490
ET042114
ABI_17 [comment=full B3 domain (RTV)] ET042973
ET051149
ABI_18 [comment=full B3 domain] ET050663
ET050023
ABI_19 [comment=full B3 domain (ARF)] ET044850
ET047576
ABI_20 [comment=missing N terminal from B3 domain] ET048931
ET048932
ABI_21 [comment=full B3 domain] ET047074
ET048996
ABI_22 [comment=full B3 domain] ET041925
ET041924
ABI_23 [comment=missing N terminal from B3 domain] ET048772
ET047009
ABI_24 [comment=missing N terminal from B3 domain] ET051063
ET051064
ABI_25 [comment=middle bit of B3 domain] ET046166
ET046165
ABI_26 [comment=full of B3 domain] ET044959
ET049383
ABI_27 [comment=full of B3 domain] ET042081
ET048591
ABI_28 [comment=full of B3 domain] ET044658
ET048824
ET048742
ABI_29 [comment=full B3 domain] ET048316
ET049749
ET047424
ABI_30 [comment=full B3 domain] ET048820
ET046762
ET048002
ABI_31 [comment=full B3 domain (RAV)] ET046682
ET051326
ET049202
ABI_32 [comment=middle bit of B3 domain] ET044054
ET047745
ET045619
ABI_33 [comment=middle bit of B3 domain] ET044324
ET044323
ET050653
ABI_34 [comment=full B3 domain] ET041784
ET041785
ET049617
ABI_35 [comment=full B3 domain] ET047099
ET046885
ET047100
ABI_36 [comment=full B3] ET044507
ET051198
ET050940
ABI_37 [comment=middle bit of B3 domain] ET050764
ET041920
ET050226
ABI_38 [comment=half of B3 domain (C terminal)] ET049403
ET050257
ET042111
ABI_39 [comment=C terminal part of B3 domain] ET043482
ET044784
ET042183
ABI_40 [comment=middle bit of B3 domain] ET046945
ET042256
ET049602
ET051364
ABI_41 [comment=full B3 domain] ET042783
ET048021
ET048020
ET042257
ABI_42 [comment=full B3 domain] ET046140
ET046053
ET046045
ET046046
ABI_43 [comment=middle bit of B3 domain] ET046495
ET046287
ET048842
ET046608
ABI_44 [comment=half of the B3 domain (C terminal)] ET051524
ET050711
ET050712
ET047790
ABI_45 [comment=C terminal part of B3 domain] ET049439
ET047605
ET047604
ET044174
ABI_46 [comment=half of the B3 domain] ET042927
ET042926
ET043318
ET050509
ABI_47 [comment=half of the B3 domain] ET042461
ET042459
ET050078
ET042460
ABI_49 [comment=half of the B3 domain] ET045102
ET046391
ET045104
ET041749
ET041750
ABI_50 [comment=full B3 domain (RAV)] ET047494
ET049539
ET043754
ET044388
ET043186
ABI_51 [comment=half of the B3 domain] ET047579
ET042607
ET047578
ET051444
ET049154
ABI_52 [comment=full B3 domain] ET042624
ET045358
ET049298
ET045357
ET049297
ABI_53 [comment=half of the B3 domain (C terminal)] ET042863
ET042862
ET042831
ET042673
ET042672
ET042830
ABI_54 [comment=half of the B3 domain (C terminal)] ET048222
ET049401
ET049400
ET046820
ET042215
ET049943
ABI_55 [comment=full B3 domain (NGA3)] ET050024
ET051618
ET045739
ET043941
ET045740
ET051617
ABI_56 [comment=full B3 domain] ET043291
ET050006
ET043890
ET044759
ET051733
ET044958
ABI_57 [comment=full B3 domain (ARF)] ET051350
ET042669
ET042668
ET043332
ET046295
ET046606
ET049818
ABI_58 [comment=full B3 domain (similar to RAV)] ET044999
ET044844
ET042158
ET042159
ET046300
ET051671
ET042074
ABI_59 [comment=half of the B3 domain (C terminal)] ET046699
ET046698
ET045056
ET043896
ET042606
ET048386
ET045055
ABI_60 [comment=half of the B3 domain (C terminal)] ET049888
ET048606
ET050791
ET050587
ET043035
ET050792
ET043034
ET050586
ABI_61 [comment=full B3 domain] ET042304
ET042620
ET050331
ET042619
ET043638
ET042059
ET042303
ET044117
ABI_62 [comment=full B3 domain] ET041866
ET045727
ET041778
ET041739
ET045749
ET041738
ET047302
ET048592
ABI_63 [comment=full B3 domain] ET050022
ET050330
ET043637
ET051479
ET048961
ET049345
ET049353
ET043764
ET048960
ABI_64 [comment=full B3 domain] ET044676
ET044326
ET044327
ET045620
ET049410
ET042801
ET049440
ET042802
ET045621
ABI_65 [comment=full B3 domain] ET042633
ET049610
ET042298
ET050700
ET042518
ET043082
ET044683
ET047361
ET045766
ET044945
ABI_66 [comment=full B3 domain] ET043674
ET043738
ET050332
ET045477
ET042713
ET044788
ET042370
ET046090
ET046409
ET048527
ABI_67 [comment=missing C terminal of B3 domain] ET051434
ABI_68 [comment=half of B3 domain (N terminal)] ET048449
ABI_69 [comment=full B3 domain] ET043214
ABI_70 [comment=missing N terminal of B3 domain] ET045292
ABI_71 [comment=missing N terminal of B3 domain] ET043389
ABI_72 [comment=missing N terminal of B3 domain] ET045201
ABI_73 [comment=missing N terminal of B3 domain] ET049236
ABI_74 [comment=missing N terminal of B3 domain] ET048112
ABI_75 [comment=half of B3 domain (C terminal)] ET043756
ABI_76 [comment=half of B3 domain (C terminal)] ET044496
ABI_77 [comment=middle bit of B3 domain] ET046390
ABI_78 [comment=full of B3 domain] ET043218
ABI_79 [comment=middle part of B3 domain] ET046970
ABI_80 [comment=missing N terminal of B3 domain] ET044585
ABI_81 [comment=missing N terminal of B3 domain] ET043255
ABI_82 [comment=middle bit B3 domain] ET043338
ABI_83 [comment=middle bit B3 domain] ET043421
ABI_84 [comment=middle bit B3 domain] ET050638
ABI_85 [comment=half of B3 domain (C terminal)] ET050812
ABI_86 [comment=missing N terminal of B3 domain] ET049944
ABI_87 [comment=half of B3 domain (C terminal)] ET042895
ABI_88 [comment=full B3 domain] ET049438
ABI_89 [comment=full B3 domain] ET049049
ABI_90 [comment=full B3 domain (ARF)] ET044891
ABI_91 [comment=full B3 domain] ET047972
ABI_92 [comment=C terminal part of B3 domain] ET042047
ABI_93 [comment=middle bit B3 domain] ET042008
ABI_94 [comment=full B3 domain] ET049998


Tobacco published genes related to transcription factor family ABI
Family Genbank ID Name
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu