Comparative genomics and evolution of proteins involved in RNA metabolism

Nucleic Acids Research

Volumn 30, Issue 7, 2002, Pages 1427-1464

  Anantharaman, Vivek ^a   Koonin, Eugene V ^a   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; RIBOZYME; RNA; RNA BINDING PROTEIN; URIDINE;

ALTERNATIVE RNA SPLICING; ARCHAEBACTERIUM; CELL FUNCTION; CONTROLLED STUDY; ENDOSYMBIOSIS; ENZYME ANALYSIS; EUKARYOTE; EVOLUTION; GENOMICS; MITOCHONDRION; NONHUMAN; PARASITE; PARSIMONY ANALYSIS; PLANT; POLYADENYLATION; PREDICTION; PRIORITY JOURNAL; PROGENOTE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN STRUCTURE; REGNUM; REGULATORY MECHANISM; REVIEW; RNA BINDING; RNA DEGRADATION; RNA METABOLISM; RNA METHYLATION; RNA PROCESSING; RNA TRANSCRIPTION; RNA TRANSLATION; SEQUENCE ANALYSIS;

ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; NEGIBACTERIA; POSIBACTERIA;

EID: 0036529621     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/30.7.1427     Document Type: Review

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104. Classification and evolution of P-loop GTPases and related ATPases
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150. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato
151. Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase
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175. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation
176. A tale of two synthetases
177. Requirement for E. coli NusG protein in factor-dependent transcription termination
178. Ribosomal RNA antitermination in vitro: Requirement for Nus factors and one or more unidentified cellular components
179. Assembly of transcription elongation complexes containing the N protein of phage lambda and the Escherichia coli elongation factors NusA, NusB, NusG and S10
180. Ribosomal protein S4 is a transcription factor with properties remarkably similar to NusA, a protein involved in both non-ribosomal and ribosomal RNA antitermination
181. Evidence that Spt4, Spt5 and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae
182. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs
183. A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins
184. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation
185. Crystal structure and induction mechanism of AmiC-AmiR: A ligand-regulated transcription antitermination complex
186. Chromodomains are protein-RNA interaction modules
187. Polyadenylation of mRNA in prokaryotes
188. An evolutionary classification of the metallo-beta-lactamase fold proteins
189. Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I
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191. Structure, mechanism and evolution of the mRNA capping apparatus
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193. An RNA 5′-triphosphatase related to the protein tyrosine phosphatases
194. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes
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196. A nuclear cap binding protein complex involved in pre-mRNA splicing
197. Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G
198. Post-transcriptional gene silencing across kingdoms
199. Transgene silencing in monocots
200. RNA silencing in plants-defense and counterdefense
201. Gene silencing as an adaptive defence against viruses
202. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance
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204. A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity and regulation
205. Identification of novel small RNAs using comparative genomics and microarrays
206. Three novel components of the human exosome
207. Musing on the structural organization of the exosome complex
208. Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach
209. CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone
210. Hsp15: A ribosome-associated heat shock protein
211. NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae
212. Nascent 60S ribosomal subunits enter the free pool bound by Nmd3p
213. Upf1p, Nmd2p and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs
214. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans
215. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae
216. The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes
217. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA
218. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in C. elegans
219. Role for a bidentate ribonuclease in the initiation step of RNA interference
220. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing
221. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA
222. Argonaute2, a link between genetic and biochemical analyses of RNAi
223. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD
224. Molecular cloning and characterization of a rabbit eIF2C protein
225. RNAi as random degradative PCR siRNA primers convert mRNA into dsRNAs that are degraded to generate new siRNAs
226. A mammalian telomerase-associated protein
227. A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors
228. Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation
229. Crystal structure and evolution of a transfer RNA splicing enzyme
230. Crystal structure of a dimeric archaeal splicing endonuclease
231. Shaping the genome-restriction-modification systems as mobile genetic elements
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233. Homologs of small nucleolar RNAs in Archaea
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235. Selfish DNA and the origin of introns
236. Intron phylogeny: A new hypothesis
237. The recent origins of spliceosomal introns revisited
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239. Intron positions correlate with module boundaries in ancient proteins
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241. Pre-mRNA splicing in the new millennium
242. Structure and assembly of the spliceosomal small nuclear ribonucleoprotein particles
243. Mechanical devices of the spliceosome: Motors, clocks, springs and things
244. Protein functions in pre-mRNA splicing
245. Spliceosomal UsnRNP biogenesis, structure and function
246. Splicing-related catalysis by protein-free snRNAs
247. Frequent alternative splicing of human genes
248. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
249. Analysis of the splicing machinery in fission yeast: A comparison with budding yeast and mammals
250. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding
251. The ubiquitin system
252. The meteoric rise of regulated intracellular proteolysis
253. The 65 and 110 kDa SR-related proteins of the U4/U6.U5 tri-snRNP are essential for the assembly of mature spliceosomes
254. A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing
255. Homologues of 26S proteasome subunits are regulators of transcription and translation
256. The PCI domain: A common theme in three multiprotein complexes
257. A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae
258. Molecular cloning and analysis of small optic lobes, a structural brain gene of Drosophila melanogaster
259. Mdm2 is a RING finger-dependent ubiquitin protein ligase for itself and p53
260. Archaea and the prokaryote-to-eukaryote transition
261. Early evolution and the origin of eukaryotes
262. A hydrogenosome with a genome
263. Origins of hydrogenesomes and mitochondria: Evolution and organelle biogenesis
264. Recent developments from the Leishmania genome project
265. Sequence survey of the Giardia lamblia genome
266. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum
267. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
268. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
269. Monophyletic origins of the metazoa: An evolutionary link with fungi
270. Large-scale comparison of fungal sequence information: Mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae
271. Initial sequencing and analysis of the human genome
272. Apoptotic molecular machinery: Vastly increased complexity in vertebrates revealed by genome comparisons
273. Evidence for a clade of nematodes, arthropods and other moulting animals
274. Did DNA replication evolve twice independently?
275. The universal ancestor
276. Interpreting the universal phylogenetic tree
277. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme
278. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors
279. HemK, a class of protein methyl transferase with similarity to methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination
280. MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase