ライフサイエンスコーパス: ribosome

1 th tRNA and other structural elements of the ribosome.

2 nascent polypeptide is still attached to the ribosome.

3 shows no activity outside the context of the ribosome.

4 to the terminal mRNA codon bound to the 70S ribosome.

5 l tRNAs to the A-site of the translating 80S ribosome.

6 force during co-translational folding at the ribosome.

7 ortant in co-chaperoning the assembly of the ribosome.

8 rfA anchors in the mRNA entry channel of the ribosome.

9 de dissociation factor of the S. aureus 100S ribosome.

10 ile the A/U-tail enables mRNA binding to the ribosome.

11 nt with its role in directing mRNAs onto the ribosome.

12 a residue-level coarse-grained model of the ribosome.

13 secondary metabolite with the eukaryotic 80S ribosome.

14 ssembly must occur in the context of the 70S ribosome.

15 to their length and lack of association with ribosomes.

16 , thereby placing the protein on translating ribosomes.

17 ain proteins that must themselves be made by ribosomes.

18 n process that would favour the recycling of ribosomes.

19 nzymes that functionally diversify mammalian ribosomes.

20 Rps23 into the nucleus for assembly into 40S ribosomes.

21 calizations previously observed for mRNA and ribosomes.

22 uality control pathways to recognize stalled ribosomes.

23 enriched transcripts are broadly occupied by ribosomes.

24 ating that it is accommodated by translating ribosomes.

25 that are translated in dendrites by neuronal ribosomes.

26 sm providing functional specificity to human ribosomes.

27 anslation leading to accumulation of stalled ribosomes.

28 All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the

29 must maintain cellular integrity, including ribosome abundance, to reinitiate the de novo protein sy

30 This approach provides maps of ribosome activity for each expressed gene in a given bio

31 lt-brain gene lists generated by Translating Ribosome Affinity Purification (TRAP) and CREB-target ge

32 Translating ribosome affinity purification (TRAP) and in vitro lucif

33 d hypothalamus) of BAC aldh1l1-translational ribosome affinity purification (TRAP) mice (both sexes).

34 Furthermore, translating ribosome affinity purification and single-cell RNA seque

35 r show that PRV circuit-directed translating ribosome affinity purification can be broadly applied to

36 By using translational ribosome affinity purification followed by RNA-Seq, we p

37 Translating ribosome affinity purification is a method initially dev

38 te such protein interactions, we establish a ribosome affinity purification method that unexpectedly

39 Directional transit of the ribosome along the messenger RNA (mRNA) template is a ke

40 leader ribosomal densities, distribution of ribosomes along coding sequences, and ribosome codon occ

41 '-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function rem

42 the nascent protein chain emerging from the ribosome and guide it along an ordered pathway toward th

43 ctor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position

44 ivated T cells showed impaired production of ribosomes and a failure to maintain proliferative capaci

45 The proximal factors that sense stalled ribosomes and initiate mammalian ribosome-associated QC

46 we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunit

47 The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent polypeptides to assist protein fol

48 the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or

49 free translation assays using both bacterial ribosomes and recombinant hybrid ribosomes carrying euka

50 on result in defective resolution of stalled ribosomes and subsequent readthrough of poly(A)-containi

51 ement factors while upregulating nucleosome, ribosome, and chromatin-modifying genes.

52 tein using a pool of messenger RNAs (mRNAs), ribosomes, and regulatory small RNAs inherited from the

53 into DHFR and IkappaB-alpha using wild-type ribosomes, and the elaborated proteins could subsequentl

54 The regulation and disassembly of the 100S ribosome are largely unknown because the temporal abunda

55 The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcript

56 enriched in binding to RPL10A/uL1-containing ribosomes are shown to require RPL10A/uL1 for their effi

57 ion codon, which cannot accommodate multiple ribosomes, are not subject to NGD.

58 the cytosolic rather than the mitochondrial ribosome as the primary drug target.

59 erated H2O2 Prx1 is synthesized on cytosolic ribosomes as a preprotein with a cleavable N-terminal pr

60 is challenges the popular conception of "the ribosome" as a homogeneous, monolithic molecular machine

61 the search for the native ribosome structure.Ribosomes assemble through the hierarchical addition of

62 hieve this, we herein report reference-based ribosome assembly (RAMBL), a computational pipeline, whi

63 Temporary functional inactivation of the 60S ribosome assembly factor Bop1 in a 3T3 cell model marked

64 or a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces ce

65 er disease virus (BDV), are required for 80S ribosomes assembly and IRES activity.

66 followed by RNA-Seq, we profiled astroglial ribosome-associated (presumably translating) mRNAs in ma

67 rgence at the ribosomal tunnel exit requires ribosome-associated complex (RAC) but not nascent polype

68 ity control of integral membrane proteins by ribosome-associated complex-stress-seventy subfamily B c

69 PGC-1alpha ribosome-associated messenger RNA in MSN subtypes was as

70 esults showed that the expression pattern of ribosome-associated mRNA profiles in astrocytes closely

71 Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that

72 singly, Ssb1, a cytoplasmic Hsp70 that binds ribosome-associated nascent polypeptide chains, also bin

73 ty readily exposes unexpected binding of the ribosome-associated protein SRA.

74 hod that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories incl

75 nse stalled ribosomes and initiate mammalian ribosome-associated QC events remain undefined.

76 uitylation plays a pivotal role in mammalian ribosome-associated QC pathways.

77 ation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by d

78 quencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq

79 nd increased translation by producing excess ribosomes, at the expense of lower steady-state growth r

80 of the encoded protein, particularly at low ribosome availability.

81 iency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of th

82 eins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of

83 imary transcript and concomitantly enhancing ribosome binding to increase expression of the transport

84 virus-like translational enhancer (PTE) and ribosome-binding 3' T-shaped structure (TSS) have been f

85 nd in viruses of different genera, while the ribosome-binding kl-TSS that provides a long-distance in

86 noprecipitation-mass spectrometry identified ribosome-binding protein 1 (RRBP1) as SYNJ2BP's ERM bind

87 n in several systems, we show that increased ribosome biogenesis and activity are a hallmark of prema

88 anine, tyrosine and tryptophan biosynthesis, ribosome biogenesis and glycolysis/gluconeogenesis were

89 osomal proteins, including those involved in ribosome biogenesis and rRNA processing.

90 TOR1) signaling, we suspected a link between ribosome biogenesis and TOR1 signaling in NKKY101.

91 While limiting ribosome biogenesis extends lifespan in several systems,

92 P2, the RNA helicase yRok1/hROK1(DDX52), the ribosome biogenesis factor yRrp7/hRRP7 and yUtp24/hUTP24

93 n yeast have established YVH1 as a novel 60S ribosome biogenesis factor.

94 ranslational proteins, especially those with ribosome biogenesis functions.

95 demonstrated reduced expression of multiple ribosome biogenesis genes and the key translation initia

96 Transcriptional profiling revealed that ribosome biogenesis genes were significantly up-regulate

97 nsequence of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts.

98 Ribosome biogenesis in Saccharomyces cerevisiae involves

99 ore the enormous complexity of 60S synthesis.Ribosome biogenesis is a dynamic process that involves t

100 As ribosome biogenesis is a well-known downstream phenomeno

101 Thus, while ribosome biogenesis represents a potential site for the

102 TCR signaling was suboptimal, was linked to ribosome biogenesis, a rate-limiting factor in both cell

103 ation and infection processes, mitochondrial ribosome biogenesis, and regulation of apoptosis and nuc

104 xpected functions, including DNA-related and ribosome biogenesis-associated activities.

105 s been associated with ssDNA interaction and ribosome biogenesis.

106 off or on RP mRNA translation and subsequent ribosome biogenesis.

107 nses to the inhibition of different steps in ribosome biogenesis.

108 g complexes highlighted proteins involved in ribosome biogenesis.

109 sitol 4-phosphate 5-kinase, and required for ribosome biogenesis.

110 cleus to suppress pre-rRNA transcription and ribosome biosynthesis during stress, thus ameliorating E

111 mTORC1, which stimulates protein, lipid, and ribosome biosynthesis, and mTORC2, which regulates cytos

112 Using RNA sequencing of ribosome-bound mRNA from hippocampal CA3 neurons, we fou

113 In eukaryotes, the ribosome-bound quality control (RQC) complex detects abe

114 In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcri

115 Ribosomes can stall during translation due to defects in

116 osphorylated puromycin, to identify modified ribosomes capable of incorporating unprotected phosphoty

117 h bacterial ribosomes and recombinant hybrid ribosomes carrying eukaryotic decoding A site cassettes.

118 In order for EF-P to associate with paused ribosomes, certain tRNAs with specific d-arm residues mu

119 ion of ribosomes along coding sequences, and ribosome codon occupancies.

120 subsequent quality control are triggered by ribosome collision.

121 We propose that ribosome collisions serve as a robust timer for translat

122 n within the elongation factor G (GDP)-bound ribosome complex.

123 Ribosomes contain proteins that must themselves be made

124 tibiotic, in the context of a functional 70S ribosome containing tRNA substrates.

125 idual cells contained either abundant or low ribosome content, compared with the wild-type strain.

126 ations targeting transcription, translation, ribosome content, replication kinetics, fatty acid and c

127 Ribosomes decode mRNA codons by selecting cognate aminoa

128 ibes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant p

129 ected, tRNASec depletion resulted in loss of ribosome density downstream of all UGA-Sec codons.

130 l, we uncover an inverse correlation between ribosome density per mRNA and cleavage efficiency.

131 mature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density wh

132 tuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' e

133 Cycloheximide had minor effects on overall ribosome density, which affected mostly mRNAs encoding r

134 t densely modified and metabolically obscure ribosome-derived molecules found in nature.

135 interaction with small and large subunits of ribosomes did not appear to change due to H2O2 treatment

136 dation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling.

137 RUNX1), telomeropathies (TERC, TERT, RTEL1), ribosome disorders (SBDS, DNAJC21, RPL5), and DNA repair

138 tion particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to

139 Conversely, the 100S ribosomes dissociate into subunits and are presumably re

140 ematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA

141 The well established phenomenon of ribosome drop-off plays crucial roles in translational a

142 ntially fast codons, are highly resilient to ribosome drop-off.

143 on also slows down the rearrangements in the ribosome-EF-Tu-GDP-Pi-Lys-tRNA(Lys) complex following GT

144 Whereas ribosomes efficiently catalyze peptide bond synthesis by

145 l level, express mRNA containing an internal ribosome entry site (IRES).

146 pression via translation through an internal ribosome entry site (IRES).

147 ynthesis of LAMB1 by activating its internal ribosome entry site, which in turn led to increased secr

148 coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the tr

149 Picornaviruses use internal ribosome entry sites (IRESs) to translate their genomes

150 independent translation mediated by internal ribosome entry sites (IRESs).

151 eractions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extend

152 nt-chain lysines immediately proximal to the ribosome exit tunnel.

153 of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize th

154 he pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin.

155 or containing ubiquitination-resistant eS10 ribosomes failed to stall efficiently on poly(A) sequenc

156 ranscriptome profiling results to an earlier ribosome footprint analysis, we have concluded that the

157 e-wide translation efficiency estimated with ribosome footprint data from the aneuploid Drosophila S2

158 Deep sequencing based ribosome footprint profiling can provide novel insights

159 ompared translation efficiency, the ratio of ribosome footprint reads to mRNA reads for each gene, to

160 Published ribosome footprinting results and the analysis of a fram

161 Ribosome footprinting using degradome data demonstrated

162 tes shows promise as a method for generating ribosome footprints.

163 RNA polymerase and ribosomes form a one-to-one complex with a micromolar di

164 tron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechani

165 Ribosomes from Mycobacterium tuberculosis (Mtb) possess

166 the human ribosome and a means of regulating ribosome function remains to be determined.

167 h the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre.

168 ility of ribosomes, such as those created by ribosome haploinsufficiency, can drive messenger RNA-spe

169 The ribosome has evolved an exit tunnel to host the elongati

170 different probes of subunit rotation in the ribosome have provided qualitatively distinct descriptio

171 ts reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circ

172 We discuss ribosome homeostasis as an overarching principle that go

173 isorders with the ubiquitous requirement for ribosomes in all cells.

174 Ribosome inactivating proteins (RIPs) are RNA N-glycosid

175 We have proposed that the ancient ribosome increased in size during early evolution by add

176 The ribosome-inhibiting protein saporin was conjugated to a

177 mparable estimations of gene expression when ribosome integrity is not compromised.

178 -terminal domain, which is required for RNAP-ribosome interaction in vitro and for pronounced cell gr

179 (RPS15A) plays a promotive role in the mRNA/ribosome interactions during early translation.

