RNL_ARATH
ID RNL_ARATH Reviewed; 1104 AA.
AC Q0WL81; Q0WVN4; Q0WWW5; Q96312; Q9LN14;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=tRNA ligase 1 {ECO:0000303|PubMed:15653639};
DE Short=AtRLG1 {ECO:0000303|PubMed:20844078};
DE Short=AtRNL {ECO:0000303|PubMed:16428247};
DE Short=AtRlg1p {ECO:0000303|PubMed:20844078};
DE EC=6.5.1.3 {ECO:0000269|PubMed:15653639, ECO:0000269|PubMed:23515942, ECO:0000269|PubMed:24554441};
DE AltName: Full=Protein AT.I.24-9 {ECO:0000303|Ref.4};
GN Name=RNL {ECO:0000303|PubMed:16428247};
GN Synonyms=RLG1 {ECO:0000303|PubMed:20844078};
GN OrderedLocusNames=At1g07910 {ECO:0000312|Araport:AT1G07910};
GN ORFNames=T6D22.1 {ECO:0000312|EMBL:AAF79821.1};
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;
RN [1]
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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 282-1103.
RC STRAIN=cv. Columbia;
RA Tremousaygue D., Bardet C., Dabos P., Regad F., Pelese F., Lescure B.;
RL Submitted (JUL-1996) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15653639; DOI=10.1093/nar/gki174;
RA Englert M., Beier H.;
RT "Plant tRNA ligases are multifunctional enzymes that have diverged in
RT sequence and substrate specificity from RNA ligases of other phylogenetic
RT origins.";
RL Nucleic Acids Res. 33:388-399(2005).
RN [6]
RP FUNCTION, MUTAGENESIS OF LYS-152; GLU-218; GLU-326; LYS-541; LYS-543;
RP SER-701; ASP-726; ARG-804; HIS-999; THR-1001 AND HIS-1060, AND DOMAIN.
RX PubMed=16428247; DOI=10.1093/nar/gkj441;
RA Wang L.K., Schwer B., Englert M., Beier H., Shuman S.;
RT "Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase
RT (Trl1) and requirements for complementation of tRNA splicing by a plant
RT Trl1 homolog.";
RL Nucleic Acids Res. 34:517-527(2006).
RN [7]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=20844078; DOI=10.1091/mbc.e10-08-0693;
RA Mori T., Ogasawara C., Inada T., Englert M., Beier H., Takezawa M.,
RA Endo T., Yoshihisa T.;
RT "Dual functions of yeast tRNA ligase in the unfolded protein response:
RT unconventional cytoplasmic splicing of HAC1 pre-mRNA is not sufficient to
RT release translational attenuation.";
RL Mol. Biol. Cell 21:3722-3734(2010).
RN [8]
RP FUNCTION, MUTAGENESIS OF LYS-152; 700-LYS-SER-701; ASP-726; HIS-999;
RP THR-1001; HIS-1060 AND THR-1062, DOMAIN, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, COFACTOR, AND ACTIVE SITE.
RX PubMed=23515942; DOI=10.1261/rna.038406.113;
RA Remus B.S., Shuman S.;
RT "A kinetic framework for tRNA ligase and enforcement of a 2'-phosphate
RT requirement for ligation highlights the design logic of an RNA repair
RT machine.";
RL RNA 19:659-669(2013).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, DOMAIN, AND MUTAGENESIS OF LYS-152;
RP 700-LYS-SER-701; ASP-726 AND THR-1001.
RX PubMed=24554441; DOI=10.1261/rna.043752.113;
RA Remus B.S., Shuman S.;
RT "Distinctive kinetics and substrate specificities of plant and fungal tRNA
RT ligases.";
RL RNA 20:462-473(2014).
RN [10]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND DEVELOPMENTAL
RP STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=25892242; DOI=10.1016/j.celrep.2015.03.054;
RA Leitner J., Retzer K., Malenica N., Bartkeviciute R., Lucyshyn D.,
RA Jaeger G., Korbei B., Bystroem A., Luschnig C.;
RT "Meta-regulation of Arabidopsis auxin responses depends on tRNA
RT maturation.";
RL Cell Rep. 11:516-526(2015).
