ライフサイエンスコーパス: ribosome

1 del, and thus mature, the 60S subunit of the ribosome.

2 continue to rearrange at the vicinity of the ribosome.

3 release factor associated with a terminating ribosome.

4 he peptidyl transferase center P-site of the ribosome.

5 e of messenger RNA (mRNA) translation by the ribosome.

6 o a variety of cellular processes beyond the ribosome.

7 ct the energetics of hybrid formation on the ribosome.

8 to be critical for binding of Stx2A1 to the ribosome.

9 e folding pathway of RNH is unchanged on the ribosome.

10 Mrf instability and dissociates Mpy from the ribosome.

11 coordinated by rRNA and deeply buried in the ribosome.

12 , especially of the large 60S subunit of the ribosome.

13 an extreme example being their mitochondrial ribosomes.

14 cell poles that is devoid of electron-dense ribosomes.

15 nsfer RNA (tRNA), respectively, from stalled ribosomes.

16 y identify proteins associated with collided ribosomes.

17 ibosome degradation and H69 cleavage of host ribosomes.

18 ves unmasking of target sites by translating ribosomes.

19 yotic ribosomes and eukaryotic mitochondrial ribosomes.

20 ts Lso2-containing, but not Stm1-containing, ribosomes.

21 e of puromycin-labeled nascent peptides from ribosomes.

22 NA by RNase H1 while the mRNA resides in the ribosomes.

23 s of peptides using wild-type and engineered ribosomes.

24 ongating polypeptide chains from translating ribosomes.

25 of translationally inactive yeast and human ribosomes.

26 ome mass fraction and the active fraction of ribosomes.

27 ytopic membrane proteins have relatively low ribosome abundance, providing evidence for translational

28 Ribosomes accurately decode mRNA by proofreading each am

29 The substrate for ribosomes actively engaged in protein synthesis is a ter

30 Here, we employed translating ribosome affinity purification (TRAP) and RNA sequencing

31 Here, we combined translating ribosome affinity purification (TRAP) with RNA sequencin

32 ess this problem, we adopted a Translational Ribosome Affinity Purification (TRAP)- approach and desi

33 Cell type-specific translating ribosome affinity purification and qPCR was used to comp

34 we have applied a combination of translating ribosome affinity purification and ribosome profiling to

35 By using translating ribosome affinity purification coupled with deep-sequenc

36 inhibition were determined using translating ribosome affinity purification followed by high-throughp

37 We used translating ribosome affinity purification sequencing and behavioral

38 Ribosomes also mediate piRNA processing in roosters and

39 alysis of the single-step displacements from ribosome and EF-Tu diffusive trajectories before and aft

40 s of the interactions between Fe(2+) and the ribosome and identify Mn(2+) as a factor capable of atte

41 bosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translat

42 Mitochondrial ribosome and mitochondria-associated genes were identifi

43 ancer patients revealed a subset with strong ribosome and protein synthesis signatures; these CTCs ex

44 degradation of all rRNA species of the yeast ribosome and that it is bound directly to RNA molecules.

45 ed for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby mainta

46 l to that of BCL11A, directly interacts with ribosomes and BCL11A mRNA.

47 l impact of m(4)C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.

48 cing the nonspecific targeting of signalless ribosomes and pre-emptive targeting of ribosomes with sh

49 l ribosome entry sites (IRES) to hijack host ribosomes and promote cap-independent translation.

50 acterial HflX dissociates antibiotic-stalled ribosomes and rescues the bound mRNA.

51 We confirmed that EBP1 associates with ribosomes and that EBP1 silencing hinders ribosomal RNA

52 e the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulat

53 ged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (

54 ed in nuclear DNA, translated on cytoplasmic ribosomes, and imported into mitochondria.

55 nding to the decoding site of the eukaryotic ribosomes appears to result in ototoxicity, but there is

56 r with Fe2+ than with Mg2+, (iii) functional ribosomes are associated with Fe2+ after purification fr

57 Ribosomes are central targets of this response, as they

58 SMN-primed ribosomes are preferentially positioned within the first

59 tographic fractions containing extracellular ribosomes are probably not silent from an immunological

60 Collided ribosomes are specifically recognised by ZNF598 to initi

61 relationship between RNA polymerase and the ribosome as well as the basis of transcriptional polarit

62 lity control mechanism in which the abundant ribosome assembly factor, RbfA, suppresses protein synth

63 e biosynthesis and with GTPases that control ribosome assembly or activity.