180 graphically derived models of aminoglycoside-ribosome interactions.

181 The RNAP-ribosome interface includes the RNAP subunit alpha carbo

182 from the ribosome, with the splitting of the ribosome into subunits being somewhat dispensable, or wh

183 ctions including dissociation of the stalled ribosome into subunits.Several protein quality control m

184 The ribosome is a complex macromolecular machine composed of

185 The bacterial hibernating 100S ribosome is a poorly understood form of the dimeric 70S

186 Stalled ribosomes iteratively served as a ruler to template prec

187 To decipher ribosome kinetics at stall sites, we induced ribosome st

188 Our results indicate that the increased ribosome loading of modified mRNAs renders them more per

189 Conversely, ribosome loading onto Ccnb2 mRNA and Cyclin B2 protein l

190 The results indicate that ribosome maintenance is key for maintaining the ability

191 irect interaction between RNA polymerase and ribosomes may contribute to the coupling of transcriptio

192 Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiq

193 In addition, codon usage regulates ribosome movement and stalling on mRNA during translatio

194 Importantly, dual-labeled ribosome-nascent chain libraries enable single-molecule

195 mulation depends on a similar fluctuation in ribosome number.

196 ion efficiency using both mRNA abundance and ribosome occupancy.

197 tome, and sequestered up to 15% of the total ribosome occupancy.

198 es indicates that cleavage requires multiple ribosomes on the mRNA.

199 but is not required for axonal transport of ribosomes or its target mRNAs.

200 ing sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of

201 0.8- to 2.3-MDa prokaryotic 30S, 50S and 70S ribosome particles and the 9-MDa Flock House virus.

202 ics of the translation process by increasing ribosome pausing and density on the mRNA.

203 gation step, but the mechanism that triggers ribosome pausing is not known.

204 of cellular factors to infect cells, and the ribosome plays an essential role in all viral infections

205 Our results show that ribosome premature termination may lead to non-intuitive

206 e major factor associated with P. aeruginosa ribosome preservation.

207 Madumycin II inhibits the ribosome prior to the first cycle of peptide bond format

208 Central to this coordination is ribosome production.

209 ovel open reading frames (ORFs) from regular ribosome profiling (rRibo-seq) data and outperform sever

210 Using a combination of ribosome profiling and in vitro biochemistry, we report

211 Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA se

212 Analysis of ribosome profiling and RNA-seq data for endogenous miRNA

213 t interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of Csr

214 t sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into th

215 Ss determined through mass spectrometry with ribosome profiling data revealed that about two-thirds o

216 tions were indeed supported by the available ribosome profiling data.

217 frame and shed light on A-site occupancy in ribosome profiling experiments more broadly.

218 Ribosome profiling in ER-stressed cells lacking these fa

219 We performed comparative ribosome profiling in yeast and mice with various ribonu

220 estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs

221 Ribosome profiling of an eIF5A-depleted strain reveals a

222 s, in vitro translation systems, and in vivo ribosome profiling of liver tissue from mice carrying ge

223 Ribosome profiling of NTT substitution R13P reveals heig

224 Using RNA sequencing (RNA-Seq) and ribosome profiling of primary human platelets, we show t

225 ide-resolution mapping of m(6)A coupled with ribosome profiling reveals that m(6)A promotes the trans

226 Ribosome profiling reveals that ribosomes stalled at the

227 Here we use an epidermis-specific, in vivo ribosome profiling strategy to investigate the translati

228 Recent functional, proteomic and ribosome profiling studies in eukaryotes have concurrent

229 Recent genome-wide ribosome profiling studies suggest that thousands of uOR

230 d this question by using parallel RNAseq and ribosome profiling to characterize the response of macro

231 Here, we use parallel RNA and ribosome profiling to study translational regulatory dyn

232 nt, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target pred

233 with genome-wide analysis of translation by ribosome profiling, we provide a global picture of SD-de

234 near-residue resolution by in vivo selective ribosome profiling.

235 RNA-Seq), chromatin immunoprecipitation, and ribosome profiling.

236 lation of 5'TOP mRNAs such as those encoding ribosome proteins (RP).

237 es Vms1 as a key player in the regulation of ribosome quality control specifically on mitochondria-lo

238 bosome recycling on the same mRNA or de novo ribosome recruitment.

