ライフサイエンスコーパス: RNA ligase

1 the crystal structure and mechanism of a T4 RNA ligase.

2 (4) ends are then sealed by an ATP-dependent RNA ligase.

3 '-kinase/3'-phosphatase and an ATP-dependent RNA ligase.

4 stablish that 7Q10 is a generally applicable RNA ligase.

5 d 5'-PO4 ends are sealed by an ATP-dependent RNA ligase.

6 timization and generality of 7Q10 as a 2'-5' RNA ligase.

7 the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase.

8 RNA ligase (Trl1) and a putative baculovirus RNA ligase.

9 , such as guanyltransferase, DNA ligase, and RNA ligase.

10 3'-OH/5'-PO4 ends, which are then sealed by RNA ligase.

11 s in mitochondrial transcripts that involves RNA ligase.

12 ed from linear oligoribonucleotides using T4 RNA ligase.

13 ng that the hairpin ribozyme is an efficient RNA ligase.

14 major polypeptides, three of which represent RNA ligase.

15 transferase, 3' U-specific exonuclease, and RNA ligase.

16 orted thus far utilize a mechanism involving RNA ligase.

17 ase altering the catalytic properties of the RNA ligase.

18 circuit, we identify RtcB as the primary UPR RNA ligase.

19 espite possessing all signature motifs of an RNA ligase.

20 karyotic RtcB as the long-sought animal 3'-P RNA ligase.

21 sequence oligonucleotide using thermostable RNA ligase.

22 at prepare broken RNA termini for sealing by RNA ligase.

23 riophages in their specification of putative RNA ligases.

24 hat the predominant cause of the bias is the RNA ligases.

25 ted a considerable degree of selectivity for RNA ligases.

26 site of classical ATP-grasp enzymes and DNA/RNA ligases.

27 T4 RNA ligase 1 (Rnl1) exemplifies an ATP-dependent RNA lig

28 t a single trifunctional baculovirus enzyme, RNA ligase 1 (Rnl1), catalyzes the identical set of RNA

29 e, we show that the bacteriophage T4 enzymes RNA ligase 1 and polynucleotide kinase/phosphatase can f

30 I from L. major, and recombinant RNA editing RNA ligase 1 from L. tarentolae.

31 adenylyltransferase domain that resembles T4 RNA ligase 1, a central domain that resembles T4 polynuc

32 plant ligase, like yeast Trl1 but unlike T4 RNA ligase 1, requires a 2'-PO4 end for tRNA splicing in

33 y wild-type CthPnkp are readily sealed by T4 RNA ligase 1, the H189D enzyme generates ends that are s

34 on-free, adapter adenylation method using T4 RNA ligase 1.

35 s of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD(+)-dependent DNA ligase

36 of DNA ligases, RNA capping enzymes, and T4 RNA ligases 1 and 2.

37 T4 RNA ligase 2 (Rnl2) and kinetoplastid RNA editing ligase

38 T4 RNA ligase 2 (Rnl2) efficiently seals 3'-OH/5'-PO4 RNA n

39 T4 RNA ligase 2 (Rnl2) exemplifies a family of RNA-joining

40 Bacteriophage T4 RNA ligase 2 (Rnl2) exemplifies a polynucleotide ligase

41 Here we report that bacteriophage T4 RNA ligase 2 (Rnl2) is an efficient catalyst of RNA liga

42 3'-ends of target RNAs, respectively, by T4 RNA ligase 2 (Rnl2).

43 100X faster than either T4 DNA Ligase or T4 RNA Ligase 2 for RNA splinted DNA ligation.

44 LISH utilizes the T4 RNA Ligase 2 to efficiently join adjacent chimeric RNA-D

45 st the most closely related bacteriophage T4 RNA ligase 2, as well as against human DNA ligase IIIbet

46 of DNA ligases, RNA capping enzymes, and T4 RNA ligase 2.

47 of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2.

48 mes for uridylyl (U) removal and addition, 2 RNA ligases, 2 proteins with RNase III-like domains, and

49 We also identified the gene for band V RNA ligase, a protein much more homologous to band IV th

50 onuclease, terminal uridylyltransferase, and RNA ligase activities as well as gRNA and both edited an

51 uridylyl transferase, 3'-exouridylylase, and RNA ligase activities.

