TF3A_ARATH
ID TF3A_ARATH Reviewed; 412 AA.
AC Q84MZ4; Q940P2; Q9C7G8;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Transcription factor IIIA {ECO:0000303|PubMed:12711688};
DE Short=AtTFIIIA {ECO:0000303|PubMed:12711688};
GN Name=TFIIIA {ECO:0000303|PubMed:12711688};
GN OrderedLocusNames=At1g72050 {ECO:0000312|Araport:AT1G72050};
GN ORFNames=F28P5.6 {ECO:0000312|EMBL:AAG51140.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702 {ECO:0000312|EMBL:AAO73339.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=12711688; DOI=10.1093/nar/gkg335;
RA Mathieu O., Yukawa Y., Prieto J.-L., Vaillant I., Sugiura M., Tourmente S.;
RT "Identification and characterization of transcription factor IIIA and
RT ribosomal protein L5 from Arabidopsis thaliana.";
RL Nucleic Acids Res. 31:2424-2433(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=15208423; DOI=10.1104/pp.104.042176;
RA Gong W., Shen Y.-P., Ma L.-G., Pan Y., Du Y.-L., Wang D.-H., Yang J.-Y.,
RA Hu L.-D., Liu X.-F., Dong C.-X., Ma L., Chen Y.-H., Yang X.-Y., Gao Y.,
RA Zhu D., Tan X., Mu J.-Y., Zhang D.-B., Liu Y.-L., Dinesh-Kumar S.P., Li Y.,
RA Wang X.-P., Gu H.-Y., Qu L.-J., Bai S.-N., Lu Y.-T., Li J.-Y., Zhao J.-D.,
RA Zuo J., Huang H., Deng X.-W., Zhu Y.-X.;
RT "Genome-wide ORFeome cloning and analysis of Arabidopsis transcription
RT factor genes.";
RL Plant Physiol. 135:773-782(2004).
RN [6]
RP GENE FAMILY.
RX PubMed=15236668; DOI=10.1186/1471-2164-5-39;
RA Englbrecht C.C., Schoof H., Boehm S.;
RT "Conservation, diversification and expansion of C2H2 zinc finger proteins
RT in the Arabidopsis thaliana genome.";
RL BMC Genomics 5:39-39(2004).
RN [7]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-185, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=17272265; DOI=10.1074/mcp.m600408-mcp200;
RA Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT "Multidimensional protein identification technology (MudPIT) analysis of
RT ubiquitinated proteins in plants.";
RL Mol. Cell. Proteomics 6:601-610(2007).
RN [8]
RP ALTERNATIVE SPLICING.
RX PubMed=19211543; DOI=10.1101/gr.086876.108;
RA Fu Y., Bannach O., Chen H., Teune J.H., Schmitz A., Steger G., Xiong L.,
RA Barbazuk W.B.;
RT "Alternative splicing of anciently exonized 5S rRNA regulates plant
RT transcription factor TFIIIA.";
RL Genome Res. 19:913-921(2009).
RN [9]
RP POTATO SPINDLE TUBER VIROID (PSTVD) RNA-BINDING.
RX PubMed=21153748; DOI=10.1007/s00705-010-0867-x;
RA Eiras M., Nohales M.A., Kitajima E.W., Flores R., Daros J.A.;
RT "Ribosomal protein L5 and transcription factor IIIA from Arabidopsis
RT thaliana bind in vitro specifically Potato spindle tuber viroid RNA.";
RL Arch. Virol. 156:529-533(2011).
RN [10]
RP FUNCTION, DISRUPTION PHENOTYPE, ALTERNATIVE SPLICING, PROTEOLYTIC CLEAVAGE,
RP DEVELOPMENTAL STAGE, AND TISSUE SPECIFICITY.
RX PubMed=22353599; DOI=10.1111/j.1365-313x.2012.04948.x;
RA Layat E., Cotterell S., Vaillant I., Yukawa Y., Tutois S., Tourmente S.;
RT "Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA
RT control 5S rRNA accumulation during Arabidopsis thaliana development.";
RL Plant J. 71:35-44(2012).