239 translation factors, elongation factor G and ribosome recycling factor, are known to be required for

240 permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome

241 Bacterial ribosome recycling requires breakdown of the post-termin

242 lays a role in translation re-initiation and ribosome recycling.

243 increased the expression of MYC-, E2F-, and ribosome-related gene sets, promoted excessive prolifera

244 th protein coding potential, as estimated by ribosome release scores.

245 he natural loss of the mRNA surveillance and ribosome rescue factor Pelota.

246 sis that substrate movements relative to the ribosome resolve through relatively long-lived late inte

247 ing the end of a transcript each terminating ribosome returns to the cytoplasmic pool before initiati

248 Early ribosome-rich cells (RRCs) have a transcriptomic signatu

249 gression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S

250 n the mRNA structure was located outside the ribosome's footprint, translation was repressed by <2-fo

251 ld, when mRNA structures overlapped with the ribosome's footprint.

252 mechanism of translation suppression by the ribosome-silencing factors.

253 d, plant-like state, poxviruses remodel host ribosomes so that adenosine repeats erroneously generate

254 S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy.

255 n during development, evidence for regulated ribosome specification within individual cells has remai

256 cific codons and codon combinations modulate ribosome speed and facilitate protein folding.

257 ng the rates of mRNA and tRNA release and of ribosome splitting in several model PoTCs.

258 .9 A cryo-electron microscopy structure of a ribosome stalled during translation of the extremely com

259 Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pai

260 d cleavage of ER-associated mRNAs results in ribosome stalling and mRNA degradation.

261 ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bac

262 lational decay and identified changes in the ribosome stalling index during stress and recovery.

263 ity was lost, indicated that the uORF causes ribosome stalling.

264 ls a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to pro

265 M) had played a central role in the study of ribosome structure and the process of translation in bac

266 of study, culminated in the determination of ribosome structure at 2.5-A resolution.

267 embly and simplify the search for the native ribosome structure.Ribosomes assemble through the hierar

268 ow even subtle shifts in the availability of ribosomes, such as those created by ribosome haploinsuff

269 ss well understood, larger-scale features of ribosomes-such as why a few ribosomal RNA molecules domi

270 mote the helicase activity of the elongating ribosome, suggesting that uS3 contacts with mRNA enhance

271 Ribosome surface properties may thus limit the compositi

272 link between defects in genes that regulate ribosome synthesis and risk of CRC.

273 complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the tr

274 mature axons in the mammalian brain contain ribosomes, the translational regulator FMRP and a subset

275 ked to a test for a key functionality of 40S ribosomes: their ability to translocate the mRNAtRNA pai

276 Emerging studies have linked the ribosome to more selective control of gene regulation.

277 nhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the seque

278 tor RF1 promotes its aggregation and enables ribosomes to continue with translation through a prematu

279 /Sup35p, the [PSI (+)] prion, empowers yeast ribosomes to read-through UGA stop codons.

280 t1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing su

281 the ubiquitin ligase ZNF598 is required for ribosomes to terminally stall during translation of poly

282 h increases stop codon read-through allowing ribosomes to translate into the 3-end of mRNAs.

283 hesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end

284 tional repression, starvation responses, and ribosome turnover.

285 In the assembled ribosome, uL23(tail) associates with Domain III of the r

286 ntrol specifically on mitochondria-localized ribosomes, ultimately preventing protein aggregate accum

287 w here that the RQC complex also exists as a ribosome-unbound complex during the escort of aberrant p

288 Here, we follow synthesis by individual ribosomes using dual-trap optical tweezers and observe s

289 n because the temporal abundance of the 100S ribosome varies considerably among different bacterial p

290 Thus, ribosomes varying in RP composition may confer specializ

291 ption-mediated amplification assay targeting ribosomes was developed and widely used to study the epi

292 rial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P s

293 Cell, Shi et al. (2017) identify translating ribosomes which lack specific proteins and associate wit

294 key difference in their interaction with the ribosome, which correlates with their ability to cause c

295 bactericidal antibiotics dissociate from the ribosome with significantly slower rates.

296 y structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the

297 sent high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs d

298 effect the release of mRNA and tRNA from the ribosome, with the splitting of the ribosome into subuni

299 enriched or depleted from select subsets of ribosomes within embryonic stem cells.

300 inately expressed for proper assembly of the ribosome yet the mechanisms that control expression of R