52 The data show that the editing RNA ligase activity is modulated by a novel mechanism, i

53 into the mechanism of how Hen1 activates the RNA ligase activity of Pnkp for RNA repair.

54 c rescue and in vitro splicing show that the RNA ligase activity of RtcB is directly required for the

55 n to be a component of this complex, to have RNA ligase activity, and to be one of two adenylatable p

56 continuously evolving RNA enzyme, also with RNA ligase activity, but with a completely independent e

57 d 3' fragments are subsequently joined by an RNA ligase activity, thereby removing a 26-base intron.

58 de of approximately 20 kilodaltons exhibited RNA ligase activity.

59 , we purified E. coli RtcB and tested it for RNA ligase activity.

60 one unusually fast-reacting RNA enzyme with RNA ligase activity.

61 contain at their catalytic core the class I RNA ligase, an artificial ribozyme with a catalytic rate

62 ntial in vitroevidence for involvement of an RNA ligase and an endoribonuclease, which are components

63 d out successive ligation reactions using T4 RNA ligase and T4 DNA ligase.

64 udes editing site-specific endoribonuclease, RNA ligase and terminal uridylnucleotidyl transferase (T

65 p45 co-purifies with RNA ligase and Tutase in a large ( approximately 700 kDa

66 nd/or protein binding domains, as do the two RNA ligases and a RNA helicase, which provide for additi

67 cipitates a small portion of the p45 and p50 RNA ligases and approximately 40% of the guide RNAs.

68 h are conserved among archaeal ATP-dependent RNA ligases and are situated on the surface of the enzym

69 unctions, except that band IV and band V are RNA ligases and genetic analysis indicates that the form

70 NA Wybutosine biosynthesis enzyme Tyw3p, DNA/RNA ligases and related nucleotidyltransferases and the

71 n of LC-4 with 2-4 proteins, including REL1 (RNA ligase) and LC-3, was suggested by chemical crosslin

72 RNA helicase, terminal uridylyl transferase, RNA ligase, and adenylation activities, which may have a

73 particle previously shown to contain TUTase, RNA ligase, and gRNAs and remains stable after salt trea

74 he hypothesis that contemporary DNA ligases, RNA ligases, and RNA capping enzymes evolved by the fusi

75 These properties of the mitochondrial RNA ligase are consistent with an expected in vivo role

76 ATP-dependent RNA ligases are agents of RNA repair that join 3'-OH and

77 T4 RNA ligases are commonly used to attach adapters to RNAs

78 seven polypeptide complex that includes two RNA ligases, band IV and band V.

79 rdate Branchiostoma floridae that encodes an RNA ligase (Bf RNL) with a strict requirement for RNA su

80 RNA ligase can then join the mRNA halves through their n

81 yme cleavage to prepare appropriate ends for RNA ligase catalyzed ligation.

82 e present the crystal structure of an active RNA ligase consisting of the C-terminal half of Pnkp (Pn

83 The approximately 20S RNA ligase-containing complex (L-complex) in trypanosoma

84 The Leishmania major RNA ligase-containing complex protein 2 expressed in ins

85 ntaining components interacting via RNA: the RNA ligase-containing L-complex, a 3' TUTase (terminal u

86 edimentation coefficient or abundance of the RNA ligase-containing L-complex, suggesting that the inh

87 Moreover, using a RNA ligase-dead mutant, we determine that the ligase act

88 These RNA ligase deoxyribozymes are the first that create nati

89 this new approach to obtain 3'-5'-selective RNA ligase deoxyribozymes is particularly important for

90 revious experiments have identified numerous RNA ligase deoxyribozymes, each of which can synthesize

91 valent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes.

92 dapter cofold structure, we conclude that T4 RNA ligases do not show significant primary sequence pre

93 Here we identify an RNA ligase (DraRnl) from the radiation-resistant bacteri

94 Deinococcus radiodurans RNA ligase (DraRnl) is a template-directed ligase that s

95 Deinococcus radiodurans RNA ligase (DraRnl) is the founding member of a family o

96 Deinococcus radiodurans RNA ligase (DraRnl) seals 3-OH/5-PO4 nicks in duplex nuc

97 nt roles in RNA metabolism as substrates for RNA ligases during tRNA restriction-repair and tRNA spli

98 ntained whereby systems typically contain: a RNA ligase (either ATP-grasp or RtcB superfamilies), nuc

99 some-editing ligases and a group of putative RNA ligases encoded by eukaryotic viruses (baculoviruses

100 trypanosome RNA-editing ligases and putative RNA ligases encoded by eukaryotic viruses and archaea.

