Pseudomonas putida tryptophan synthetase: partial sequence of the subunit

Understanding microbial metabolism

Metabolism encompasses the biochemical basis of life and as such spans all biological disciplines. Many decades of basic research, primarily in microbes, have resulted in extensive characterization of metabolic components and regulatory paradigms. With this basic knowledge in hand and the technologies currently available, it has become feasible to move toward an understanding of microbial metabolism as a system rather than as a collection of component parts. Insight into the system will be generated by continued efforts to rigorously define metabolic components combined with renewed efforts to discover components and connections using in vivo-driven approaches. On the tail of a detailed understanding of components and connections that comprise metabolism will come the ability to generate a comprehensive mathematical model that describes the system. While microbes provide the logical organism for this work, the value of such a model would span biological disciplines. Described herein are approaches that can provide insight into metabolism and caveats of their use. The goal of this review is to emphasize that in silico, in vitro, and in vivo approaches must be used in combination to achieve a full understanding of microbial metabolism.

Evolutionary differences in chromosomal locations of four early genes of the tryptophan pathway in fluorescent pseudomonads: DNA sequences and characterization of Pseudomonas putida trpE and trpGDC

Pseudomonas putida possesses seven structural genes for enzymes of the tryptophan pathway. All but one, trpG, which encodes the small (beta) subunit of anthranilate synthase, have been mapped on the circular chromosome. This report describes the cloning and sequencing of P. putida trpE, trpG, trpD, and trpC. In P. putida and Pseudomonas aeruginosa, DNA sequence analysis as well as growth and enzyme assays of insertionally inactivated strains indicated that trpG is the first gene in a three-gene operon that also contains trpD and trpC. In P. putida, trpE is 2.2 kilobases upstream from the trpGDC cluster, whereas in P. aeruginosa, they are separated by at least 25 kilobases (T. Shinomiya, S. Shiga, and M. Kageyama, Mol. Gen. Genet., 189:382-389, 1983). The DNA sequence in P. putida shows an open reading frame on the opposite strand between trpE and trpGDC; this putative gene was not characterized. Evidence is also presented for sequence similarities in the 5' untranslated regions of trpE and trpGDC in both pseudomonads; the function of these regions is unknown, but it is possible that they play some role in regulation of these genes, since all the genes respond to repression by tryptophan. The sequences of the anthranilate synthase genes in the fluorescent pseudomonads resemble those of p-aminobenzoate synthase genes of the enteric bacteria more closely than the anthranilate synthase genes of those organisms; however, no requirement for p-aminobenzoate was found in the Pseudomonas mutants created in this study.

DNA sequence of the tryptophan synthase genes of Pseudomonas putida

Genes encoding the 2 subunits of tryptophan synthase in Pseudomonas putida have been identified and cloned by their similarity to the corresponding genes in Pseudomonas aeruginosa. The deduced amino acid sequences were confirmed by comparison with regions ascertained earlier by protein sequencing. The Pseudomonas amino acid sequences are 85% identical for the beta subunit and 70% identical for the alpha subunit. These sequences are compared to those of Salmonella typhimurium, where the structure is known from X-ray crystallography. Although amino acid conservation drops to 54% and 36% for the beta and alpha subunits, only 3 single residue gaps are required to maintain alignment throughout and most of the residues identified as important for catalysis or cofactor binding are conserved. The 23 residues surrounding the beta chain lysine that enters into a Schiff base linkage with the pyridoxal phosphate cofactor are compared in 13 species, including representatives from the eukaryotic and both prokaryotic kingdoms; appreciable conservation is apparent. The approximately 100 base pairs separating the trpB gene from its divergently transcribed activator gene are similar in the 2 pseudomonads, but do not resemble those of any other bacterium or fungus studied to date.

Tryptophan biosynthetic pathway in the Enterobacteriaceae: some physical properties of the enzymes

Several physical properties of the first four enzymatic activities of the tryptophan pathway were examined using gel filtration and ion exchange chromatography. Five different patterns were noted. Differences in the anthranilate synthetase (AS) and phosphoribosylanthranilate transferase (PRT) defined these patterns. In all the organisms studied phosphoribosylanthranilate isomerase and indoleglycerol phosphate synthetase co-eluted from both diethylaminoethyl-cellulose and G-200 and thus probably are contained in a single polypeptide of 50,000 daltons. An AS-PRT complex was found in Citrobacter species, Enterobacter cloacae, and Erwinia dissolvens. In all the other bacteria examined AS and PTR were separate molecules. In Serratia marcescens, S. marinorubra, and Enterobacter liquefaciens, AS was 140,000 daltons and PRT was 45,000 daltons. In Erwinia carotavora and Enterobacter hafniae the AS was the same size as the Serratia species but the PRT was larger at 67,000 daltons. Two Proteus species had an AS and PRT of the same size as E. carotavora and E. halfniae but the Proteus AS was different in that it partially dissociated upon gel filtration. Aeromonas formicans was unique in its possession of an AS with a molecular weight of 220,000. The PRT of A. formicans was found to elute at 67,000 daltons. Possible paths of evolution of the tryptophan enzymes are discussed in terms of the results of this study. The results presented here are also considered with respect to existing taxonomic schemes of the enteric bacteria.