CC -!- FUNCTION: Essential component of stress-response pathways entailing
CC repair of RNA breaks with 2',3'-cyclic phosphate and 5'-OH ends
CC (PubMed:23515942). Tri-functional enzyme that repairs RNA breaks with
CC 2',3'-cyclic-PO(4) and 5'-OH ends. The ligation activity requires three
CC sequential enzymatic activities: opening of the 2'3'-cyclic
CC phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester
CC (CPDase activity), phosphorylation of the 5' terminus of the 3' half-
CC tRNA in the presence of ATP (kinase activity) and ligation of the two
CC tRNA halves in an ATP-dependent reaction (ligase activity)
CC (PubMed:24554441, PubMed:23515942). Deficient in transferring AMP to
CC pRNA(OH) to form AppRNA(OH) but proficient at sealing pre-adenylylated
CC AppRNA(OH) (PubMed:23515942). CPDase and kinase reactions are almost
CC insensitive to RNA length, whereas the ligase activity decreases with
CC shorter RNA size. Can also splice DNA ended by a single 3'-terminal
CC ribonucleoside 2',3'-cyclic-PO(4) (PubMed:24554441). Binds to mRNA,
CC mature and immature (PubMed:20844078). Exhibits tRNA ligase activity in
CC vitro (PubMed:15653639, PubMed:24554441). Required for the splicing of
CC precursor tRNA molecules containing introns (PubMed:16428247,
CC PubMed:20844078). Can circularize an intron cleaved from a pre-tRNA by
CC splicing endonuclease in vitro (PubMed:20844078). Seems not involved in
CC unfolded protein response (UPR) in the endoplasmic reticulum
CC (PubMed:20844078). Involved in auxin signaling and polar transport
CC during organ morphogenesis (PubMed:25892242).
CC {ECO:0000269|PubMed:15653639, ECO:0000269|PubMed:16428247,
CC ECO:0000269|PubMed:20844078, ECO:0000269|PubMed:23515942,
CC ECO:0000269|PubMed:24554441, ECO:0000269|PubMed:25892242}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.;
CC EC=6.5.1.3; Evidence={ECO:0000269|PubMed:15653639,
CC ECO:0000269|PubMed:23515942, ECO:0000269|PubMed:24554441};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:23515942};
CC Note=Requires the presence of Mg(2+) to exhibit tRNA ligase activity.
CC {ECO:0000269|PubMed:23515942};
CC -!- ACTIVITY REGULATION: Requires the presence of NTP, preferentially ATP
CC rather than dATP, UTP, CTP and GTP, respectively, to mediate
CC ribonucleotide 5'-phosphorylation. {ECO:0000269|PubMed:23515942}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}. Cytoplasm
CC {ECO:0000269|PubMed:20844078}. Note=Associated on polysomes.
CC {ECO:0000269|PubMed:20844078}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Comment=Additional isoforms seem to exist.
CC {ECO:0000312|Araport:AT1G07910};
CC Name=1;
CC IsoId=Q0WL81-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q0WL81-2; Sequence=VSP_058828;
CC -!- TISSUE SPECIFICITY: Mainly expressed in proliferating cells and tissues
CC such as root meristems, the vasculature of developing plantlets,
CC flowers and elongating tissue. {ECO:0000269|PubMed:25892242}.
CC -!- DEVELOPMENTAL STAGE: During lateral root formation, already visible in
CC stage I lateral root primordia, and accumulates at strong levels during
CC later stages of root development. {ECO:0000269|PubMed:25892242}.
CC -!- DOMAIN: Has three domains each corresponding to an enzymatic activity,
CC namely in N- to C-terminal order: ligase, kinase and cyclic
CC phosphodiesterase (CPDase). {ECO:0000269|PubMed:23515942,
CC ECO:0000269|PubMed:24554441, ECO:0000305|PubMed:16428247}.