101 000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible delet

102 hod is demonstrated by the generation of new RNA ligase enzymes.

103 of the founding members of the ATP-dependent RNA ligase family (T4 RNA ligase 1; Rnl1) and the NAD(+)

104 ligase 1 (Rnl1) exemplifies an ATP-dependent RNA ligase family that includes fungal tRNA ligase (Trl1

105 Pnkp defines a new RNA ligase family with signature structural and function

106 -paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chima

107 Using RNA ligase for the reaction instead of the existing chem

108 verts host DNA ligase 1, converting it to an RNA ligase, for the final step.

109 It is indeed an RNA ligase, for when expressed in Escherichia coli, the

110 tion was performed with a partially purified RNA ligase from isolated mitochondria of Leishmania tare

111 ext-generation sequencing using thermostable RNA ligase from Methanobacterium thermoautotrophicum (Mt

112 An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (Mt

113 Here, we identified another RNA ligase from the bacterial domain--a second RNA ligas

114 Here, we report the characterization of an RNA ligase from the thermophilic archaeon, Methanobacter

115 An RNA ligase from the Thermus scotoductus bacteriophage TS

116 We now describe the isolation of novel RNA ligases from a library that is based on a zinc finge

117 ive inhibitors that will block the essential RNA ligase function in a number of major protozoan patho

118 RNA ligases function pervasively across the three kingdo

119 recently cloned 1104 amino acid Arabidopsis RNA ligase functions in lieu of yeast Trl1 in vivo and i

120 fected RNA editing in vivo, whereas the REL2 RNA ligase gene could be down-regulated with no effect o

121 taining transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA gen

122 Bacteriophage T4 RNA ligase (gp63) is the best-studied member of this cla

123 decades of investigation, neither of the two RNA ligases has been identified.

124 hitecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently,

125 We further demonstrate that RNA ligases have strong sequence-specific biases which d

126 rometric analysis of the core L-complex: two RNA ligases; homologs of the four Trypanosoma brucei edi

127 RtcB exemplifies a family of RNA ligases implicated in tRNA splicing and repair.

128 tcB enzymes are a newly discovered family of RNA ligases, implicated in tRNA splicing and other RNA r

129 The chromosomal gene encoding RNA ligase in E. coli was disrupted, abolishing ligase a

130 shown previously that the REL1 mitochondrial RNA ligase in Trypanosoma brucei was a vital gene and di

131 After excision of the intron, transfer RNA ligase joins the severed exons, lifting the translat

132 re-sensitive phenotype in both wild-type and RNA ligase knockout strains.

133 mall interaction protein A6, and the editing RNA ligase L2.

134 TbREX1 or TbREX2 in combination with either RNA ligase, LmREL1, or LmREL2.

135 These findings suggest that ATP-dependent RNA ligase may act on a specific set of 3'-adenylated RN

136 r in vitro, these data suggest that the REL1 RNA ligase may be active in vivo in both U-insertion and

137 We have used RNA ligase mediated RACE and in silico analyses to locat

138 of gene expression (CAGE) tags, 1.2 million RNA ligase mediated rapid amplification of cDNA ends (RL

139 Results of RNA ligase mediated rapid amplification of cDNA ends fol

140 RNA ligase-mediated 3'-RACE showed that SRT is not polya

141 RNA ligase-mediated rapid amplification of 5' cDNA ends

142 at myelin basic protein gene promoters using RNA ligase-mediated rapid amplification of 5' cDNA ends.

143 ied the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay

144 5' RNA ligase-mediated rapid amplification of cDNA ends (RL

145 on sites have been identified by full-length RNA ligase-mediated rapid amplification of cDNA ends (RL

146 We used 5' RNA ligase-mediated rapid amplification of cDNA ends (RL

147 5'-RNA ligase-mediated rapid amplification of cDNA ends eva

148 of two cases with ETV5 outlier expression by RNA ligase-mediated rapid amplification of cDNA ends ide

149 man-derived P. carinii was obtained using an RNA ligase-mediated rapid amplification of cDNA ends tec

150 Using RNA ligase-mediated rapid amplification of cDNA ends to

151 RNA sequencing and 5' RNA ligase-mediated rapid amplification of complementary

152 RNA ligase-mediated rapid amplification of complementary

153 mapped by primer extension and confirmed by RNA ligase-mediated reverse transcription-PCR, a techniq

154 Using RNA ligase-mediated-5' rapid amplification of cDNA end a

155 ility matrices can produce higher yields for RNA ligase motifs than random pools.