64 oles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell.

65 hough evolutionally conserved, the mammalian ribosome assembly system is more complex than in yeasts.

66 ontrol function in the process from accurate ribosome assembly to rRNA processing.

67 We propose that during TRAP, assembled ribosomes associated with misfolded nascent chains move

68 , we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes

69 Single-cell RNA-sequencing, ribosome-associated mRNA profiling and chromatin analyse

70 s 3'->5' exosomal degradation of mRNA during ribosome-associated mRNA surveillance pathways.

71 rom the ribosome exit tunnel, where multiple ribosome-associated protein biogenesis factors (RPBs) di

72 The ribosome-associated protein quality control (RQC) system

73 We also discuss alterations of ribosome-associated proteins (RAPs), with a particular f

74 gate the role in antigen presentation of the ribosome-associated quality control (RQC) pathway for th

75 the integrated stress response (ISR) or the ribosome-associated quality control (RQC) pathway stimul

76 Ribosome-associated quality control (RQC) pathways prote

77 nked nascent chains, which are substrates of ribosome-associated quality control (RQC).

78 de these nascent chains via a process called ribosome-associated quality control (RQC).

79 ptide protein 5 (TTC5) as a tubulin-specific ribosome-associating factor that triggers cotranslationa

80 Disassembly, but not ribosome association, requires 40S ubiquitination by ZNF

81 binding of eight analogues to the bacterial ribosome at high resolution, revealing binding interacti

82 However, ribosomes at this position also yielded some 53-nucleoti

83 so that translation can be initiated at the ribosome binding site.

84 d with ribosome biogenesis, rRNA processing, ribosome binding, GTP binding, and hydrolase activity.

85 role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initia

86 re maintenance (dyskeratosis congenita), and ribosome biogenesis (Diamond-Blackfan anemia, Shwachman-

87 cation, transcription, nucleotide synthesis, ribosome biogenesis and function, as well as lipid metab

88 While ribosome biogenesis and global protein synthesis were un

89 tion (LLPS) facilitates the initial steps of ribosome biogenesis and other functions.

90 pports transcriptional programs that promote ribosome biogenesis and protein synthesis in cells stimu

91 ilization of RNA structure and regulation of ribosome biogenesis and protein synthesis.

92 disassembly of the 90S/SSU processome during ribosome biogenesis and repress nucleolar stress.

93 r pathways associated with mRNA translation, ribosome biogenesis and stress signaling.

94 Nucleoli, the sites of ribosome biogenesis and the largest structures in human

95 RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly p

96 ed in all stages of protein biosynthesis and ribosome biogenesis during both stages of hibernation th

97 The ribosome biogenesis factor Las1 is an essential endoribo

98 is purification method for the dissection of ribosome biogenesis in human cells.

99 regulation of the translation initiation and ribosome biogenesis machinery.

100 ress from chemotherapy or radiation therapy, ribosome biogenesis stress, and possibly inflammation ma

101 ependent, cNHEJ-independent functions during ribosome biogenesis that require the kinase activity of

102 nvolved in central and energy metabolism and ribosome biogenesis were dysregulated more in physiologi

103 t appeared to change at the RNA level (e.g., ribosome biogenesis) did not do so at the protein level,

104 lation for RP-mRNAs, enhancing RP synthesis, ribosome biogenesis, and the overall protein synthesis i

105 ar protein that regulates rRNA synthesis and ribosome biogenesis, interacts with CSA and CSB.

106 ginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth

107 mTORC1 mediates ribosome biogenesis, protein translation, and autophagy,

108 s have significant functions associated with ribosome biogenesis, rRNA processing, ribosome binding,

109 tion regulation, mRNA processing and export, ribosome biogenesis, translation initiation, and protein

110 tial cellular processes, such as splicing or ribosome biogenesis, where they remodel large RNA-protei

111 Ribosome biogenesis, which takes place mainly in the nuc

112 olymerase I (Pol I) is the first key step of ribosome biogenesis.

113 in particle assembly, primarily dedicated to ribosome biogenesis.

114 structure that colocalizes genes involved in ribosome biogenesis.

115 al GTPase of bacteria recently implicated in ribosome biogenesis.

116 se eIF6 recruitment to the nucleolus and 60S ribosome biogenesis.

117 y of 5S rRNA is preserved due to its role in ribosome biogenesis.

118 owing this pattern primarily associated with ribosome biogenesis.

