A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and protein sequence data, respectively. They contain various options to help users in analyzing DNA/RNA and protein sequence data. With program NUCDAT, it is also possible to get access to the EMBO Nucleotide Data Library. This can be achieved by running program COPY to create two data files from the library. Program LITRAT enables users to prepare a scientific literature file convenient for writing scientific articles, and program STRAIN for storing information concerning bacterial and/or plasmid strains.

Sequence (biology)

Fortran

10.1093/nar/12.1part1.101

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Citations (24)

Systematic mapping of autonomously replicating sequences on chromosome V ofSaccharomyces cerevisiae using a novel strategy

Yeast (1996)

Seiji Tanaka Yoshimi Tanaka Katsumi Isono

We have developed a new procedure for easy and rapid identification of autonomously replicating sequences (ARSs) and have applied it to the analysis of chromosome V of Saccharomyces cerevisiae. The procedure makes use of the ordered λ phage clone bank of this chromosome that we have constructed, and includes transposition of a mini-transposon and selection of transposon-containing derivatives, isolation of their DNA and circularization at their cos-ends, transformation of yeast cells with the circularized DNA, and scoring transformation frequency. The transposon used was derived from Tn5supF, contained the yeast LEU2 gene, and was placed, together with the hyperactive transposase gene, on a mini-F plasmid for stable maintenance in Escherichia coli K-12. Sixteen regions of chromosome V showing ARS activity were identified, of which 12 were newly found in this work. Thus, the procedure will be useful for systematic genomic scale analysis of ARSs in yeast and related organisms in which ordered clone banks have been established. The average distance between adjacent ARS-containing regions was approximately 40 kb. Two-dimensional gel electrophoretic analysis of chromosome replication indicated that one of the newly identified ARSs was functional as an actual in situ replication origin, at least under the conditions employed.

Transposase

Transposition (logic)

Yeast artificial chromosome

Autonomously replicating sequence

10.1002/(sici)1097-0061(199602)12:2<101::aid-yea885>3.0.co;2-2

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Citations (12)

Primary structure of Escherichia co gene rpsA

Brigitte Wittmann‐Liebold Alap-Raman Subramanian Katsumi Isono

The primary structure of protein SI, the largest protein component of the Escherichia coli ribosome, has been elucidated by determining the amino acid sequence of the protein (from E. coli MRE600) and the nucleotide sequence of the S 1gene (rpsA, of a K-12 strain). The two methods gave results in perfect agreement except at two positions where possible strain-specific differences were found. Protein S1 (MRE600) is composed of 557 amino acid residues (no modified amino acids were detected) and has Mr 61,159. The DNA sequence for protein S1 (K-12) suggests 556 amino acid residues. A computer survey of the sequence re- vealed three regions in SI with a high degree of internal homology. The ribosome binding domain of SI (NH2 terminus) does not show any preponderance of basic amino acids. The two cysteine and the majority 'of tryptophan residues of S1 as well as two of the three homologous regions are located in its middle region which contains the nucleic acid binding domain. The pattern of degenerate codon usage in the S1 gene is nonrandom and similar to that reported for other ribosomal protein genes.

Protein primary structure

Ribosomal protein

Homology

Ribosomal binding site

Source

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Citations (0)

Role of Ribosomal Protein S1 in Protein Synthesis: Effects of Its Addition to Bacillus stearothermophilus Cell‐Free System

European Journal of Biochemistry (1975)

Setsuko Isono Katsumi Isono

Products of the f2 phage RNA-directed protein synthesizing systems in vitro, derived from Escherichia coli and Bacillus stearothermophilus, were analyzed. In contrast to other reports, it was found that B. stearothermophilus ribosomes synthesized phage coat protein when the high-speed (100 000 X g) supernatant (S100) and ribosomal wash (crude initiation factors) of homologous origin were used. Furthermore, a marked stimulation of coat protein synthesis was observed with B. stearothermophilus ribosomes when either S100 or ribosomal wash or both from E. coli cells were used instead of the respective homologous components. The principle responsible for this stimulation was identified as the 30-S ribosomal protein S1 present in S100 and ribosomal wash. Purified S1 from E. coli at roughly one-to-one molar ratio to ribosomes resulted in about 10-fold stimulation of the incorporation of [14C]valine when added to the B. stearothermophilus system. This stimulation was observed mainly in the synthesis of coat protein and replicase.

Ribosomal protein

Cell-free system

50S

10.1111/j.1432-1033.1975.tb02202.x

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Citations (47)