Expression of the Pseudomonas aeruginosa gentamicin resistance gene aacC3 in Escherichia coli

MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria

Background

A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons and regulons in a genome. Here we implement and report a strategy to computationally identify transcriptional units and operons of mycobacteria and construct a database-MycoperonDB.

Description

We have predicted transcriptional units and operons in mycobacteria and organized these predictions in the form of relational database called MycoperonDB. MycoperonDB database at present consists of 18053 genes organized as 8256 predicted operons and transcriptional units from five closely related species of mycobacteria. The database further provides literature links for experimentally characterized operons. All known promoters and related information is collected, analysed and stored. It provides a user friendly interface to allow a web based navigation of transcription units and operons. The web interface provides search tools to locate transcription factor binding DNA motif upstream to various genes. The reliability of operon prediction has been assessed by comparing the predicted operons with a set of known operons.

Conclusion

MycoperonDB is a publicly available structured relational database which has information about mycobacterial genes, transcriptional units and operons. We expect this database to assist molecular biologists/microbiologists in general, to hypothesize functional linkages between operonic genes of mycobacteria, their experimental characterization and validation. The database is freely available from our website .

Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on matrix assisted laser desorption/ionization whole cell protein fingerprints

Rapid identification of microorganisms using matrix assisted laser desorption/ionization (MALDI) is a rapidly growing area of research due to the minimal sample preparation, speed of analysis and broad applicability of the technique. This approach relies on expressed biochemical markers, often proteins, to identify microorganisms. Therefore, variations in culture conditions that affect protein expression may limit the ability of MALDI-MS to correctly identify an organism. We have expanded our efforts to investigate the effects of culture conditions on MALDI-MS signatures to specifically examine the effects of pH, growth rate and temperature. Continuous cultures maintained in bioreactors were used to maintain specific growth rates and pH for E. coli HB 101. Despite measurable morphological differences between growth conditions, the MALDI-MS data associated each culture with the appropriate library entry (E. coli HB 101 generated using batch culture on a LB media), independent of pH or growth rate. The lone exception was for a biofilm sample collected from one of the reactors which had no appreciable degree of association with the correct library entry. Within the data set for planktonic organisms, variations in growth rate created the largest variation between fingerprints. The effect of varying growth temperature on Y. enterocolitica was also examined. While the anticipated effects on phenotype were observed, the MALDI-MS technique provided the proper identification.

Serovar determination, drug resistance patterns and plasmid profiles of Pseudomonas aeruginosa isolated from burn patients at two hospitals of Tehran (IRAN)

The serovars and drug susceptibility patterns of 265 isolates of Pseudomonas aeruginosa cultured from burn patients during 2001-2002 at Motahari and Tohid Hospital were determined. Distribution of serovars was different at two hospitals. Most of the isolates at Tohid Hospital belonged to serovar 0:1, but 21 and 13% of them were untypeable or polyagglutinable, respectively. Serovar 0:11 was the most prevalent serovar at Motahari Hospital. All the strains were multi resistant to tetracyclin, carbenicillin, amikacin, ceftazidime, sulfamethoxazol, ciprofloxacin, tobramycin, kanamycin, cefotaxime and gentamicin. Further analysis of the strains by plasmid profiling demonstrated that 95% of the isolates carried two megaplasmids. However, there was not any correlation between the serotyping and presence of plasmids. Changes in the drug susceptibility patterns and beta-lactamase production of some cured derivatives were observed after the strains lost their plasmids. The emergence of multi-drug resistant strains of P. aeruginosa is a serious concern in burn patients who are hospitalized in Tehran.

Characterization of the chromosomal aac(6')-Iz gene of Stenotrophomonas maltophilia

The aac(6')-Iz gene of Stenotrophomonas maltophilia BM2690 encoding an aminoglycoside 6'-N-acetyltransferase was characterized. The gene was identified as a coding sequence of 462 bp corresponding to a protein with a calculated mass of 16,506 Da, a value in good agreement with that of ca. 16,000 found by in vitro coupled transcription-translation. Analysis of the deduced amino acid sequence indicated that the protein was a member of the major subfamily of aminoglycoside 6'-N-acetyltransferases. The enzyme conferred resistance to amikacin but not to gentamicin, indicating that it was an AAC(6') of type I. The open reading frame upstream from the aac(6')-Iz gene was homologous to the fprA gene of Myxococcus xanthus (61% identity), which encodes a putative pyridoxine (pyridoxamine) 5'-phosphate oxidase. Pulsed-field gel electrophoresis of total DNA from BM2690 and S. maltophilia ATTC 13637 digested with XbaI, DraI, and SpeI followed by hybridization with rRNA and aac(6')-Iz-specific probes indicated that the gene was located in the chromosome. The aac(6')-Iz gene was detected by DNA-DNA hybridization in all 80 strains of S. maltophilia tested. The MICs of gentamicin against these strains of S. maltophilia were lower than those of amikacin, netilmicin, and tobramycin, indicating that production of AAC(6')-Iz contributes to aminoglycoside resistance in S. maltophilia.