Homeodomain Genomic sequences Homeodomain Phylogeny file Homeodomain Phylogeny file with bootstrap Homeodomain Phylogeny JPEG Homeodomain Phylogeny PDF

Minimum number of tobacco Homeodomain genes: 129

Count of tobacco Homeodomain sequences: 142

Pfam accession: Homeobox KNOX1 KNOX2

SHOULD possess Homeobox KNOX1 KNOX2 domains and COULD   possess ELK HALZ HD-ZIP_N PHD domains

Homeodomain proteins were initially discovered during the study of homeotic mutants in Drosophila and have since been shown to play important roles in the developmental regulation of all eukaryotic lineages. The homeodomain is a 60 amino acid domain that consists of three helices and an N-terminal arm . The third helix lies in the major groove of the DNA, and along with the N-terminal arm, is responsible for DNA recognition. The first homeobox gene found in plants was knotted1 (kn1) that was isolated from maize plants carrying a dominant mutation that alters leaf development . Subsequently, other plant homeodomain proteins were found and these include hooded in barley that gives rise to modified flowers, glabra2 that results in a failure to develop trichomes and Bell1 that is involved in ovule development. Additionally, the homeodomain proteins WUSCHEL (WUS) and SHOOTMERISTEM-LESS (STM) have positive functions in regulating stem cell fate in the shoot apical meristem . Plants also contain homeodomain leucine zipper proteins (HDZip) where the homeodomain is associated with a leucine zipper. These are found exclusively in the plant kingdom and appear to be regulators that response to environmental factors .

Papers

Bharathan, G; Janssen, BJ; Kellogg, EA; Sinha, N. Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa? Proc. Natl. Acad. Sci. U.S.A. 1997. 94(25):13749-53 PMID: 9391098

Chan, RL; Gago, GM; Palena, CM; Gonzalez, DH. Homeoboxes in plant development. Biochim. Biophys. Acta 1998. 1442(1):1-19 PMID: 9767075

Scott, MP; Tamkun, JW; Hartzell, GW. The structure and function of the homeodomain. Biochim. Biophys. Acta 1989. 989(1):25-48 PMID: 2568852

Sessa G, Morelli G, Ruberti I. DNA-binding specificity of the homeodomain-leucine zipper domain. J Mol Biol. 1997 Dec 5;274(3):303-9. PMID: 9405140



Homeodomain genes were isolated from the tobacco GSSs by searches with the homeodomain from at least one member of each of the major subgroups of plant homeodomain protein (Chan et al., 1998). This approach was crucial to success as, unlike the other transcription factor families, searches with a homeodomain from one family often only resulted in isolation of genes from that family and not the complete homeodomain family. The different groups of tobacco homeodomain genes are quite dissimilar. To illustrate this, searches with the homeodomain from glabra2 resulted in 74 hits whereas searches with knotted1 only yielded 15 hits and none of these were present in those obtained with glabra2. The combined results from all searches revealed a minimum of 128 homeodomain genes in the tobacco genome.

Number of N terminal – 19

Number of C terminal – 29

Number of full – 88

Number of genes with middle part of domain – 6

Total – 117

There are 13 published homeodomain genes that were not present in GSSs search (except knotted1) and they were added manually to the data set.