CC -!- DISRUPTION PHENOTYPE: Abnormal auxin responses leading to altered root
CC physiology (e.g. elongation, meristem morphology and gravitropism) and
CC aberrations in cotyledon number and venation. At later developmental
CC stages, reduced apical dominance and aberrations in lateral organ
CC positioning at inflorescence stems. {ECO:0000269|PubMed:25892242}.
CC -!- SIMILARITY: Belongs to the TRL1 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79821.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC026875; AAF79821.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE28210.1; -; Genomic_DNA.
DR EMBL; AK226218; BAE98383.1; -; mRNA.
DR EMBL; AK226707; BAE98814.1; -; mRNA.
DR EMBL; AK230326; BAF02126.1; -; mRNA.
DR EMBL; U63815; AAB07881.1; -; Genomic_DNA.
DR RefSeq; NP_172269.2; NM_100665.3. [Q0WL81-1]
DR AlphaFoldDB; Q0WL81; -.
DR STRING; 3702.AT1G07910.2; -.
DR PaxDb; Q0WL81; -.
DR PRIDE; Q0WL81; -.
DR ProteomicsDB; 227966; -. [Q0WL81-1]
DR EnsemblPlants; AT1G07910.1; AT1G07910.1; AT1G07910. [Q0WL81-1]
DR GeneID; 837306; -.
DR Gramene; AT1G07910.1; AT1G07910.1; AT1G07910. [Q0WL81-1]
DR KEGG; ath:AT1G07910; -.
DR Araport; AT1G07910; -.
DR TAIR; locus:2205085; AT1G07910.
DR eggNOG; ENOG502QSM5; Eukaryota.
DR HOGENOM; CLU_008781_0_0_1; -.
DR InParanoid; Q0WL81; -.
DR PhylomeDB; Q0WL81; -.
DR BioCyc; ARA:AT1G07910-MON; -.
DR PRO; PR:Q0WL81; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q0WL81; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0003972; F:RNA ligase (ATP) activity; IDA:UniProtKB.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0010928; P:regulation of auxin mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0042245; P:RNA repair; IDA:UniProtKB.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; IDA:UniProtKB.
DR InterPro; IPR015965; tRNA_lig_PDEase.
DR InterPro; IPR038837; tRNA_ligase_1.
DR PANTHER; PTHR35460; PTHR35460; 1.
DR Pfam; PF08302; tRNA_lig_CPD; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Auxin signaling pathway; Cytoplasm;
KW Endonuclease; Hydrolase; Kinase; Ligase; Magnesium; Metal-binding;
KW Multifunctional enzyme; Nuclease; Nucleotide-binding; Nucleus;
KW Protein biosynthesis; Reference proteome; RNA repair; RNA-binding;
KW Stress response; Transferase; tRNA processing.
FT CHAIN 1..1104
FT /note="tRNA ligase 1"
FT /id="PRO_0000439342"
FT ACT_SITE 152
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000269|PubMed:23515942"
FT VAR_SEQ 1..576
FT /note="Missing (in isoform 2)"
FT /id="VSP_058828"
FT MUTAGEN 152
FT /note="K->A: Loss of tRNA ligase activity due to impaired
FT ligase activity, but normal end-healing."
FT /evidence="ECO:0000269|PubMed:16428247,
FT ECO:0000269|PubMed:23515942, ECO:0000269|PubMed:24554441"
FT MUTAGEN 218
FT /note="E->A: Loss of tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 326
FT /note="E->A: Loss of tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 541
FT /note="K->A: Loss of tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 543
FT /note="K->A: Loss of tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 700..701
FT /note="KS->AA: Loss of kinase activity, but conserved
FT CPDase activity."
FT /evidence="ECO:0000269|PubMed:23515942,
FT ECO:0000269|PubMed:24554441"
FT MUTAGEN 701
FT /note="S->A: Loss of tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 726
FT /note="D->A: Loss of tRNA ligase activity due to impaired
FT kinase activity, but conserved CPDase activity."
FT /evidence="ECO:0000269|PubMed:16428247,
FT ECO:0000269|PubMed:23515942, ECO:0000269|PubMed:24554441"
FT MUTAGEN 804
FT /note="R->A: Reduced tRNA ligase activity."
