Physical map of the extremely thermophilic bacterium Thermus thermophilus HB27 chromosome

The alpha-aminoadipate pathway for lysine biosynthesis is widely distributed among Thermus strains

We previously reported that lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus HB27 (T. Kosuge and T. Hoshino, FEMS Microbiol. Lett., 169, 361-367, 1998), which was the first report demonstrating the synthesis of lysine through the alpha-aminoadipate pathway in Bacteria. LYS20 and LYS4, which respectively encode homocitrate synthase and homoaconitate hydratase have already been identified as the lysine biosynthetic genes in T. thermophilus HB27. In the present work, we examined eight other Thermus strains for the existence of genes belonging to the alpha-aminoadipate pathway. BamHI- or BglII-digested total DNAs from the eight strains were analyzed by Southern hybridization using LYS20 or LYS4 as a DNA probe. DNA fragments that hybridized with one or both of the genes were detected in seven of the Thermus strains but not in T. ruber. The sizes of the fragments that hybridized with the LYS20 and LYS4 probes were the same among T. thermophilus HB27, T. thermophilus HB8, "T. caldophilus" GK24, and four "T. flavus" strains. For example, a similar 4.3-kb fragment was detected in each of the above seven strains. In this fragment, four open reading frames were found downstream of the LYS4 gene in T. thermophilus HB27. Gene disruption experiments revealed that three open reading frames are involved in lysine biosynthesis in T. thermophilus HB27. These results strongly suggest that the lysine biosynthetic gene cluster for the alpha-aminoadipate pathway is widely distributed in the genus Thermus.

High thermal and chemical stability of Thermus thermophilus seven-iron ferredoxin. Linear clusters form at high pH on polypeptide unfolding

To probe the stability of the seven-iron ferredoxin from Thermus thermophilus (FdTt), we investigated its chemical and thermal denaturation processes in solution. As predicted from the crystal structure, FdTt is extremely resistant to perturbation. The guanidine hydrochloride-induced unfolding transition shows a midpoint at 6.5 m (pH 7, 20 degrees C), and the thermal midpoint is above boiling, at 114 degrees C. The stability of FdTt is much lower at acidic pH, suggesting that electrostatic interactions are important for the high stability at higher pH. On FdTt unfolding at alkaline pH, new absorption bands at 520 nm and 610 nm appear transiently, resulting from rearrangement of the cubic clusters into linear three-iron species. A range of iron-sulfur proteins has been found to accommodate these novel clusters in vitro, although no biological function has yet been assigned.

Analysis of the methionine biosynthetic pathway in the extremely thermophilic eubacterium Thermus thermophilus

Four DNA fragments that could rescue the mutations of four Met- mutants were cloned from Thermus thermophilus HB27 and their complete nucleotide sequences were determined. Two of the four fragments respectively contained the greater parts of the metF and metH genes, the predicted amino acid sequences of which showed identities of 30.8% and 32.7% with 5,10-methylenetetrahydrofolate reductase (EC 1.7.99.5) and vitamin B12-dependent homocysteine transmethylase (EC 2.1.1.13) of Escherichia coli. The other two DNA fragments, which overlapped one another, contained two open reading frames whose predicted amino acid sequences were respectively similar to those of O-acetylhomoserine sulfhydrylase (EC 4.2.99.10, the product of the MET17 gene) and homoserine O-acetyltransferase (EC 2.3.1.31, the product of the MET2 gene) of Saccharomyces cerevisiae. The metF, metH, MET2, and MET17 genes of T. thermophilus were disrupted by introducing the heat-stable kanamycin nucleotidyltransferase gene into the genome. Each transformant showed methionine auxotrophy. Both the MET2- and MET17-disrupted mutants could grow in a minimal medium containing homocysteine but not in the same medium containing succinylhomoserine or cystathionine. In contrast, the metF- and metH-disrupted mutants could not grow in the minimal medium containing homocysteine. These results suggest that in T. thermophilus, homoserine is directly converted to homocysteine via O-acetylhomoserine and that homocysteine is methylated to synthesize methionine.

Lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus

A 3.8-kb DNA fragment which was able to complement the mutation of a lysine auxotrophic Thermus thermophilus mutant was cloned from T. thermophilus HB27. Sequence analysis of the 3.8-kb fragment indicated the presence of three open reading frames including a truncated one. The predicted amino acid sequences of two of the three open reading frames showed 55.2% and 45.0% identity with homocitrate synthase and homoaconitate hydratase of Saccharomyces cerevisiae, respectively. These two enzymes act as lysine biosynthetic enzymes through the alpha-aminoadipate pathway which has been reported in S. cerevisiae and fungi. Each of the two open reading frames in T. thermophilus was disrupted by integration of the heat-stable kanamycin nucleotidyltransferase gene. The resulting mutants showed lysine auxotrophy, which could be complemented with alpha-aminoadipate but not with diaminopimelate. These results indicate that lysine was synthesized through the alpha-aminoadipate pathway and not through the diaminopimelate pathway in T. thermophilus.

Construction of a proline-producing mutant of the extremely thermophilic eubacterium Thermus thermophilus HB27

Growth of Thermus thermophilus HB27 was inhibited by a proline analog, 3,4-dehydroproline (DHP). This result suggested that the gamma-glutamyl kinase (the product of the proB gene) was inhibited by feedback inhibition in T. thermophilus. DHP-resistant mutants were reported previously for Escherichia coli (A. M. Dandekar and S. L. Uratsu, J. Bacteriol. 170:5943-5945, 1988) and Serratia marcescens (K. Omori, S. Suzuki, Y. Imai, and S. Komatsubara, J. Gen. Microbiol. 138:693-699, 1992), and their mutated sites in the proB gene were identified. Comparison of the amino acid sequence of T. thermophilus gamma-glutamyl kinase with those of E. coli and S. marcescens mutants revealed that the DHP resistance mutations occurred in the amino acids conserved among the three organisms. For eliminating the feedback inhibition, we first constructed a DHP-resistant mutant, TH401, by site-directed mutagenesis at the proB gene as reported for the proline-producing mutant of S. marcescens. The mutant, TH401, excreted about 1 mg of L-proline per liter at 70 degreesC after 12 h of incubation. It was also suggested that T. thermophilus had a proline degradation and transport pathway since it was able to grow in minimal medium containing L-proline as sole nitrogen source. In order to disrupt the proline degradation or transport genes, TH401 was mutated by UV irradiation. Seven mutants unable to utilize L-proline for their growth were isolated. One of the mutants, TH4017, excreted about 2 mg of L-proline per liter in minimal medium at 70 degreesC after 12 h of incubation.

Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes

Two aspartyl-tRNA synthetases (AspRSs) were isolated from Thermus thermophilus HB8. Both are alpha2 dimers but differ in the length of their polypeptide chains (AspRS1, 68 kDa; and AspRS2, 51 kDa). Both chains start with Met and are deprived of common sequences to a significant extent. This rules out the possibility that AspRS2 is derived from AspRS1 by proteolysis, in agreement with specific recognition of each AspRS by the homologous antibodies. DNA probes derived from N-terminal amino acid sequences hybridize specifically to different genomic DNA fragments, revealing that the two AspRSs are encoded by distinct genes. Both enzymes are present in various strains from T. thermophilus and along the growth cycle of the bacteria, suggesting that they are constitutive. Kinetic investigations show that the two enzymes are specific for aspartic acid activation and tRNAAsp charging. tRNA aspartylation by the thermostable AspRSs is governed by thermodynamic parameters which values are similar to those measured for mesophilic aspartylation systems. Both thermophilic AspRSs are deprived of species specificity for tRNA aspartylation and exhibit N-terminal sequence signatures found in other AspRSs, suggesting that they are evolutionarily related to AspRSs from mesophilic prokaryotes and eukaryotes. Comparison of the efficiency of tRNA aspartylation by each enzyme under conditions approaching the physiological ones suggests that in vivo tRNAAsp charging is essentially ensured by AspRS1, although AspRS2 is the major species. The physiological significance of the two different AspRSs in T. thermophilus is discussed.

