Published in Nature on February 03, 2005
Ab initio gene identification in metagenomic sequences. Nucleic Acids Res (2010) 4.47
tRNA biology charges to the front. Genes Dev (2010) 4.07
Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A (2009) 2.48
Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A (2010) 2.12
Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol Direct (2013) 1.75
A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol (2008) 1.60
Origin and evolution of the ribosome. Cold Spring Harb Perspect Biol (2010) 1.47
The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res (2011) 1.43
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis. Nucleic Acids Res (2012) 1.41
Transfer RNA genes in pieces. EMBO Rep (2008) 1.35
The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. Proc Natl Acad Sci U S A (2005) 1.29
Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proc Natl Acad Sci U S A (2005) 1.27
Hyperthermophiles in the history of life. Philos Trans R Soc Lond B Biol Sci (2006) 1.27
The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea (2007) 1.22
Identification and characterization of a tRNA decoding the rare AUA codon in Haloarcula marismortui. RNA (2007) 1.19
A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Res (2009) 1.19
Diversity and roles of (t)RNA ligases. Cell Mol Life Sci (2012) 1.18
The origin and evolution of tRNA inferred from phylogenetic analysis of structure. J Mol Evol (2007) 1.18
tRNADB-CE: tRNA gene database curated manually by experts. Nucleic Acids Res (2008) 1.16
Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol (2011) 1.10
RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol (2012) 1.07
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci U S A (2009) 1.07
Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota. Genome Biol Evol (2014) 1.07
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04
Discovery of a minimal form of RNase P in Pyrobaculum. Proc Natl Acad Sci U S A (2010) 1.01
On origin of genetic code and tRNA before translation. Biol Direct (2011) 0.97
Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells. Proc Natl Acad Sci U S A (2008) 0.96
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves. PLoS One (2008) 0.95
tRNA gene diversity in the three domains of life. Front Genet (2014) 0.94
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms. Genes (Basel) (2011) 0.94
Disrupted tRNA gene diversity and possible evolutionary scenarios. J Mol Evol (2009) 0.93
Handling tRNA introns, archaeal way and eukaryotic way. Front Genet (2014) 0.91
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Nucleic Acids Res (2009) 0.89
Transfer RNA processing in archaea: unusual pathways and enzymes. FEBS Lett (2010) 0.89
tRNA creation by hairpin duplication. J Mol Evol (2005) 0.88
One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation. Biol Direct (2009) 0.88
A comparison among the models proposed to explain the origin of the tRNA molecule: A synthesis. J Mol Evol (2009) 0.86
Formal proof that the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character. J Mol Evol (2009) 0.84
Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution. Life (Basel) (2015) 0.84
Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment. Nat Commun (2016) 0.83
Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop. Nucleic Acids Res (2011) 0.82
Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development. Front Genet (2014) 0.82
Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genet (2015) 0.81
Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol (2013) 0.81
Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep (2013) 0.81
The presence in tRNA molecule sequences of the double hairpin, an evolutionary stage through which the origin of this molecule is thought to have passed. J Mol Evol (2011) 0.80
Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One (2012) 0.80
Processing of multiple-intron-containing pretRNA. Proc Natl Acad Sci U S A (2009) 0.79
The last universal common ancestor (LUCA) and the ancestors of archaea and bacteria were progenotes. J Mol Evol (2010) 0.78
X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res (2012) 0.78
Long-distance splicing. Proc Natl Acad Sci U S A (2008) 0.77
A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality. J Mol Evol (2011) 0.76
Evolutionary Insights into RNA trans-Splicing in Vertebrates. Genome Biol Evol (2016) 0.76
Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes. Proc Natl Acad Sci U S A (2012) 0.76
Evolution of initiator tRNAs and selection of methionine as the initiating amino acid. RNA Biol (2016) 0.75
Methodology for constructing problem definitions in bioinformatics. Bioinform Biol Insights (2008) 0.75
Circularization restores signal recognition particle RNA functionality in Thermoproteus. Elife (2015) 0.75
Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans. J Mol Evol (2017) 0.75
A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature (2002) 4.68
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A (2003) 4.36
PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 3.93
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics (2005) 2.82
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res (2003) 2.81
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res (2005) 2.60
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
Expanding the genetic code of Escherichia coli with phosphoserine. Science (2011) 2.49
RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A (2006) 2.34
Trans-editing of mischarged tRNAs. Proc Natl Acad Sci U S A (2003) 2.33
Natural expansion of the genetic code. Nat Chem Biol (2007) 2.09
HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Science (2011) 2.03
The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J (2009) 2.00
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J (2003) 1.98
An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Natl Acad Sci U S A (2004) 1.96
From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res (2008) 1.88
VBASE2, an integrative V gene database. Nucleic Acids Res (2005) 1.86
Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol (2011) 1.86
Bacillus megaterium--from simple soil bacterium to industrial protein production host. Appl Microbiol Biotechnol (2007) 1.85
Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev (2004) 1.85
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans. EMBO J (2005) 1.74
The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science (2009) 1.70
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res (2006) 1.69
Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase. FEBS Lett (2006) 1.66
Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. Proc Natl Acad Sci U S A (2011) 1.65
Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation. Proc Natl Acad Sci U S A (2007) 1.65
Severe oxidative stress induces protein mistranslation through impairment of an aminoacyl-tRNA synthetase editing site. Proc Natl Acad Sci U S A (2010) 1.65
Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol (2004) 1.63
RhlR expression in Pseudomonas aeruginosa is modulated by the Pseudomonas quinolone signal via PhoB-dependent and -independent pathways. J Bacteriol (2006) 1.59
Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc Natl Acad Sci U S A (2010) 1.57
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res (2007) 1.55
Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc Natl Acad Sci U S A (2002) 1.55
The biochemistry of heme biosynthesis. Arch Biochem Biophys (2008) 1.53
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci U S A (2013) 1.52
A freestanding proofreading domain is required for protein synthesis quality control in Archaea. Proc Natl Acad Sci U S A (2004) 1.52
Structure and function of enzymes in heme biosynthesis. Protein Sci (2010) 1.48
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett (2012) 1.46
Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Science (2006) 1.45
Pyrrolysine is not hardwired for cotranslational insertion at UAG codons. Proc Natl Acad Sci U S A (2007) 1.45
Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat Struct Biol (2002) 1.43
Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev (2005) 1.40
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res (2008) 1.39
Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates. Proc Natl Acad Sci U S A (2003) 1.36
Quality control despite mistranslation caused by an ambiguous genetic code. Proc Natl Acad Sci U S A (2008) 1.36
Transfer RNA genes in pieces. EMBO Rep (2008) 1.35
Ignicoccus hospitalis sp. nov., the host of 'Nanoarchaeum equitans'. Int J Syst Evol Microbiol (2007) 1.33
JVirGel: Calculation of virtual two-dimensional protein gels. Nucleic Acids Res (2003) 1.33
Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol Cell (2003) 1.33
Upgrading protein synthesis for synthetic biology. Nat Chem Biol (2013) 1.32
Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12. J Bacteriol (2003) 1.32
Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proc Natl Acad Sci U S A (2008) 1.32
A truncated aminoacyl-tRNA synthetase modifies RNA. Proc Natl Acad Sci U S A (2004) 1.32
Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J Biol Chem (2002) 1.32
The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. Proc Natl Acad Sci U S A (2005) 1.29
The Fnr regulon of Bacillus subtilis. J Bacteriol (2006) 1.29
The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration. J Bacteriol (2007) 1.29
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature (2008) 1.28
The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett (2005) 1.28
Life without RNase P. Nature (2008) 1.27
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci U S A (2011) 1.27
The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase. J Biol Chem (2005) 1.24
Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol (2010) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung. Int J Med Microbiol (2010) 1.23
Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei. Proc Natl Acad Sci U S A (2006) 1.23
The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. Res Microbiol (2003) 1.22
Emergence of the universal genetic code imprinted in an RNA record. Proc Natl Acad Sci U S A (2006) 1.22
Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli. J Biol Chem (2002) 1.22
Mutations disrupting selenocysteine formation cause progressive cerebello-cerebral atrophy. Am J Hum Genet (2010) 1.21
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucleic Acids Res (2007) 1.20
The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. Proc Natl Acad Sci U S A (2009) 1.20
Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase. J Biol Chem (2004) 1.19
Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Proc Natl Acad Sci U S A (2002) 1.19
The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln. J Biol Chem (2007) 1.19
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. Nucleic Acids Res (2008) 1.18
Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J (2006) 1.16
A short story about a big magic bug. Bioeng Bugs (2010) 1.16
Structure and function of radical SAM enzymes. Curr Opin Chem Biol (2004) 1.16
Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase. Nucleic Acids Res (2007) 1.15
N-acetyl lysyl-tRNA synthetases evolved by a CcdB-based selection possess N-acetyl lysine specificity in vitro and in vivo. FEBS Lett (2012) 1.15
Characterization of JG024, a pseudomonas aeruginosa PB1-like broad host range phage under simulated infection conditions. BMC Microbiol (2010) 1.15
Production and secretion of recombinant Leuconostoc mesenteroides dextransucrase DsrS in Bacillus megaterium. Biotechnol Bioeng (2005) 1.14
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proc Natl Acad Sci U S A (2012) 1.14
Mitochondrial tRNA import--the challenge to understand has just begun. Biol Chem (2009) 1.13
Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium. Biochem J (2003) 1.13
Protein aggregation caused by aminoglycoside action is prevented by a hydrogen peroxide scavenger. Mol Cell (2012) 1.12