Total minimum number – 129




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
Homeodomain_1 ET042736
Homeodomain_2 ET051710
ET048600
ET048244
Homeodomain_3 ET048384
ET043171
Homeodomain_4 ET048523
ET046428
ET043144
ET046427
Homeodomain_5 ET043145
ET045475
Homeodomain_6 ET050805
ET042035
Homeodomain_7 ET042016
ET047394
ET047390
Homeodomain_8 ET042253
ET047010
Homeodomain_9 ET043727
Homeodomain_10 ET051702
ET051484
Homeodomain_11 ET045067
ET045066
Homeodomain_12 ET045923
ET050533
ET043514
Homeodomain_13 ET050062
ET048147
ET048446
Homeodomain_14 ET043112
ET042129
Homeodomain_15 ET046152
ET046149
Homeodomain_16 ET049973
ET046083
ET050219
ET049171
ET049108
ET049972
Homeodomain_17 ET047906
ET046933
ET050635
ET051119
Homeodomain_18 ET042446
ET042639
Homeodomain_19 ET044300
ET051162
ET049580
Homeodomain_20 ET048311
ET046466
Homeodomain_21 ET045306
ET050452
ET048430
Homeodomain_22 ET044407
ET044408
Homeodomain_23 ET045174
ET041686
ET044988
ET049254
ET042722
Homeodomain_24 ET049536
ET046164
ET046169
ET042795
Homeodomain_25 ET050665
ET050153
ET042144
ET047759
Homeodomain_26 ET046467
ET050507
ET046405
Homeodomain_27 ET048689
ET049308
ET048688
Homeodomain_28 ET045437
ET048633
ET050536
Homeodomain_29 ET047353
ET044103
ET044224
ET051215
ET049527
ET044225
Homeodomain_30 ET045121
ET049563
ET049314
Homeodomain_31 ET051842
ET043609
ET045672
Homeodomain_32 ET044654
ET042228
ET042227
Homeodomain_33 ET050699
ET045989
ET050733
Homeodomain_34 ET051038
ET050101
ET046289
ET050760
Homeodomain_35 ET051233
ET045829
ET045720
ET046144
ET045521
ET044026
Homeodomain_36 ET044005
ET047862
ET042271
ET046957
Homeodomain_37 ET047348
ET042161
ET050658
ET051520
ET042162
Homeodomain_38 ET045901
ET049933
ET049636
ET043989
Homeodomain_39 ET051441
ET043879
ET051028
ET050305
ET051442
ET042917
ET051027
Homeodomain_40 ET048285
ET041935
ET043493
ET043182
ET045016
ET047726
ET041934
ET048502
ET043319
Homeodomain_41 ET047092
ET048298
ET044308
ET043553
ET044516
Homeodomain_42 ET046247
ET045550
ET045541
ET046998
ET051519
Homeodomain_43 ET051467
ET047114
ET043642
ET049112
Homeodomain_44 ET051020
ET048691
ET042086
ET047045
Homeodomain_45 ET046056
ET048423
ET048260
ET048590
ET047618
ET043871
Homeodomain_46 ET045831
ET042953
ET042773
ET049373
ET045832
ET049809
ET042772
ET044629
Homeodomain_47 ET051066
ET051260
ET051499
ET050235
ET047905
Homeodomain_48 ET042012
ET042013
ET050729
ET050694
ET045346
Homeodomain_49 ET044131
ET046588
ET050044
ET050045
ET048918
ET048399
ET044132
Homeodomain_50 ET042085
ET044869
ET042369
ET042364
ET047218
Homeodomain_51 ET046671
ET051704
ET043433
ET050528
ET051065
ET048028
Homeodomain_52 ET044874
ET051539
ET046564
ET046563
ET048248
Homeodomain_53 ET048505
ET046180
ET041897
ET041896
ET047783
ET051465
ET043413
Homeodomain_54 ET046033
ET042766
ET045958
ET044422
ET043932
ET046254
ET045654
ET046032
ET042014
Homeodomain_55 ET045698
ET041967
ET051180
ET045653
ET047403
ET042453
ET045199
ET045685
ET041966
Homeodomain_56 ET047978
ET044475
ET048148
ET049581
ET046221
ET045368
ET043685
ET047979
ET044930
Homeodomain_57 ET043734
Homeodomain_58 ET042199
ET051443
ET048953
ET047815
ET045034
ET045035
ET043248
ET049816
Homeodomain_59 ET048966
ET043915
ET043816
ET048976
ET051766
ET051337
ET045640
ET048465
Homeodomain_60 ET047569
ET051485
ET050854
ET043660
ET051648
ET051884
ET047253
ET049884
ET047501
Homeodomain_61 ET047029
ET046541
ET049209
ET051275
ET047098
ET045744
ET047028
ET048018
ET046542
ET051603
ET049119
ET042283
ET042284
ET042188
ET043902
ET045745
ET050329
Homeodomain_62 ET046516
ET048029
ET044150
ET046782
Homeodomain_63 ET045350
Homeodomain_64 ET042577
Homeodomain_65 ET042652
Homeodomain_66 ET049791