Experimental surgery to create subgenomes of Bacillus subtilis 168

The 4,188-kb circular genome of Bacillus subtilis 168 was artificially dissected into two stable circular chromosomes in vivo, one being the 3,878-kb main genome and the other the 310-kb subgenome that was recovered as covalently closed circular DNA in CsCl-ethidium bromide ultracentrifugation. The minimal requirements to physically separate the 310-kb DNA segment out of the genome were two interrepeat homologous sequences and an origin of DNA replication between them. The subgenome originated from the 1,255-1, 551-kb region of the B. subtilis genome was essential for the cell to survive because the subgenome was not lost from the cell. The finding that the B. subtilis genome has a potential to be divided and the resulting two replicons stably maintained may shed light on origins and formation mechanisms of giant plasmids or second chromosomes present in many bacteria. Similar excision or its reversal process, i.e., integration of large sized covalently closed circular DNA pieces into the main genome, implies significant roles of subgenomes in the exchange of genetic information and size variation of bacterial genomes in bacterial evolution.

Mapping of 61 genes on the refined physical map of the chromosome of Thermus thermophilus HB27 and comparison of genome organization with that of T. thermophilus HB8

We have constructed refined physical maps of the chromosome (1 center dot 82 Mb) and the large plasmid pTT27 (250 kb) of Thermus thermophilus HB27. A total of 49 cleavage sites with five restriction enzymes, EcoRI, SspI, MunI, EcoRV and ClaI, were determined on the maps. The location of 61 genes was determined by using as probes 64 genes cloned from T. thermophilus or other Thermus strains. Comparison of the genomic organization of the chromosomes of T. thermophilus HB27 and HB8 revealed that they were basically identical, but some genes were located in different regions. Among 32 genes whose locations were determined on both the HB27 and the HB8 chromosomes, the copy number of rpsL-rpsG-fus-tufA, the locations of glyS, pol, and one copy of nusG-rplK-rplA were different. The IS1000 sequence was located only in one region on the HB27 chromosome. In contrast, IS1000 sequences were scattered over four regions on the chromosome of HB8. As each region in which glyS, pol, or one copy of nusG-rplK-rplA are present also contained IS1000 in HB8, it is suggested that IS1000 may play an important role in genomic rearrangements in Thermus strains.

Molecular cloning and sequence analysis of the proBA operon from an extremely thermophilic eubacterium Thermus thermophilus

A 3.6 kb DNA fragment carrying the Thermus thermophilus proBA region, which encodes the first two steps in the proline biosynthetic pathway, was cloned from the Thermus thermophilus gene library, and its complete nucleotide sequence was determined. The deduced amino acid sequence of gamma-glutamyl kinase (40,657 Da), the product of proB gene, and gamma-glutamyl phosphate reductase (48,747 Da), the product of proA gene, showed 44.1% and 44.4% identity to those of Escherichia coli, respectively. The termination codon of the proB gene and the initiation codon of the proA gene overlapped by 2 bp. A possible transcriptional termination structure was found downstream of the proA gene but not downstream of the proB gene. These results indicate that the proBA genes of T. thermophilus form a single operon as in E. coli.

A carotenogenic gene cluster exists on a large plasmid in Thermus thermophilus

In Thermus thermophilus HB27, the crtB gene encoding phytoene synthase was found to exist on the large plasmid, pTT27. One of the carotenoid under-producing mutants, Crt31, carried a derivative of pTT27 (pTT27') in which deletion and inversion were observed near the crtB gene. T. thermophilus HB8 also contained a large plasmid which showed homology to pTT27 and the crtB gene. These results suggested that genes for carotenoid biosynthesis occurred as a cluster on a large plasmid in Thermus thermophilus. This is the first report to show directly that carotenogenesis is plasmid-encoded in microorganisms.