156 we describe the ability of the thermophilic RNA ligase MthRnl from Methanobacterium thermoautotrophi

157 Methanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodieste

158 The 381-amino acid Methanobacterium RNA ligase (MthRnl) catalyzes intramolecular ligation of

159 Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sea

160 sites of P. aerophilum ligase and that of T4 RNA ligase, nor ligases from plants and fungi.

161 that catalyzes accurate RNA editing contains RNA ligases of approximately 57 kDa (band IV) and approx

162 The band IV and band V RNA ligases of the RNA editing complex therefore serve d

163 ar derivative was made in vitro by action of RNA ligase on a derivative of lambda cro RNA containing

164 RNA ligases participate in repair, splicing and editing

165 RNA ligases participate in repair, splicing, and editing

166 An RNA ligase previously detected in extracts of Escherichi

167 The RNA ligase reaction was studied in vitro using purified

168 ose transesterification or endonuclease plus RNA ligase reactions and may involve a guide RNA-mRNA ch

169 e to act as RNA-dependent RNA polymerase and RNA ligase, respectively.

170 des, we used in vitro evolution to obtain an RNA ligase ribozyme that lacks cytidine.

171 lymerase ribozyme, derived from an efficient RNA ligase ribozyme, can achieve the very fast k(cat) of

172 The class I RNA ligase ribozyme, isolated previously from random seq

173 e template segment of a representative 2'-5' RNA ligase ribozyme, the class II ligase, and its ligati

174 dy the behavior of an evolving population of RNA ligase ribozymes in response to selection pressures

175 , local fitness landscapes for two different RNA ligase ribozymes were examined using a continuous in

176 f Wright and Joyce, who continuously evolved RNA ligase ribozymes with an in vitro replication cycle

177 rt the first crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,be

178 A ligase from the bacterial domain--a second RNA ligase (Rnl2) encoded by phage T4.

179 Rtca along with the RNA ligase Rtcb and its catalyst Archease operate in the

180 Here we show that the Escherichia coli RNA ligase RtcB can splice these dirty DNA ends via a un

181 Activity of the RNA ligase RtcB has only two known functions: tRNA ligat

182 The RNA ligase RtcB splices broken RNAs with 5'-OH and eithe

183 entially ligated, apparently by adenylylated RNA ligase since exogenously added ATP was not required

184 d uridylyl transferase directly from UTP and RNA ligase steps and are incompatible with models involv

185 Mitochondrial RNA ligase subsequently rejoins the mRNA.

186 DNA ligases are available, only fragments of RNA ligases such as Rnl2 are known.

187 rminated ssDNA microarray elements with a T4 RNA ligase surface reaction.

188 tic motif is based on a previously described RNA ligase that can undergo either self- or cross-replic

189 ata demonstrate that RtcB is the long-sought RNA ligase that catalyzes unconventional RNA splicing du

190 s recently been identified as a 3'-phosphate RNA ligase that directly joins an RNA strand ending with

191 RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3

192 RtcB enzymes are novel RNA ligases that join 2',3'-cyclic phosphate and 5'-OH e

193 dely distributed Rnl5 family of nick-sealing RNA ligases, the physiological functions of which are un

194 he complex was trapped by the addition of T4 RNA ligase to a cleavage reaction, resulting in covalent

195 ed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to

196 ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs w

197 single stranded DNA (ssDNA) are used with T4 RNA ligase to capture various short 20-24 base single-st

198 he mRNA cleavage products are then joined by RNA ligase to generate partially edited mRNAs with uridy

199 The procedure involves use of RNA ligase to link a specific oligoribonucleotide to the

200 RNA ligase type 1 from bacteriophage T4 (Rnl1) is involv

201 MthRnl and TS2126 RNA ligases were not able to modify a 3'p in nicked doub

202 sis by RNA capping enzymes, DNA ligases, and RNA ligases, which comprise a superfamily of covalent nu

203 In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by

204 h hydroxyl groups, as they can be labeled by RNA ligase with [32P]-cytidine-3',5'-bisphosphate.