FT /evidence="ECO:0000269|PubMed:16428247"
FT MUTAGEN 999
FT /note="H->A: Reduced tRNA ligase activity due to reduced
FT CPDase activity."
FT /evidence="ECO:0000269|PubMed:16428247,
FT ECO:0000269|PubMed:23515942"
FT MUTAGEN 1001
FT /note="T->A: Loss of tRNA ligase activity due to impaired
FT CPDase activity, but conserved kinase activity."
FT /evidence="ECO:0000269|PubMed:16428247,
FT ECO:0000269|PubMed:23515942, ECO:0000269|PubMed:24554441"
FT MUTAGEN 1060
FT /note="H->A: Loss of tRNA ligase activity due to reduced
FT CPDase activity."
FT /evidence="ECO:0000269|PubMed:16428247,
FT ECO:0000269|PubMed:23515942"
FT MUTAGEN 1062
FT /note="T->A: Reduced CPDase activity."
FT /evidence="ECO:0000269|PubMed:23515942"
FT CONFLICT 945
FT /note="Missing (in Ref. 4; AAB07881)"
FT /evidence="ECO:0000305"
FT CONFLICT 1088
FT /note="R -> H (in Ref. 3; BAE98814)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1104 AA; 123205 MW; 0FBDC8D6C2597FA6 CRC64;
MDAPFESGDS SATVVAEAVN NQFGGLSLKE SNTNAPVLPS QTTSNHRVQN LVWKPKSYGT
VSGSSSATEV GKTSAVSQIG SSGDTKVGLN LSKIFGGNLL EKFSVDKSTY CHAQIRATFY
PKFENEKTDQ EIRTRMIEMV SKGLATLEVS LKHSGSLFMY AGHKGGAYAK NSFGNIYTAV
GVFVLSRMFR EAWGTKAPKK EAEFNDFLEK NRMCISMELV TAVLGDHGQR PLDDYVVVTA
VTELGNGKPQ FYSTSEIISF CRKWRLPTNH VWLFSTRKSV TSFFAAFDAL CEEGIATSVC
RALDEVADIS VPASKDHVKV QGEILEGLVA RIVSSQSSRD MENVLRDHPP PPCDGANLDL
GLSLREICAA HRSNEKQQMR ALLRSVGPSF CPSDVEWFGD ESHPKSADKS VITKFLQSQP
ADYSTSKLQE MVRLMKEKRL PAAFKCYHNF HRAEDISPDN LFYKLVVHVH SDSGFRRYHK
EMRHMPSLWP LYRGFFVDIN LFKSNKGRDL MALKSIDNAS ENDGRGEKDG LADDDANLMI
KMKFLTYKLR TFLIRNGLSI LFKDGAAAYK TYYLRQMKIW GTSDGKQKEL CKMLDEWAAY
IRRKCGNDQL SSSTYLSEAE PFLEQYAKRS PKNHILIGSA GNLVRTEDFL AIVDGDLDEE
GDLVKKQGVT PATPEPAVKE AVQKDEGLIV FFPGIPGSAK SALCKELLNA PGGFGDDRPV
HTLMGDLVKG KYWPKVADER RKKPQSIMLA DKNAPNEDVW RQIEDMCRRT RASAVPIVAD
SEGTDTNPYS LDALAVFMFR VLQRVNHPGK LDKESSNAGY VLLMFYHLYE GKNRNEFESE
LIERFGSLIK MPLLKSDRTP LPDPVKSVLE EGIDLFNLHS RRHGRLESTK GTYAAEWTKW
EKQLRDTLVA NSEYLSSIQV PFESMVHQVR EELKTIAKGD YKPPSSEKRK HGSIVFAAIN
LPATQVHSLL EKLAAANPTM RSFLEGKKKS IQEKLERSHV TLAHKRSHGV ATVASYSQHL
NREVPVELTE LIYNDKMAAL TAHVGSVDGE TVVSKNEWPH VTLWTAEGVT AKEANTLPQL
YLEGKASRLV IDPPVSISGP LEFF
