LIM Genomic sequences

Minimum number of tobacco LIM genes: 22

Count of tobacco LIM sequences: 27

Pfam accession: LIM

SHOULD possess LIM domain

The AC-rich motif, Pal-box, is an important cis-acting element for gene expression involved in phenylpropanoid biosynthesis. A cDNA clone (Ntlim1) encoding a Pal-box binding protein was isolated by Southwestern screening. The deduced amino acid sequence is highly similar to the members of the LIM protein family that contain a zinc finger motif. Moreover, Ntlim1 had a specific DNA binding ability and transiently activated the transcription of a beta-glucuronidase reporter gene driven by the Pal-box sequence in tobacco protoplasts. The transgenic tobacco plants with antisense Ntlim1 showed low levels of transcripts from some key phenylpropanoid pathway genes such as phenylalanine ammonia-lyase, hydroxycinnamate CoA ligase and cinnamyl alcohol dehydrogenase. Furthermore, a 27% reduction of lignin content was observed in the transgenic tobacco with antisense Ntlim1.

Papers

Eliasson, A; Gass, N; Mundel, C; Baltz, R; Kräuter, R; Evrard, JL; Steinmetz, A. Molecular and expression analysis of a LIM protein gene family from flowering plants. Mol. Gen. Genet. 2000. 264(3):257-67 PMID: 11085265

Kawaoka, A; Kaothien, P; Yoshida, K; Endo, S; Yamada, K; Ebinuma, H. Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. Plant J. 2000. 22(4):289-301 PMID: 10849346



Number of contigs: 25

Number of singlets: 2

Number of N terminal – 1

Number of N terminal with middle part of domain – 3

Number of C terminal – 3

Number of genes with middle part of domain with C terminal – 3

Number of genes with middle part of domain – 2

Number of full – 14

Total minimum number – 22




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
LIM_1 [comment=3 prime end] ET050159
LIM_2 [comment=middle part] ET049658
LIM_3 [comment=3 prime end] ET046253
ET048749
LIM_4 [comment=3 prime end] ET043404
ET048291
LIM_5 [comment=is WLIM2 (2 bp different)] ET043349
ET048341
LIM_6 [comment=This is PLIM2] ET044194
ET042452
LIM_7 [comment=middle divergent type] ET043773
ET044095
LIM_8 [comment=middle and 3 prime end] ET047810
ET043643
LIM_9 [comment=Complete. All three exons] ET048755
ET043001
LIM_10 [comment=5 prime and middle] ET042790
ET042789
ET049744
LIM_11 [comment=is PLIM1] ET042293
ET050475
ET042292
LIM_12 [comment=5 prime end and middle] ET044625
ET044617
ET044626
LIM_13 [comment=middle and 3 prime] ET044032
ET050008
ET045287
LIM_14 [comment=complete] ET046423
ET042517
ET046464
LIM_15 [comment=Similar to NtLIM1 but not the same complete] ET045206
ET050493
ET046320
LIM_16 [comment=full length] ET050494
ET046321
ET046527
ET045205
LIM_17 [comment=complete] ET049160
ET046155
ET050880
ET049159
LIM_18 [comment=full length] ET047858
ET051308
ET045718
ET043596
LIM_19 [comment=5 prime and middle] ET046535
ET050139
ET046846
ET043262
ET048182
LIM_20 [comment=Full length] ET048183
ET043644
ET043263
ET049234
ET050571
LIM_21 [comment=Full length] ET047708
ET047706
ET047707
ET046577
ET046576
LIM_22 [comment=Complete] ET046336
ET046422
ET051236
ET046337
ET049087
ET042597
LIM_23 [comment=is WLIM2 (as is #5)] ET049346
ET049356
ET044276
ET048317
ET044199
ET044692
ET049347
ET044691
LIM_24 [comment=is NtLIM1] ET049600
ET041691
ET042950
ET043184
ET048145
ET042117
ET048146
ET043183
LIM_25 [comment=Full length] ET043084
ET043086
ET048971
ET043085
ET050073
ET043087
ET050280
ET048970
ET047885
ET045356
LIM_26 [comment=middle and 3 prime] ET049537
LIM_27 [comment=5 prime end only] ET043143


Tobacco published genes related to transcription factor family LIM
Family Genbank ID Name
LIM AF184109 WLIM1
LIM AF116851 PLIM-2
LIM AB023479 Ntlim1
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