Homeodomain_67 ET047154
Homeodomain_68 ET046750
ET051860
ET049207
ET048900
Homeodomain_69 ET048653
Homeodomain_70 ET042843
Homeodomain_71 ET044188
Homeodomain_72 ET043373
Homeodomain_73 ET043477
Homeodomain_74 ET048920
ET044299
Homeodomain_75 [alias=knotted1] ET047295
ET041939
ET041938
ET045565
Homeodomain_76 ET042963
Homeodomain_77 ET049104
ET043281
Homeodomain_78 ET043786
Homeodomain_79 ET045610
ET044472
Homeodomain_80 ET050636
Homeodomain_81 ET043171
ET048423
Homeodomain_82 ET046750
Homeodomain_83 ET044906
ET050189
ET048329
ET051099
Homeodomain_84 ET049080
Homeodomain_85 ET044299
Homeodomain_86 ET049662
Homeodomain_87 ET044234
Homeodomain_88 ET048194
ET049609
ET042365
ET042708
ET047243
ET048657
ET044076
ET042709
ET043634
Homeodomain_89 ET047821
ET049961
ET043208
ET042763
ET041894
ET045538
ET049022
ET048344
ET043209
Homeodomain_90 ET048226
ET043233
ET050133
ET049865
ET049673
ET047462
ET050483
Homeodomain_91 ET045695
ET044987
ET043610
ET047374
ET046204
ET044986
Homeodomain_92 ET044157
ET043306
ET048699
ET048179
ET050824
ET050823
Homeodomain_93 ET041797
ET045353
ET043735
ET050447
ET051798
ET050178
ET043734
ET045355
ET048421
ET050436
Homeodomain_94 ET043307
ET043301
ET050033
ET042083
ET042066
Homeodomain_95 ET051834
ET042337
ET048731
ET043573
Homeodomain_96 ET044143
ET047267
ET048205
ET047367
Homeodomain_97 ET048581
ET048582
ET045557
ET049014
Homeodomain_98 ET046611
ET044741
ET047402
ET046610
Homeodomain_99 ET044013
ET042963
ET045799
Homeodomain_100 ET051694
ET047411
ET042622
Homeodomain_101 ET041905
ET041906
ET043727
Homeodomain_102 ET047066
ET050083
ET047067
Homeodomain_103 ET049104
ET043281
Homeodomain_104 ET049027
ET043032
Homeodomain_105 ET051353
ET050916
ET050915
ET049635
Homeodomain_106 ET043234
ET050134
Homeodomain_107 ET049719
ET050312
Homeodomain_108 ET048249
Homeodomain_109 ET042333
Homeodomain_110 ET046508
Homeodomain_111 ET047588
Homeodomain_112 ET044837
Homeodomain_113 ET045436
Homeodomain_114 ET049096
Homeodomain_115 ET048207
ET046340
Homeodomain_116 ET049687
ET047773
Homeodomain_117 ET050427
ET051602
Homeodomain_118 ET043786
ET044463
Homeodomain_119 ET043836
ET047014
Homeodomain_120 ET050813
ET050686
Homeodomain_121 ET047603
ET048069
Homeodomain_122 ET044149
ET045217
Homeodomain_123 ET042603
ET042602
Homeodomain_124 ET042867
ET042866
Homeodomain_125 ET045610
ET044472
Homeodomain_126 ET043933
ET045116
Homeodomain_127 ET048652
ET044944
Homeodomain_128 ET051195
ET048323
ET051322
Homeodomain_129 ET047295
ET041939
ET041938
ET045565
Homeodomain_130 ET043607
ET050833
ET047410
ET047002
Homeodomain_131 ET048104
Homeodomain_132 ET050543
ET042697
Homeodomain_133 ET048601
ET049927
Homeodomain_134 ET045992
ET045991
Homeodomain_135 ET050388
ET042738
ET048540
Homeodomain_136 ET045902
ET050563
ET048656
ET050043
Homeodomain_137 ET051656
ET046185
ET046752
ET048771
Homeodomain_138 ET050179
ET047985
ET048928
ET050200
ET045125
Homeodomain_139 ET044290
ET050498
ET046380
ET046035
ET044466
ET046959
ET049765
Homeodomain_140 ET045742
ET048070
ET046889
ET050948
ET050761
ET045996
ET050947
ET045658
ET046630
ET047301
Homeodomain_141 ET049503
Homeodomain_142 ET043462


Tobacco published genes related to transcription factor family Homeodomain
Family Genbank ID Name
Homeodomain AF544054 knotted 3
Homeodomain AF544053 knotted 2
Homeodomain AF544052 knotted 1
Homeodomain AY169493 H1
Homeodomain AY101610 Hfi22
Homeodomain AB025715 homeobox 22
Homeodomain AB025714 homeobox 20
Homeodomain AB025713 homeobox 9
Homeodomain AJ006180 NTHD2
Homeodomain AJ006179 HD1
Homeodomain AB025573 NTH1
Homeodomain AB004797 NTH23
Homeodomain AB004785 NTH15
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