119 SIN RNA-seq for profiling intact nuclei with ribosome-bound mRNA and MIRACL-seq for label-free enrich

120 a translation initiation factor eIF4E and by ribosome-bound nascent chain ribopuromycylation.

121 ural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal alpha-helix into t

122 This suggested that ribosomes bypass tryptophan codons in the absence of try

123 The pioneering ribosome can both physically associate and kinetically c

124 Thus, nascent chain ejection times from the ribosome can vary greatly between proteins due to differ

125 ibosomal profiling has shed new light on how ribosomes can ignore stop codons in messenger RNA.

126 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact.

127 Ribosomes can produce proteins in minutes and are largel

128 shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger

129 stimulates TORC1 and liberates proteasomes, ribosomes, chaperones and metabolic enzymes from non-mem

130 stalled translation events is activated when ribosomes collide and form disome, trisome, or higher-or

131 the MAPKKK ZAK functions as the sentinel for ribosome collisions and is required for immediate early

132 This tiered response to ribosome collisions would allow cells to dynamically tun

133 The collided ribosome complex must be disassembled to initiate downst

134 f a posttermination Thermus thermophilus 70S ribosome complexed with EF-G, RRF and two transfer RNAs

135 Seed ribosome complexes are associated with mRNA-binding prot

136 promote dissociation of EF-G from FA-stalled ribosome complexes.

137 Moreover, with age, ribosome coverage gradually decreased in the vicinity of

138 nosa deploys a virulence mechanism to induce ribosome degradation and H69 cleavage of host ribosomes.

139 l mRNA translatability, but they also reveal ribosome-dependent and ribosome-independent mRNA-surveil

140 Ribosome dimerization is thought to be reversible, with

141 The procedure entails a single round of ribosome display using the sybody libraries encoded by m

142 The contribution of poly ribosomes dominates at faster and soluble proteins at sl

143 e messenger RNAs and undergo stalling at the ribosome during translation.

144 F1) as a novel protein recruited to collided ribosomes during translational distress.

145 We modeled codon-specific ribosome dwell times from ribosome profiling, considerin

146 t molecular dynamics simulations of the full ribosome-EF-Tu complex.

147 Here we used ribosome engineering to investigate whether 5S rRNA auto

148 Viruses use internal ribosome entry sites (IRES) to hijack host ribosomes and

149 nascent polypeptides rapidly dissociate from ribosomes even in the presence of elongation inhibitors.

150 izations and confirm its position within the ribosome excluded region.

151 when a nascent polypeptide emerges from the ribosome exit tunnel, where multiple ribosome-associated

152 ting ribosomal RNA synthesis and processing, ribosome export into the cytoplasm, and global protein s

153 rage of multiple metrics for a wide range of ribosome footprint lengths.

154 bo files store all essential data grouped by ribosome footprint lengths.

155 ation and could include clearance of stalled ribosomes from mRNA, poising mRNA for degradation and re

156 In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolv

157 nsional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3

158 ate whether 5S rRNA autonomy is critical for ribosome function and cell survival.

159 and gene families, including Wnt signaling, ribosome function, DNA binding, and clustered protocadhe

160 K63 ubiquitination of ribosomes has emerged as a new posttranslational modific

161 Specifically, we show that ribosome hibernation in a batch culture is induced at an

162 Together, we propose that ribosome hibernation is a specific and conserved respons

163 ight on a conserved mechanism for eukaryotic ribosome hibernation.

164 modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on

165 the ASCC3 helicase disassembles the leading ribosome in an ATP-dependent reaction.

166 H) nascent chains stalled on the prokaryotic ribosome in vitro We found that ribosome-stalled RNH has

167 This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are boun

168 is an indispensable component of cytoplasmic ribosomes in all species.

169 Eukaryotic ribosomes in some lineages appear to be logarithmically

170 Jasmonate-induced protein 60 (JIP60) is a ribosome-inactivating protein (RIP) from barley (Hordeum

171 In contrast, ribosomes incorporating the missense variant erroneously

172 irs are present in the A- and P-sites of the ribosome independent of other factors known to influence

173 but they also reveal ribosome-dependent and ribosome-independent mRNA-surveillance pathways.

174 er length beyond 6 nt destabilizes mRNA-tRNA-ribosome interactions and results in a 5- to 10-fold red

175 ops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translat

176 licase then facilitates the translocation of ribosomes into the uORF downstream regions (UDRs).

