Nucleotide sequence of the trpB gene in Escherichia coli and Salmonella typhimurium

We have obtained the entire nucleotide sequence of the penultimate gene of the tryptophan operon, trpB, in Escherichia coli and Salmonella typhimurium. The amino acid sequence deduced for the E. coli gene product is in agreement with earlier, fragmentary protein sequence results. The trpB nucleotide sequences for the two bacterial species are perfectly colinear and show 85% identity. Most of the nucleotide differences found are without consequence for the amino acid sequence, which shows greater than 96% identity. The degree of conservation of both the nucleotide and amino acid sequences is significantly greater than for trpA, the adjacent gene encoding the other subunit of the same enzyme. When synonymous third codon position nucleotide differences are examined, they seem to be distributed at random throughout trpB and trpA, except for one completely conserved 66 basepair long region within trpB.     

Nucleotide sequence of the Salmonella typhimurium mutB gene, the homolog of Escherichia coli mutY.

The mutB gene of Salmonella typhimurium is involved in a methylation-independent repair pathway specific for A/G or A/C mismatches and is the homolog of the Escherichia coli mutY gene. The mutB gene of S. typhimurium was cloned and sequenced. The isolated mutB clone reduced the mutation rate of the mutB mutant to wild-type levels and also restored A/G mismatch-specific nicking activity, which is defective in mutB extracts. The amino acid sequence encoded by the mutB gene is 91% homologous to that encoded by the E. coli mutY gene.     

Nucleotide sequence analysis of purH and purD genes from Salmonella typhimurium

The purH and purD genes coding for the 5'-phosphoribosyl 5-amino-imidazole-4-carboxamide (AICAR) transformylase and 5'-phosphoribosyl-glycinamide (GAR) synthetase, respectively, were identified on a 4.8 kb Eco RI fragment of chromosomal DNA from Salmonella typhimurium. Nucleotide sequence analysis of the cloned fragment revealed the presence of two large open reading frames (O.R.F.), which were separated by 11 base pairs (bp). Substantial DNA and amino acid sequence homology was noted between the purH and purD genes of S. typhimurium and Escherichia coli. Expression of the Salmonella purD gene in a T7 polymerase/promoter system revealed the presence of a 49 kDa protein band by SDS-PAGE and subsequent autoradiography. The purH gene of Salmonella was not expressed since the 5' end of this gene was not cloned.     

Nucleotide sequence of the trpC-trpB intercistronic region from Salmonella typhimurium.

We have sequenced a DNA segment that contains the Salmonella typhimurium trpC-trpB junction. A series of 11 amino acids predicted from the sequence are identical to the amino-terminal amino acid sequence of Escherichia coli tryptophan synthetase β (Crawford et al., 1979). Carboxypeptidase A digestion of phosphoribosyl-anthranilate isomerase-indoleglycerolphosphate synthetase identified its carboxy-terminal amino acids allowing us to specify the end of trpC. Nine nucleotides separate the terminator codon of trpC from the initiator codon of trpB. The messenger RNA around the trpB initiation site, as well as around many other prokaryotic ribosome binding sites, has the potential to form stable stem and loop structures. These secondary structures share the property of having most, if not all, of the sequences complementary to the 3′ end of 16 S ribosomal RNA, as well as the initiator codon, included in single-stranded regions.     

Nucleotide sequence of the Escherichia coli hisD gene and of the Escherichia coli and Salmonella typhimurium hisIE region

Summary In this paper we report the nucleotide sequence of the hisD gene of Escherichia coli and of the hisIE region of both E. coli and Salmonella typhimurium. The hisD gene codes for a bifunctional enzyme, l-histidinol: NAD⁺ oxidoreductase, of 434 amino acids with a molecular mass of 46,199 daltons. We established that the hisIE region of both S. typhimurium and E. coli is composed of a single gene and not, as previously believed, of two separate genes. The derived amino acid sequence indicates that the hisIE gene codes for a bifunctional protein of 203 amino acids with an approximate molecular mass of 22,700 daltons. We also determined the nucleotide sequence of a deletion mutant in S. typhimurium which abolishes the hisF and hisI functions but retains the hisE function. We deduced that the mutant produces a chimeric protein fusing the aminoterminal region of the upstream hisF gene to the carboxylterminal domain of the hisIE gene which encodes for the hisE function. In view of these results the structural and functional organization of the histidine operon in enteric bacteria needs to be revised. The operon is composed of only 8 genes and the pathway leading to the biosynthesis of the amino acid requires 11 enzymatic steps.     

The nucleotide sequence of rpsL and its flanking regions in Salmonella typhimurium

The ribosomal protein (r-protein)-encoding gene, rpsL, and regions flanking it, from Salmonella typhimurium, have been sequenced directly from polymerase chain reaction-amplified chromosomal DNA. The deduced amino acid sequence is identical to that of the Escherichia coli rpsL encoded r-protein. At the nucleotide level, the similarity is 98%, suggesting a strong pressure for the conservation of this important protein. More surprisingly, the noncoding sequences surrounding the gene are also conserved at the 98% level, suggesting that they too are functionally important.     

Nucleotide sequences of the trpG regions of Escherichia coli,Shigella dysenteriae,Salmonella typhimurium and Serratia marcescens

The nucleotide sequences of Serratia marcescens trpG and the corresponding regions of Escherichia coli, Shigella dysenteriae and Salmonella typhimurium trpD have been determined. Analysis of the nucleotide sequence divergence suggests the following evolutionary relationships: Serratia-[Salmonella, (Escherichia, Shigella)]. Partial reconstruction of ancestral nucleotide sequences and subsequent analysis of nucleotide substitutions show that the majority of nucleotide substitutions in the evolution of trp(G)D are transitions that result in a reduction of G + C content. Since most of the nucleotide substitutions are in the third position of codons, bias in synonymous codon usage also reflects G + C content. The trpE-trp(G)D junction in the four organisms is characterized by overlapping translation termination and initiation codons. The relative positions of trpE and trp(G)D thus became fixed in evolution before the fusion of trpG and trpD. Nucleotide sequences representing the fusion of trpG and trpD in Escherichia, Shigella and Salmonella are not more nor less divergent than other portions of the trp(G)D coding sequences.