Amino-terminal sequence of the tryptophan synthetase alpha chain of Bacillus subtilis

The sequence of the 46 NH(2)-terminal residues of the tryptophan synthetase alpha chain of Bacillus subtilis was determined and compared with the corresponding sequences of Escherichia coli, Shigella dysenteriae, Salmonella typhimurium, Aerobacter aerogenes, Serratia marcescens, and Pseudomonas putida. A deletion of six residues was found at the NH(2)-terminal end of the alpha chain of B. subtilis.

The evolutionary stability of cytochrome c-551 in Pseudomonas aeruginosa and Pseudomonas fluorescens biotype C

Cytochrome c-551 was prepared from nine different strains of Pseudomonas aeruginosa and six of Pseudomonas fluorescens biotype C, and their amino acid sequences were compared with the sequences previously determined for the cytochromes of type strains of each species. The standard of sequence examination was such that all single amino acid substitutions, delections or insertions ought to have been detected. Balanced double changes in sites in the same part of the sequence might have escaped detection. The standard of some of the quantitative amino acid analyses was not as high as would be required for the investigation of completely unknown sequences. Eight of the Ps. aeruginosa sequences could not be distinguished from the type sequence, whereas the ninth had a single amino acid substitution. The sequences from Ps. fluorescens biotype C were more varied, differing in from zero to four substitutions from the type sequence, with the most diverse sequences differing in seven positions. The results for Ps. aeruginosa are interpreted as evidence that neutral mutations are not responsible for much molecular evolution. The superficially paradoxical differences in the results for the two species are discussed.

Functional correspondence between 30S ribosomal proteins of Escherichia coli and Bacillus stearothermophilus

30S ribosomal proteins from Bacillus stearothermophilus (B. proteins) have been fractionated and characterized with respect to their ability to replace various E. coli 30S proteins (E. proteins) in the E. coli 30S ribosome reconstitution system. The functional counterparts of all the E. proteins, except S1, S6, S9, and S13, have been tested. In all cases, B. proteins can substitute for E. proteins. Several purified B. proteins are chemically different from their functionally homologous E. proteins. Five B. proteins are immunochemically related to E. proteins; this set includes two proteins that could not be tested in the reconstitution system (S9 and S13). Thus most, if not all, of the E. proteins have functionally equivalent counterparts among B. proteins, even though properties of the two ribosomes are different in several respects. These results suggest that the fundamental structural organization of ribosomes may be the same throughout prokaryotic organisms.

Amino terminal sequence of the tryptophan synthetase alpha chain of Serratia marcescens

The sequence of the amino terminal 28 residues of the tryptophan synthetase alpha chain of Serratia marcescens is presented and compared with the related sequences of alpha chains of other bacteria.

Mapping of the tryptophan genes of Acinetobacter calcoaceticus by transformation

Auxotrophs of Acinetobacter calcoaceticus blocked in each reaction of the synthetic pathway from chorismic acid to tryptophan were obtained after N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. One novel class was found to be blocked in both anthranilate and p-aminobenzoate synthesis; these mutants (trpG) require p-aminobenzoate or folate as well as tryptophan (or anthranilate) for growth. The loci of six other auxotrophic classes requiring only tryptophan were defined by growth, accumulation, and enzymatic analysis where appropriate. The trp mutations map in three chromosomal locations. One group contains trpC and trpD (indoleglycerol phosphate synthetase and phosphoribosyl transferase) in addition to trpG mutations; this group is closely linked to a locus conferring a glutamate requirement. Another cluster contains trpA and trpB, coding for the two tryptophan synthetase (EC 4.2.1.20) subunits, along with trpF (phosphoribosylanthranilate isomerase); this group is weakly linked to a his marker. The trpE gene, coding for the large subunit of anthranilate synthetase, is unlinked to any of the above. This chromosomal distribution of the trp genes has not been observed in other organisms.

Comparative immunological and enzymatic study of the tryptophan synthetase beta 2 subunit in the Enterobacteriaceae

The beta(2) subunits of tryptophan synthetase, formula alpha(2)beta(2), from Escherichia coli, Shigella dysenteriae, Enterobacter aerogenes, Salmonella typhimurium, and Serratia marcescens were compared by three criteria. (i) alphabeta association constants for the various beta(2) subunits and E. coli alpha subunit varied between 3.6 x 10(8)m(-1) for E. coli and 0.33 x 10(8)m(-1) for S. marcescens; values for the other organisms were intermediate. (ii) Antiserum neutralization of the beta(2) subunit enzyme activity using anti-E. coli beta(2) serum showed significant cross-reaction among the organisms (E. coli, 1.0; S. dysenteriae, 0.98; S. typhimurium, 0.67; E. aerogenes, 0.61; S. marcescens, 0.42). (iii) Quantitative microcomplement fixation showed E. coli beta(2) and S. marcescens beta(2) subunits to have an index of dissimilarity of 1.8 while the other organisms had intermediate indexes. Similar complement fixation data were obtained with antisera from separate rabbits and from first course and boost sera. These findings suggest that the general surface structure and the respective alpha subunit binding site of the beta(2) subunits from these Enterobacteriaceae have been strongly conserved.

Pseudomonas putida tryptophan synthetase: partial sequence of the subunit

There is 50% identity in the sequences of the first 50 residues of the alpha chains of Escherichia coli and Pseudomonas putida. No deletions or additions of residues are found in this region, except for the N-terminal methionine residue which is missing in the polypeptide isolated from P. putida. Most of the residues which differ are chemically dissimilar, and half of them are specified by codons which differ by more than a single base. The two residues known by mutational analysis to be essential for catalysis in E. coli are conserved in P. putida. The potential taxonomic usefulness of information of this sort is analyzed.