177 produces the proteome, while the dissociable ribosome is committed to the translation of a specific m

178 tion, translation of the genetic code by the ribosome is hypothesized to be exceptionally sensitive t

179 fraction of Fe2+ that is associated with the ribosome is not exchangeable with surrounding divalent c

180 The bacterial ribosome is recycled into subunits by two conserved prot

181 The function of a ribosome is to build ribosomes; to accomplish this task,

182 These findings suggest that the ribosome itself does not necessarily rewire protein fold

183 erevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indica

184 Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demon

185 Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misa

186 e appreciation of relevance of the extent of ribosome loading for recoding.

187 d, GCN2 kinase preferentially suppressed the ribosome loading of mRNAs for functions such as mitochon

188 to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes,

189 This work expands the scope of ribosome-mediated polymerization, setting the stage for

190 Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon.

191 The human mitochondrial ribosome (mitoribosome) and associated proteins regulate

192 hesized within mitochondria on mitochondrial ribosomes (mitoribosomes) with over 70 polypeptides enco

193 Nascent peptide-mediated anchoring of ribosome-mRNA translation complexes to the inclusions is

194 formational sampling of translation-arrested ribosome nascent chain complexes is key to understand co

195 ng the 3'->5' RNA helicase Ski2 binds to 80S ribosomes near the mRNA entrance and facilitates 3'->5'

196 Bacterial ribosomes never left stasis.

197 1 assembly, exhibit constitutively high psbA ribosome occupancy in the dark and differ in this way fr

198 Ribosome occupancy measurements enable protein abundance

199 rylated TBK1 levels), and the expression and ribosome occupancy of cGAS-dependent inflammatory genes

200 nd N-terminal peptide elongation, regulating ribosome occupancy of these codons.

201 a global scale, and pinpoint characteristic ribosome occupancy patterns at single codon resolution.

202 Importantly, the polarity of ribosomes on mRNAs encoding multiple TMDs was disproport

203 Our results uncover a function for ribosomes on non-coding regions of RNAs and reveal the m

204 Regulon-level coordination by ribosomes on sensory short ORFs illustrates one utility

205 g, HiPR-FISH shows the diverse strategies of ribosome organization that are exhibited by taxa in the

206 translation and folding, and within this the ribosome particle is the key player.

207 the mouse brain also leads to codon-specific ribosome pausing and neurodegeneration, suggesting that

208 ses function in the same pathway to mitigate ribosome pausing.

209 the major bacterial target sites such as the ribosome, penicillin-binding proteins, and topoisomerase

210 Ribosome profiling (Ribo-seq) is a powerful technology f

211 Here, by ribosome profiling (Ribo-seq) we find specific dysregula

212 We have adapted ribosome profiling (RP) workflows from the Illumina to t

213 Ribosome profiling data revealed that ORF-Y is translate

214 be possible to produce a "one-size-fits-all" ribosome profiling data set.

215 Ribosome profiling demonstrated Ebp1-60S binding is high

216 Here, we developed ribosome profiling in a model archaeon, Haloferax volcan

217 Here we used ribosome profiling in melanoma cells to investigate the

218 boR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate ess

219 Ribosome profiling revealed an uncharacterized complexit

220 We used ribosome profiling to characterize the biological role o

221 anslating ribosome affinity purification and ribosome profiling to identify biologically relevant pri

222 Through comparative genomic analysis and ribosome profiling we here identify and confirm the expr

223 By coupling in vivo ribosome profiling with genetic screening, we provide di

224 use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mech

225 using a combination of multiscale modeling, ribosome profiling, and gene ontology analyses.

226 d a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine

227 led codon-specific ribosome dwell times from ribosome profiling, considering codon pair interactions

228 e our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a co

229 fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data.

230 ESSyourself brings robust, rapid analysis of ribosome-profiling data to a broad and ever-expanding au

231 Here, using a suite of ribosome-profiling techniques(2-4), we present a high-re

232 mino acids frequent in ribosomal proteins on ribosome progression.

233 ays predominate including the Wnt, MAPK, the ribosome, proteasome, endocytosis and tight junction pat

234 g mRNA for degradation and rendering stalled ribosomes recyclable by Pelota/Hbs1/ABCE1.

235 s, providing insights into the mechanisms of ribosome recycling and tRNA translocation.

236 The molecular basis for ribosome recycling by RRF and EF-G remains unclear.

237 iling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli.

238 proteins, elongation factor G (EF-G) and the ribosome recycling factor (RRF).

239 dissociation of the 100S complexes enabling ribosome recycling for participation in new rounds of tr

240 a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.

241 ltilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing,

242 al electrostatic interactions, can influence ribosome recycling, and could be particularly relevant t

243 translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it

244 itin resolved at 4.4-2.7 angstrom showed 80S ribosomes represented in multiple states of translation,

245 -dependent factors, including the Pelo-Hbs1L ribosome rescue complex.

246 arrest leads to the futile activation of the ribosome rescue systems.

247 mitoribosomal large subunits trapped during ribosome rescue.

248 hment of zinc to cells harboring hibernating ribosomes restores Mrf instability and dissociates Mpy f

249 ts bound to cognate and wobble codons on the ribosome revealed the disruption of a C(32-)A(38) cross-

250 For example, the presence of proline in the ribosome's P- or A-site slows down translation, but the

251 The ribosome shows that protein folding initiated with intri

252 One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 prot

253 considering codon pair interactions between ribosome sites.

254 r results point out that in addition to poly ribosomes, soluble cytoplasmic proteins have a significa

255 prokaryotic ribosome in vitro We found that ribosome-stalled RNH has an increased unfolding rate com

256 arising during translation of mRNAs lead to ribosome stalling and collisions that trigger a series o

257 In vivo, the AtaT2 activity induces ribosome stalling at all four glycyl codons but does not

258 heir mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their m

259 ovide insight into common principles causing ribosome stalling under physiological conditions.

260 also highlight the influence of drug-induced ribosome stalling, which causes bias at translation star

261 ivated by a similar set of agents that cause ribosome stalling, with maximal activation of Hel2 obser

262 fine molecular mechanisms that lead to these ribosome stalls.

263 derstanding on how this modification affects ribosome structure and function.

264 is establishes a direct relationship between ribosome structure and large-scale dynamics, and it sugg

265 The natural product-ribosome structure enabled the synthesis of simplified a

266 The 70S ribosome structure of E. faecalis now extends our knowle

267 calis now extends our knowledge of bacterial ribosome structures and may serve as a basis for the dev

268 S rRNA precursors, and an imbalanced 40S:60S ribosome subunit ratio.

269 ess this limitation, we leverage an in vitro ribosome synthesis platform to build and test every poss

270 lling muscle growth and greater induction of ribosome synthesis.

271 abolism and chromatin regulation and repress ribosome synthesis.

272 , the RNAp/NTPs machinery, and the cell-free ribosome t-RNA machinery leads to the CDNs-guided transc

273 tral component of protein synthesis, and the ribosome TE is a focal point of gene expression control

274 We show first that a ribosome-tethered nanobody can be used to trap GFP in th

275 lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis.

276 codon sequences alters interactions with the ribosome that directly contribute to misreading.

277 We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA bi

278 nt fibroblasts were reduced presence of free ribosomes, the appearance of elongated endoplasmic retic

279 s the conformational landscape of SRP on the ribosome to regulate its interaction kinetics with SR, t

280 following infection to clear the template of ribosomes to allow efficient replication.

281 reveals that SD motifs are not necessary for ribosomes to determine where initiation occurs, though t

282 f conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to spe

283 The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribos

284 mal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleopla

285 Here, we show that 80S ribosomes translate the 5'-proximal short ORFs (uORFs) o

286 Made from RNA and protein, the ribosome translates mRNA to coded protein in all living

287 The ribosome translates the genetic code into proteins in al

288 gical isomers during its biosynthesis at the ribosome-translocon complex.

289 pacts the translation apparatus (composed of ribosome, tRNA, mRNA, and translation factors) and regul

290 This study investigated ribosome ubiquitination-mediated translational controls

291 Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tR

292 nt metals may play in the maintenance of the ribosome under oxidative stress conditions.

293 results in a significant accumulation of 70S ribosomes upon erythromycin exposure.

294 o examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit wi

295 mbly G3BP paralogs, or release of mRNAs from ribosomes via translation elongation.

296 t are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the interge

297 these tryptophan-associated accumulations of ribosomes-which we term 'W-bumps'-showed that they were

298 ic subunit, RTA, which inactivates mammalian ribosomes with near-perfect efficiency.

299 lless ribosomes and pre-emptive targeting of ribosomes with short nascent chains.

300 l volume, thereby maintaining the density of ribosomes within single cells.