RN [11]
RP REVIEW, AND GENE FAMILY.
RX PubMed=23142779; DOI=10.1016/j.bbagrm.2012.10.013;
RA Layat E., Probst A.V., Tourmente S.;
RT "Structure, function and regulation of Transcription Factor IIIA: From
RT Xenopus to Arabidopsis.";
RL Biochim. Biophys. Acta 1829:274-282(2013).
CC -!- FUNCTION: Essential protein (PubMed:22353599). Isoform 1 is a
CC transcription activator the binds both 5S rDNA and 5S rRNA and
CC stimulates the transcription of 5S rRNA gene (PubMed:12711688,
CC PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development
CC (PubMed:22353599). {ECO:0000269|PubMed:12711688,
CC ECO:0000269|PubMed:22353599}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768,
CC ECO:0000269|PubMed:12711688}. Nucleus, nucleolus
CC {ECO:0000269|PubMed:12711688}. Note=Accumulates in several nuclear foci
CC including the nucleolus. {ECO:0000269|PubMed:12711688}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=exon-skipped {ECO:0000303|PubMed:19211543,
CC ECO:0000303|PubMed:22353599}, ES {ECO:0000303|PubMed:19211543,
CC ECO:0000303|PubMed:22353599};
CC IsoId=Q84MZ4-1; Sequence=Displayed;
CC Name=2; Synonyms=exon-including {ECO:0000303|PubMed:19211543,
CC ECO:0000303|PubMed:22353599}, EI {ECO:0000303|PubMed:19211543,
CC ECO:0000303|PubMed:22353599};
CC IsoId=Q84MZ4-2; Sequence=VSP_058071;
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and
CC seeds. {ECO:0000269|PubMed:22353599}.
CC -!- DEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in
CC seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in
CC 10-day-old seedlings (at protein level). In correlation with the
CC reorganization of 5S rDNA chromatin to a mature state, full-length
CC isoform 1 protein TFIIIA with transcriptional activity accumulates and
CC permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts
CC accumulate in various tissues of the reproductive phase, including
CC flowers and siliques, but only isoform 2 is present in mature seeds. In
CC flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at
CC protein level). Very low amounts of TFIIIA are found in extracts from
CC fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA
CC protein progressively increases from fresh siliques to seeds
CC concomitant with lower proportions of the shorter TFIIIA-C protein (at
CC protein level) thus leading to 5S rRNA accumulation in the seed.
CC {ECO:0000269|PubMed:22353599}.
CC -!- PTM: [Isoform 1]: Protein product TFIIIA (44 kDa) is proteolytically
CC cleaved into TFIIIA-C (34 kDa). {ECO:0000269|PubMed:22353599}.
CC -!- DISRUPTION PHENOTYPE: Lethal. {ECO:0000269|PubMed:22353599}.
CC -!- MISCELLANEOUS: Binds in vitro potato spindle tuber viroid (PSTVd) RNA.
CC {ECO:0000269|PubMed:21153748}.
CC -!- MISCELLANEOUS: [Isoform 2]: Degraded through the nonsense-mediated mRNA
CC decay (NMD) pathway in a regulated unproductive splicing and
CC translation (RUST) process. {ECO:0000269|PubMed:19211543,
CC ECO:0000269|PubMed:22353599}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG51140.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY186610; AAO73339.1; -; mRNA.
DR EMBL; AC069273; AAG51140.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE35267.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE35268.1; -; Genomic_DNA.
DR EMBL; AY054225; AAL06885.1; -; mRNA.
DR EMBL; AY066042; AAL47409.1; -; mRNA.
DR EMBL; AJ630478; CAG25851.1; -; mRNA.
DR EMBL; AY568650; AAS79540.1; -; mRNA.
DR PIR; F96743; F96743.
DR RefSeq; NP_565033.1; NM_105863.3. [Q84MZ4-2]
DR RefSeq; NP_974128.1; NM_202399.2. [Q84MZ4-1]
DR AlphaFoldDB; Q84MZ4; -.
DR SMR; Q84MZ4; -.
DR IntAct; Q84MZ4; 5.
DR STRING; 3702.AT1G72050.2; -.
DR iPTMnet; Q84MZ4; -.
DR PaxDb; Q84MZ4; -.
DR PRIDE; Q84MZ4; -.
DR ProteomicsDB; 234172; -. [Q84MZ4-1]
DR EnsemblPlants; AT1G72050.1; AT1G72050.1; AT1G72050. [Q84MZ4-2]
DR EnsemblPlants; AT1G72050.2; AT1G72050.2; AT1G72050. [Q84MZ4-1]
DR GeneID; 843536; -.
DR Gramene; AT1G72050.1; AT1G72050.1; AT1G72050. [Q84MZ4-2]
DR Gramene; AT1G72050.2; AT1G72050.2; AT1G72050. [Q84MZ4-1]
DR KEGG; ath:AT1G72050; -.
DR Araport; AT1G72050; -.
DR TAIR; locus:2030362; AT1G72050.
DR eggNOG; KOG1721; Eukaryota.
DR HOGENOM; CLU_045458_1_0_1; -.
DR InParanoid; Q84MZ4; -.
DR PhylomeDB; Q84MZ4; -.
DR PRO; PR:Q84MZ4; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q84MZ4; baseline and differential.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0080084; F:5S rDNA binding; IDA:TAIR.
DR GO; GO:0008097; F:5S rRNA binding; IDA:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF00096; zf-C2H2; 4.
DR SMART; SM00355; ZnF_C2H2; 9.
DR SUPFAM; SSF57667; SSF57667; 3.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 7.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 5.
PE 1: Evidence at protein level;
KW Activator; Alternative splicing; Developmental protein; DNA-binding;
KW Isopeptide bond; Metal-binding; Nucleus; Reference proteome; Repeat;
KW RNA-binding; rRNA-binding; Transcription; Transcription regulation;
KW Ubl conjugation; Zinc; Zinc-finger.
FT CHAIN 1..412
FT /note="Transcription factor IIIA"
FT /id="PRO_0000435410"
FT ZN_FING 20..43
FT /note="C2H2-type 1; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 66..88
FT /note="C2H2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 94..118
FT /note="C2H2-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 123..148
FT /note="C2H2-type 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 215..239
FT /note="C2H2-type 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 247..272
FT /note="C2H2-type 6; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 275..296
FT /note="C2H2-type 7; degenerate"
FT /evidence="ECO:0000255"
FT ZN_FING 305..330
FT /note="C2H2-type 8"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 336..362
FT /note="C2H2-type 9; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT REGION 144..207
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 384..391
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 144..183
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..207
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CROSSLNK 185
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:17272265"
FT VAR_SEQ 1..90
FT /note="MAEEAKVDVKTSAKKDIRNYLCQYCGISRSKNYLITKHIQSHHQMELEEERD
FT DEACEVDEESSSNHTCQECGAEFKKPAHLKQHMQSHSL -> MF (in isoform
FT 2)"
FT /id="VSP_058071"
SQ SEQUENCE 412 AA; 46653 MW; AC171F610724C09F CRC64;
MAEEAKVDVK TSAKKDIRNY LCQYCGISRS KNYLITKHIQ SHHQMELEEE RDDEACEVDE
ESSSNHTCQE CGAEFKKPAH LKQHMQSHSL ERSFTCYVDD CAASYRRKDH LNRHLLTHKG
KLFKCPKENC KSEFSVQGNV GRHVKKYHSN DNRDKDNTGL GDGDKDNTCK GDDDKEKSGS
GGCEKENEGN GGSGKDNNGN GDSQPAECST GQKQVVCKEI GCGKAFKYPS QLQKHQDSHV
KLDSVEAFCS EPGCMKYFTN EECLKSHIRS CHQHINCEIC GSKHLKKNIK RHLRTHDEDS
SPGEIKCEVE GCSSTFSKAS NLQKHMKAVH DDIRPFVCGF PGCGMRFAYK HVRNKHENSG
YHVYTCGDFV ETDEDFTSRP RGGLKRKQVT AEMLVRKRVM PPRFDAEEHE TC
