Identification and structural analysis of a ribosomal RNA gene promoter from Thiobacillus ferrooxidans

Organization of ribosomal RNA genes from the footrot pathogen Dichelobacter nodosus

Southern hybridization analysis revealed that there were three rrn loci within the genome of Dichelobacter nodosus, the causative organism of ovine footrot. These loci (rrnA, rrnB and rrnC) were isolated on recombinant lambda clones, and comprised 16S, 23S and 5S rRNA genes closely linked in that order. Sequence and primer extension analysis revealed the presence of putative genes encoding tRNA(Ile) and tRNA(Ala) within the 16S-23S spacer region, as well as a number of potential regulatory features. These elements included a single promoter, which was mapped upstream of the 16S rRNA gene and which was similar to Escherichia coli consensus promoter sequences, an AT-rich upstream region, a GC-rich motif that may be involved in stringent control, leader and spacer antitermination sequences, sites for ribonuclease processing, and a putative factor-independent terminator sequence. Potential open reading frames (ORFS) were identified within the regions flanking the rrn loci, with identical copies of the 3' terminal ORF present downstream of each rRNA operon. Determination of the complete sequence of the 5S rRNA gene, and derivation of the 5S rRNA secondary structure, further substantiated the 16S rRNA-based placement of D. nodosus within the gamma division of the Proteobacteria.

Thiobacillus ferrooxidans tyrosyl-tRNA synthetase functions in vivo in Escherichia coli

The tyrosyl-tRNA synthetase gene (tyrZ) from Thiobacillus ferrooxidans, an acidophilic, autotrophic, gram-negative bacterium that participates in bioleaching of minerals, was cloned and sequenced. The encoded polypeptide (TyrRZ) is 407 amino acids in length (molecular mass; 38 kDa). The predicted protein sequence has an extensive overall identity (44%) to the sequence of the protein encoded by the Bacillus subtilus tyrZ gene, one of the two genes encoding tyrosyl-tRNA synthetases in this microorganism. Alignment with Escherichia coli TyrRS revealed limited overall identity (24%), except in the regions of the signature sequence for class I aminoacyl-tRNA synthetases. Complementation of an E. coli strain with a thermosensitive mutation in TyrRS showed that the protein encoded by the T. ferrooxidans tyrZ gene is functional and recognizes the E. coli tRNA(Tyr) as a substrate. TyrZ is a single-copy gene as revealed by Southern blot analysis. The gene was localized upstream from the putative promoters of the rrnT2 ribosomal RNA operon. Although no rho-independent transcription terminator was found between the two genes, a 1.3-kb RNA hybridized to a DNA probe derived from the tyrZ gene. The functional relationship between these two transcription units is discussed.

Molecular genetics of Thiobacillus ferrooxidans

Thiobacillus ferrooxidans is a gram-negative, highly acidophilic (pH 1.5 to 2.0), autotrophic bacterium that obtains its energy through the oxidation of ferrous iron or reduced inorganic sulfur compounds. It is usually dominant in the mixed bacterial populations that are used industrially for the extraction of metals such as copper and uranium from their ores. More recently, these bacterial consortia have been used for the biooxidation of refractory gold-bearing arsenopyrite ores prior to the recovery of gold by cyanidation. The commercial use of T. ferrooxidans has led to an increasing interest in the genetics and molecular biology of the bacterium. Initial investigations were aimed at determining whether the unique physiology and specialized habitat of T. ferrooxidans had been accompanied by a high degree of genetic drift from other gram-negative bacteria. Early genetic studies were comparative in nature and concerned the isolation of genes such as nifHDK, glnA, and recA, which are widespread among bacteria. From a molecular biology viewpoint, T. ferrooxidans appears to be a typical member of the proteobacteria. In most instances, cloned gene promoters and protein products have been functional in Escherichia coli. Although T. ferrooxidans has proved difficult to transform with DNA, research on indigenous plasmids and the isolation of the T. ferrooxidans merA gene have resulted in the development of a low-efficiency electroporation system for one strain of T. ferrooxidans. The most recent studies have focused on the molecular genetics of the pathways associated with nitrogen metabolism, carbon dioxide fixation, and components of the energy-producing mechanisms.