Cloning, Sequence Analysis and Three-dimensional Structure Prediction of DNA Pol I from Thermophilic Geobacillus sp. MKK Isolated from an Iranian Hot Spring

A systematic review of the genera Geobacillus and Parageobacillus: their evolution, current taxonomic status and major applications

The genus Geobacillus, belonging to the phylum Firmicutes, is one of the most important genera and comprises thermophilic bacteria. The genus Geobacillus was erected with the taxonomic reclassification of various Bacillus species. Taxonomic studies of Geobacillus remain in progress. However, there is no comprehensive review of the characteristic features, taxonomic status and study of various applications of this interesting genus. The main aim of this review is to give a comprehensive account of the genus Geobacillus. At present the genus acomprises 25 taxa, 14 validly published (with correct name), nine validly published (with synonyms) and two not validly published species. We describe only validly published species of the genera Geobacillus and Parageobacillus. Vegetative cells of Geobacillus species are Gram-strain-positive or -variable, rod-shaped, motile, endospore-forming, aerobic or facultatively anaerobic, obligately thermophilic and chemo-organotrophic. Growth occurs in the pH range 6.08.5 and a temperature of 37-75 °C. The major cellular fatty acids are iso-C15:o, iso-C16:0 and iso-C17:o. The main menaquinone type is MK-7. The G-+C content of the DNA ranges between 48.2 and 58 mol%. The genus Geobacillus is widely distributed in nature, being mostly found in many extreme locations such as hot springs, hydrothermal vents, marine trenches, hay composts, etc. Geobacillus species have been widely exploited in various industrial and biotechnological applications, and thus are promising candidates for further studies in the future.

Thirty-minute screening of antibiotic resistance genes in bacterial isolates with minimal sample preparation in static self-dispensing 64 and 384 assay cards

In a clinical setting, molecular assays such as polymerase chain reaction offer a rapid means to infer or confirm identity and therapeutic decisions. Accordingly, a number of molecular assays targeting identity and antibiotic resistance (AR) genes have been developed; however, these methods can be technically complex and relatively expensive. Herein, we describe a diagnostic concept utilizing isothermal amplification technology with non-purified heat-lysed cells and self-dispensing cards for testing multiple primers in parallel. This proof-of-concept study, performed with Staphylococcus aureus isolates and associated AR genes, was compared with culture-based susceptibility and quantitative PCR (qPCR). Results demonstrate reduced sample processing steps resulting in a turnaround time (starting from bacterial culture to ending in the antibiotic resistance gene profile) in less than 30 min. For antibiotics tested in which an associated AR gene was targeted on the Gene-Z card, 69 % (18/26) of culture-based resistance events were positive for related AR genes. A comparison of loop-mediated isothermal amplification (LAMP) and qPCR assays targeting the same antibiotic resistance genes showed a 98.2 % agreement in terms of presence and absence calls. Identity-based discrepancies between conventional (phenotypic) and molecular (genotypic) results were further resolved, and we were able to demonstrate higher accuracy in identification with the molecular analysis.

A new DNA polymerase I from Geobacillus caldoxylosilyticus TK4: cloning, characterization, and mutational analysis of two aromatic residues

DNA polymerase I gene was cloned and sequenced from the thermophilic bacterium Geobacillus caldoxylosilyticus TK4. The gene is 2,634 bp long and encodes a protein of 878 amino acids in length. The enzyme has a molecular mass of 99 kDa and shows sequence homology with DNA polymerase I from Bacillus species (89% identity). The gene was overexpressed in Escherichia coli and the purified enzyme was biochemically characterized. It has all of the primary structural elements necessary for DNA polymerase and 5' --> 3' exonuclease activity, but lacks the motifs required for 3' --> 5' exonuclease activity. 5' nuclease and 3' --> 5' exonuclease assays confirmed that Gca polymerase I has a double-stranded DNA-dependent 5' --> 3' nuclease activity but no 3' --> 5' exonuclease activity. Its specific activity was observed to be 495,000 U/mg protein, and K (D) (DNA) , K (D) (dNTP) , and K (pol) were found to be 0.19 nM, 22.64 microM, and 24.99 nucleotides(-1), respectively. The enzyme showed significant reverse-transcriptase activity (RT) with Mn(2+), but very little RT activity with Mg(2+). Its error rate was found to be 2.5 x 10(-5) which is comparable to that of the previously reported error rate for the E. coli DNA polymerase I. Two aromatic residues required for dideoxyribonucleotide triphosphate sensitivity (F712Y) and strand displacement activity (Y721F) were identified.