Comparison of synonymous codon distribution patterns of bacteriophage and host genomes.

PubWeight™: 0.98‹?› | Rank: Top 15%

🔗 View Article (PMID 10048480)

Published in DNA Res on December 31, 1998

Authors

T Kunisawa1, S Kanaya, E Kutter

Author Affiliations

1: Department of Applied Biological Sciences, Science University of Tokyo, Noda, Japan. kunisawa@rs.noda.sut.ac.jp

Articles citing this

Bacteriophage T4 genome. Microbiol Mol Biol Rev (2003) 5.20

Causes for the intriguing presence of tRNAs in phages. Genome Res (2007) 1.93

Molecular Genetics of Mycobacteriophages. Microbiol Spectr (2014) 1.26

Genome landscapes and bacteriophage codon usage. PLoS Comput Biol (2008) 1.18

Codon bias is a major factor explaining phage evolution in translationally biased hosts. J Mol Evol (2008) 1.06

Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol (2008) 0.96

Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays. BMC Genomics (2005) 0.93

Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting. Mol Syst Biol (2012) 0.92

Efficacy of RNA amplification is dependent on sequence characteristics: implications for gene expression profiling using a cDNA microarray. Genomics (2007) 0.88

CBDB: the codon bias database. BMC Bioinformatics (2012) 0.86

Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli. Mol Biol Evol (2014) 0.84

Relative codon adaptation index, a sensitive measure of codon usage bias. Evol Bioinform Online (2010) 0.84

Detecting horizontally transferred and essential genes based on dinucleotide relative abundance. DNA Res (2008) 0.84

The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage. Genetics (2014) 0.80

Identification of H-2d restricted T cell epitope of foot-and-mouth disease virus structural protein VP1. Virol J (2011) 0.76

Articles by these authors

(truncated to the top 100)

A restriction map of the bacteriophage T4 genome. Mol Gen Genet (1980) 6.37

The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol (2000) 2.77

A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A (1976) 2.59

Three-dimensional structure of ribonuclease H from E. coli. Nature (1990) 2.58

Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nat Cell Biol (2001) 2.53

The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles. Nature (1985) 2.23

DNA sequence of the gene coding for Escherichia coli ribonuclease H. J Biol Chem (1983) 2.15

Regulation of a bacteriophage T4 late gene, soc, which maps in an early region. Genetics (1984) 2.14

The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol (1999) 1.83

Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol (1992) 1.78

Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. Biochemistry (1999) 1.71

The production of undegraded cytosine-containing DNA by bacteriophage T4 in the absence of dCTPase and endonucleases II and IV, and its effects on T4-directed protein synthesis. J Mol Biol (1975) 1.70

A model for the involvement of the small nucleolar RNA (U3) in processing eukaryotic ribosomal RNA. Mol Biol Rep (1983) 1.59

Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution. J Mol Biol (1993) 1.57

Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res (1996) 1.49

The rnh gene is essential for growth of Escherichia coli. Proc Natl Acad Sci U S A (1984) 1.44

Molecular cloning and nucleotide sequence of Thermus thermophilus HB8 trpE and trpG. Biochim Biophys Acta (1988) 1.29

How does RNase H recognize a DNA.RNA hybrid? Proc Natl Acad Sci U S A (1991) 1.27

The roles of the bacteriophage T4 r genes in lysis inhibition and fine-structure genetics: a new perspective. Genetics (1998) 1.26

Molecular diversities of RNases H. J Biosci Bioeng (1999) 1.21

A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc. J Biol Chem (1994) 1.20

Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry (1994) 1.19

Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core. Biochemistry (1993) 1.17

Role of histidine 124 in the catalytic function of ribonuclease HI from Escherichia coli. J Biol Chem (1993) 1.14

Assignments of backbone 1H, 13C, and 15N resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy. Biochemistry (1991) 1.13

Radiofrequency catheter ablation of left ventricular outflow tract tachycardia: report of two cases. J Cardiovasc Electrophysiol (1998) 1.10

Isolation of RNase H genes that are essential for growth of Bacillus subtilis 168. J Bacteriol (1999) 1.09

Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Protein Sci (2001) 1.08

Isolation and characterization of long-chain-alkane degrading Bacillus thermoleovorans from deep subterranean petroleum reservoirs. J Biosci Bioeng (2001) 1.05

Identification and characterization of the alc gene product of bacteriophage T4. Genetics (1984) 1.04

Bacteriophage T4 Alc protein: a transcription termination factor sensing local modification of DNA. Cell (1993) 1.02

Stabilization of Escherichia coli ribonuclease HI by strategic replacement of amino acid residues with those from the thermophilic counterpart. J Biol Chem (1992) 1.02

Active subtilisin-like protease from a hyperthermophilic archaeon in a form with a putative prosequence. Appl Environ Microbiol (2001) 0.99

Low levels of RNase H activity in Escherichia coli FB2 rnh result from a single-base change in the structural gene of RNase H. J Bacteriol (1983) 0.98

Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core. J Biol Chem (1997) 0.97

Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance. J Biol Chem (1997) 0.97

Thermostabilization of Escherichia coli ribonuclease HI by replacing left-handed helical Lys95 with Gly or Asn. J Biol Chem (1992) 0.97

High resistance of Escherichia coli ribonuclease HI variant with quintuple thermostabilizing mutations to thermal denaturation, acid denaturation, and proteolytic degradation. Biochemistry (1995) 0.96

The use of substituent constants in the quantitative treatment of hapten-antibody interaction. Arch Biochem Biophys (1969) 0.96

Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate. Biochemistry (2000) 0.95

1H NMR studies of deuterated ribonuclease HI selectively labeled with protonated amino acids. J Biomol NMR (1992) 0.93

Gene Cloning of an alcohol dehydrogenase from thermophilic alkane-degrading Bacillus thermoleovorans B23. J Biosci Bioeng (2001) 0.92

Unusual enzyme characteristics of aspartyl-tRNA synthetase from hyperthermophilic archaeon Pyrococcus sp. KOD1. FEBS Lett (1996) 0.92

Overproduction in Escherichia coli, purification and characterization of a family I.3 lipase from Pseudomonas sp. MIS38. Biochim Biophys Acta (2000) 0.91

Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: analysis of an ATPase-deficient mutant enzyme. Appl Environ Microbiol (1999) 0.91

Binding of metal ions to E. coli RNase HI observed by 1H-15N heteronuclear 2D NMR. J Biomol NMR (1991) 0.90

Diltiazem and verapamil preferentially block inactivated cardiac calcium channels. J Mol Cell Cardiol (1983) 0.90

Folding pathway of Escherichia coli ribonuclease HI: a circular dichroism, fluorescence, and NMR study. Biochemistry (1995) 0.89

Cooperative stabilization of Escherichia coli ribonuclease HI by insertion of Gly-80b and Gly-77-->Ala substitution. Biochemistry (1993) 0.89

Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI. Protein Eng (1996) 0.89

Isometric contraction and relaxation times of right and left ventricles in normal subjects and in patients with right ventricular overloading measured with bidirectional echocardiography. Jpn Heart J (1978) 0.89

Characterization of the internal motions of Escherichia coli ribonuclease HI by a combination of 15N-NMR relaxation analysis and molecular dynamics simulation: examination of dynamic models. Biochemistry (1995) 0.89

A novel strategy for stabilization of Escherichia coli ribonuclease HI involving a screen for an intragenic suppressor of carboxyl-terminal deletions. J Biol Chem (1994) 0.88

[Anti-ulcer agent pirenzepine (LS 519)--a tricyclic compound with particular physico-chemical properties (author's transl)]. Arzneimittelforschung (1977) 0.88

Crystal structures of ribonuclease HI active site mutants from Escherichia coli. J Biol Chem (1993) 0.88

Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability. Protein Eng (1993) 0.88

Cuticlin: a noncollagen structural protein from Ascaris cuticle. Arch Biochem Biophys (1973) 0.88

Kinetic analysis of Escherichia coli ribonuclease HI using oligomeric DNA/RNA substrates suggests an alternative mechanism for the interaction between the enzyme and the substrate. Eur J Biochem (1995) 0.88

Subtilisin-like serine protease from hyperthermophilic archaeon Thermococcus kodakaraensis with N- and C-terminal propeptides. Protein Eng Des Sel (2010) 0.87

Secretion into the culture medium of a foreign gene product from Escherichia coli: use of the ompF gene for secretion of human beta-endorphin. EMBO J (1985) 0.87

Isolation and characterization of psychotrophic bacteria from oil-reservoir water and oil sands. Appl Microbiol Biotechnol (2001) 0.87

An effective chemotherapy regimen for liver metastasis from retroperitoneal fibrosarcoma: report of a case. Surg Today (1997) 0.87

Transient neonatal hypothyroidism probably related to immaturity of thyroidal iodine organification. J Pediatr (1986) 0.85

Thermostable glycerol kinase from a hyperthermophilic archaeon: gene cloning and characterization of the recombinant enzyme. Protein Eng (1998) 0.85

Effects of increased physical activity and mild calorie restriction on heart rate variability in obese women. Jpn Heart J (2001) 0.84

Overproduction, purification, and characterization of ferrochelatase from Escherichia coli. J Biochem (1994) 0.84

Family I.3 lipase: bacterial lipases secreted by the type I secretion system. Cell Mol Life Sci (2006) 0.84

Steric parameters in drug design. Monoamine oxidase inhibitors and antihistamines. J Med Chem (1969) 0.84

Characterization of ribonuclease HII from Escherichia coli overproduced in a soluble form. J Biochem (2000) 0.84

Tryptic digestion of NADH dehydrogenase from alkalophilic Bacillus. J Biochem (1989) 0.84

Characterization of a RecA/RAD51 homologue from the hyperthermophilic archaeon Pyrococcus sp. KOD1. Nucleic Acids Res (1997) 0.84

Reconstitution of Escherichia coli RNase HI from the N-fragment with high helicity and the C-fragment with a disordered structure. J Biol Chem (1995) 0.84

Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon. J Bacteriol (1998) 0.84

Effect of heat treatment on proper oligomeric structure formation of thermostable glutamate dehydrogenase from a hyperthermophilic archaeon. Biochem Biophys Res Commun (1997) 0.83

A unique DNase activity shares the active site with ATPase activity of the RecA/Rad51 homologue (Pk-REC) from a hyperthermophilic archaeon. FEBS Lett (1999) 0.83

Purification of ribonuclease T1 by affinity chromatography. J Biochem (1981) 0.83

Identification of catalytically essential residues in Escherichia coli esterase by site-directed mutagenesis. FEBS Lett (1999) 0.83

Effects of diltiazem on transmembrane potential and current of right ventricular papillary muscle of ferrets. J Pharmacol Exp Ther (1984) 0.83

Identification of the gene encoding esterase, a homolog of hormone-sensitive lipase, from an oil-degrading bacterium, strain HD-1. J Biochem (1999) 0.83

Interaction of TIP26 from a hyperthermophilic archaeon with TFB/TBP/DNA ternary complex. Extremophiles (2001) 0.82

Comparative absorption of zinc picolinate, zinc citrate and zinc gluconate in humans. Agents Actions (1987) 0.82

Ca(2+)-induced folding of a family I.3 lipase with repetitive Ca(2+) binding motifs at the C-terminus. FEBS Lett (2001) 0.82

Stabilization of ribonuclease HI from Thermus thermophilus HB8 by the spontaneous formation of an intramolecular disulfide bond. Biochemistry (1998) 0.82

Elevated immunoglobulin M levels in low birth-weight neonates with chronic respiratory insufficiency. Early Hum Dev (1983) 0.82

Extracellular secretion of Escherichia coli alkaline phosphatase with a C-terminal tag by type I secretion system: purification and biochemical characterization. Protein Eng Des Sel (2006) 0.82

Heat labile ribonuclease HI from a psychrotrophic bacterium: gene cloning, characterization and site-directed mutagenesis. Protein Eng (2001) 0.82

Cloning and sequence analysis of cDNA for rat liver uricase. J Biol Chem (1988) 0.82

Diffuse endocardial thrombus in left ventricle associated with a case of hypereosinophilic syndrome. Jpn Heart J (1991) 0.82

Isolation of TBP-interacting protein (TIP) from a hyperthermophilic archaeon that inhibits the binding of TBP to TATA-DNA. FEBS Lett (1999) 0.82

Malignant fibrous histiocytoma of the stomach: report of two cases. Surg Today (1998) 0.82

Cloning of the RNase H genes from a metagenomic DNA library: identification of a new type 1 RNase H without a typical active-site motif. J Appl Microbiol (2010) 0.81

Importance of an extreme C-terminal motif of a family I.3 lipase for stability. Protein Eng Des Sel (2011) 0.81

Surgery for cholecystocholedocholithiasis in a patient with asymptomatic essential thrombocythemia: report of a case. Surg Today (1998) 0.81

Comparison of the primary structures of ribonuclease U2 isoforms. Biochem J (1986) 0.81

Duodenum-preserving resection of the head of the pancreas--modified procedures and long-term results-. Hepatogastroenterology (1996) 0.81

Effect of cavity-modulating mutations on the stability of Escherichia coli ribonuclease HI. Eur J Biochem (1992) 0.81

Investigating the role of conserved residue Asp134 in Escherichia coli ribonuclease HI by site-directed random mutagenesis. Eur J Biochem (1994) 0.80

Directed evolution of Tk-subtilisin from a hyperthermophilic archaeon: identification of a single amino acid substitution responsible for low-temperature adaptation. Protein Eng Des Sel (2007) 0.80

Combination of heteronuclear 1H-15N and 1H-13C three-dimensional nuclear magnetic resonance experiments for amide-directed sequential assignment in larger proteins. J Biochem (1990) 0.80

[Post sequence genome analysis of Escherichia coli]. Tanpakushitsu Kakusan Koso (2001) 0.80