The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences

Bibb, Mervyn J.; Findlay, P.R.; I, Maria Johnson

doi:10.1016/0378-1119(84)90116-1

Cited by 810 publications

(423 citation statements)

References 27 publications

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“…Therefore, the ORF of 1512 bp was considered to represent the sole resistance gene pur8. The codon usage of pur8 is typical of Streptornyces (data not shown) [29]. Although several other putative initiation codons are present both upstream and downstream from the presumed ATG initiator codon (Fig.…”

Section: Cloning and Nucleotide Sequence Of Pur8mentioning

confidence: 80%

The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

Tercero

Lacalle²,

Jiménez

1993

European Journal of Biochemistry

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A novel puromycin‐resistancer determinant (pur8) was isolated from one end of the pur cluster that encodes the puromycin biosynthetic pathway from Streptomyces alboniger and expressed in Streptomyces lividans. The gene pur8 induced antibiotic resistance that was highly specific for puromycin. The nucleotide sequence of pur8 contains an open reading frame of 1512 bp whose deduced amino acid sequence encodes a polypeptide (Pur8) with 14 possible transmembrane spanning segments. It shows significant similarities to other known or putative transmembrane proteins, including a number which confer drug resistance in a variety of antibiotic‐producing Streptomyces, Gram‐positive and Gram‐negative bacteria, and some solute transporters of prokaryotic and eukaryotic origin. As is probably the case for most of these proteins, Pur8 may be involved in active puromycin efflux energized by a proton‐dependent electrochemical gradient. In addition, it could be implicated in secreting N‐acetylpuromycin, the last intermediate of the biosynthesis pathway, to the environment.

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Section: Cloning and Nucleotide Sequence Of Pur8mentioning

confidence: 80%

The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

Tercero

Lacalle²,

Jiménez

1993

European Journal of Biochemistry

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“…The DNA and protein sequences were analyzed by using the PC/GENE package (IntelliGenetics, Inc., Mountain View, Calif.). ORFs were identified by using a program similar to the FRAME program developed by Bibb et al (4). The predicted proteins were scanned for similarities to the Swissprot protein sequence data base by using the FASTA program (32).…”

Section: Methodsmentioning

confidence: 99%

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene

et al. 1997

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A regulatory gene, reg1, was identified in Streptomyces lividans. It encodes a 345-amino-acid protein (Reg1) which contains a helix-turn-helix DNA-binding motif in the N-terminal region. Reg1 exhibits similarity with the LacI/GalR family members over the entire sequence. It displays 95% identity with MalR (the repressor of malE in S. coelicolor), 65% identity with ORF-Sl (a putative regulatory gene of ␣-amylase of S. limosus), and 31% identity with CcpA (the carbon catabolite repressor in Bacillus subtilis). In S. lividans, the chromosomal disruption of reg1 affected the expression of several genes. The production of ␣-amylases of S. lividans and that of the ␣-amylase of S. limosus in S. lividans were enhanced in the reg1 mutant strains and relieved of carbon catabolite repression. As a result, the transcription level of the ␣-amylase of S. limosus was noticeably increased in the reg1 mutant strain. Moreover, the induction of chitinase production in S. lividans was relieved of carbon catabolite repression by glucose in the reg1 mutant strain, while the induction by chitin was lost. Therefore, reg1 can be regarded as a pleiotropic regulatory gene in S. lividans.Streptomyces species, gram-positive soil bacteria with a high GC content, have the capacity to produce a vast array of secondary metabolites and extracellular proteins. The latter comprise many hydrolytic enzymes such as cellulases, chitinases, amylases, and xylanases allowing Streptomyces to grow on polymeric substrates (12). Genes encoding these enzymes are generally induced by degradation products of their polymeric substrates and repressed by readily metabolizable carbon sources such as glucose by a process known as catabolite repression. Several cis-acting sequences, displaying no apparent similarity, have been shown to be involved in the regulation of genes encoding such hydrolytic enzymes in various species of Streptomyces (10,11,44,49). However, no specific regulatory gene among those encoding extracellular proteins has so far been characterized for Streptomyces.␣-Amylases are secreted by several species of Streptomyces and catalyze the cleavage of the ␣-1,4 linkage of starch, yielding short linear maltodextrins which are finally converted to glucose. The highest ␣-amylase production was obtained when the ␣-amylase gene aml of Streptomyces limosus was cloned in S. lividans, which has a negligible ␣-amylase activity (43). In S. lividans, aml expression was induced by maltose and repressed by glucose. The regulation occurs at the level of transcription from the unique promoter. This led to the assumption that a regulatory protein(s) in S. lividans controlling the expression of aml might exist. A putative repressor, called open reading frame R (ORFR) in the present work, which is homologous to the regulatory proteins LacI and GalR of Escherichia coli has been located upstream of the ␣-amylase gene of S. venezuelae (45) and is also present upstream of the ␣-amylase genes of S. limosus (27) and S. griseus (42). Therefore, it was assumed that an ORF homo...

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“…Sequencing the regions flanking this gene as described previously revealed a 939-bp putative ORF immediately upstream of cs2. The DNA sequence was examined by using the algorithm of Bibb et al (5,48), which predicts the reading frame of the gene by the GϩC content at the third position of each potential codon. The GϩC content was approximately 90%, as is typical of a Streptomyces coding sequence (data not shown).…”

Section: Identification Of the Putative Pah Gene From S Clavuligerusmentioning

confidence: 99%

Identification, cloning, sequencing, and overexpression of the gene encoding proclavaminate amidino hydrolase and characterization of protein function in clavulanic acid biosynthesis

Busby

Houston

et al. 1995

J Bacteriol

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The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences

Cited by 810 publications

References 27 publications

The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene

Identification, cloning, sequencing, and overexpression of the gene encoding proclavaminate amidino hydrolase and characterization of protein function in clavulanic acid biosynthesis

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The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences

Cited by 810 publications

References 27 publications

The pur8 gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

The pur8 gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

Amylase and chitinase genes in Streptomyces lividans are regulated by reg1, a pleiotropic regulatory gene

Identification, cloning, sequencing, and overexpression of the gene encoding proclavaminate amidino hydrolase and characterization of protein function in clavulanic acid biosynthesis

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Product

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The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

The pur⁸ gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin