[The use of molecular genetics techniques in clinical microbiology--final report from the workshop of the Molecular Microbiology Working Group TIDE]. / Aplikace metod molekulární genetiky v klinické mikrobiologii: zpráva z jednání Pracovní skupiny molekulárni mikrobiologie--TIDE.

In the last decade, there has been a rapid development in the use of molecular genetics methods in clinical microbiology. Novel technologies bring new knowledge and approaches to various disciplines of microbiology--taxonomy, identification of microbes, clinical diagnosis, epidemiology of infectious diseases and antibiotic resistance. This article summarizes the conclusions from the workshop of the Molecular Microbiology Working Group TIDE held during the Second Annual Meeting of the Society for Medical Microbiology of the J. E. Purkyne Czech Medical Association.

Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis.

The gene cluster catRABC, involved in catechol degradation, was isolated from Rhodococcus erythropolis CCM2595. The genes catA, catB, catC, and the divergently transcribed catR code for catechol 1,2-dioxygenase, cis,cis-muconate cycloisomerase, muconolactone isomerase, and an IclR-type transcriptional regulator, respectively. Measurements of catechol 1,2-dioxygenase activity showed that the expression of catA is induced by phenol but not by catechol or cis,cis-muconate. The activity of catechol 1,2-dioxygenase was repressed by succinate, but no repression by glucose was observed. The transcription start points of catA and catR were determined by primer extension analysis, and the respective promoters (P-catA and P-catR) were thus localized. Measurements of promoter activity during batch cultivation using transcriptional fusion with the gfpuv reporter gene showed that expression of the catR-catABC operon is regulated at the level of transcription. Both P-catR and P-catA are repressed by CatR, and the induction of P-catA by phenol is maintained in the absence of the repressor (in R. erythropolis DeltacatR). Two different potential binding sites for the IclR-type regulator and a recognition site for the cyclic AMP receptor protein (CRP) were identified within the intergenic region between catR and catA.

Host-vector system for phenol-degrading Rhodococcus erythropolis based on Corynebacterium plasmids.

The strain Rhodococcus erythropolis CCM2595, which was shown to degrade phenol, was chosen for genetic studies. To facilitate strain improvement using the methods of gene manipulation, the technique of genetic transfer was introduced and cloning vectors were constructed. Using the plasmid pFAJ2574, an electrotransformation procedure yielding up to 7x10(4) transformants/microg DNA was optimized. Escherichia coli- R. erythropolis shuttle vectors were constructed using the replicons pSR1 and pGA1 from Corynebacterium glutamicum. The small vector pSRK21 (5.8 kb) provides six unique cloning sites and selection of recombinant clones using alpha-complementation of beta-galactosidase in E. coli. This vector, exhibiting high segregational stability under non-selective conditions in R. erythropolis CCM2595, was applied to cloning and efficient expression of the gene coding for green fluorescent protein (gfpuv).

Atypical location of double-strand origin of replication (nic site) on the plasmid pGA1 from Corynebacterium glutamicum.

The double-strand origin of replication (dso) of the rolling-circle-replicating (RC) plasmid pGA1 from Corynebacterium glutamicum was analyzed using the runoff DNA synthesis assay. The site- and strand-specific breakage of double-stranded plasmid DNA, representing the nic site of dso, was localized precisely within the sequence 5'-CTGG decreases AT-3' in the distal part of the pGA1 rep gene. This location of dso differs from the dso positions found on other RC plasmids and is in agreement with the classification of the plasmid pGA1 into a new group of RC plasmids.

Identification of a novel gene involved in stable maintenance of plasmid pGA1 from Corynebacterium glutamicum.

The cryptic plasmid pGA1 (4.8 kb) from Corynebacterium glutamicum, replicating in the rolling-circle mode, has been reported to contain four open reading frames longer than 200 bp (ORFA/per, ORFA2, ORFB, ORFC/rep). Here we present another pGA1 gene, ORFE (174 bp), located in the region downstream of the per-ORFA2 gene cluster. The ORFE is transcribed into two RNA species in a direction opposite to that of the per-ORFA2 RNA. Introduction of ORFE in trans into the cells harboring the pGA1 derivatives carrying the main stability determinant, the per gene coding for a product that positively influences the pGA1 copy number and maintenance, increased their segregational stability. Mutation of the putative translational start of the ORFE abolished this observed positive effect in trans. ORFE thus codes for a protein acting as an accessory element involved in stable maintenance of plasmid pGA1 and was hence designated the aes gene (accessory effector of stable maintenance).

Analysis of the Corynebacterium glutamicum dapA promoter.

Deletion and mutational analysis of the promoter P-dapA from Corynebacterium glutamicum was performed to identify regions and particular nucleotides important for its function. An extended -10 region and a stretch of six T's at positions -55 to -50 were found to be the most important elements in the promoter function. The results of mutational analysis of P-dapA are consistent with the conclusions of statistical computer-aided analysis of 44 C. glutamicum promoter sequences.

An integron of class 1 is present on the plasmid pCG4 from gram-positive bacterium Corynebacterium glutamicum.

The streptomycin/spectinomycin resistance determinant of the 29-kb plasmid pCG4 from Corynebacterium glutamicum was found to be a part of a typical class 1 integron. The sequence analysis revealed that the integron (designated InCg) identified in this Gram-positive bacterium is almost identical to the integron InC present on the plasmid pSA1700 from the Gram-negative bacterium Pseudomonas aeruginosa. Differences in only two base pairs were found in the 3.8-kb sequence. One base substitution (G-->C) is present in the streptomycin/spectinomycin resistance determinant which is thus identical to the aadA2a gene from the integron In6 of the broad-host-range plasmid pSa. The other one (C-->G) is present in the extended -10 region of the integron promoter involved in expression of the antibiotic resistance gene. It was shown that this novel version of the integron promoter displays five times higher activity in both C. glutamicum and Escherichia coli than the original one.

Analysis of the leuB gene from Corynebacterium glutamicum.

The leuB gene of Corynebacterium glutamicum was found to be present on a 2.2-kb BamHI-SacI chromosomal fragment which complemented the leuB mutation of Escherichia coli. The activity of 3-isopropylmalate dehydrogenase (EC 1.1.1.85), encoded by the leuB gene, was significantly increased in C. glutamicum cells harbouring a plasmid containing the 2.2-kb fragment. The nucleotide sequence of the C. glutamicum leuB coding region (an open reading frame, ORF, of 1020 bp encoding a polypeptide of 340 amino acids with M(r) of 36 144) was determined. The deduced amino acid sequence of the product of this ORF is highly homologous to those of 3-isopropylmalate dehydrogenases from three species of mycobacteria. The transcriptional start site of the leuB gene was localized 35 bp upstream of its translational start; a functional terminator was detected in the 3' flanking region. Northern hybridization analysis showed that the C. glutamicum leuB gene is transcribed as a single monocistronic RNA (approximately 1.2 kb in size). Activity of the leuB promoter was significantly reduced when leucine was present in the growth medium. This suggests the negative regulation of the leuB expression on the transcriptional level in C. glutamicum cells.

Plasmid pGA1 from Corynebacterium glutamicum codes for a gene product that positively influences plasmid copy number.

The complete nucleotide sequence (4,826 bp) of the cryptic plasmid pGA1 from Corynebacterium glutamicum was determined. DNA sequence analysis revealed four putative coding regions (open reading frame A [ORFA], ORFA2, ORFB, and ORFC). ORFC was identified as a rep gene coding for an initiator of plasmid replication (Rep) according to the high level of homology of its deduced amino acid sequence with the Rep proteins of plasmids pSR1 (from C. glutamicum) and pNG2 (from Corynebacterium diphtheriae). This function was confirmed by deletion mapping of the minimal replicon of pGA1 (1.7 kb) which contains only ORFC. Deletion derivatives of pGA1 devoid of ORFA exhibited significant decreases in the copy number in C. glutamicum cells and displayed segregational instability. Introduction of ORFA in trans into the cells harboring these deletion plasmids dramatically increased their copy number and segregational stability. The ORFA gene product thus positively influences plasmid copy number. This is the first report on such activity associated with a nonintegrating bacterial plasmid. The related plasmids pGA1, pSR1, and pNG2 lacking significant homology with any other plasmid seem to be representatives of a new group of plasmids replicating in the rolling-circle mode.

Transfer of the broad-host-range IncQ plasmid RSF1010 and other plasmid vectors to the gram-positive methylotroph Brevibacterium methylicum by electrotransformation.

Gram-positive facultative methylotrophic coryneform bacterium Brevibacterium methylicum was efficiently transformed with various plasmids using electroporation of intact cells. In addition to the plasmid vectors pEC71 and pZ6-1 constructed on the basis of cryptic plasmids from coryneform bacteria, broad-host-range plasmids pLS5 (derivative of plasmid pMV158 from Streptococcus agalactiae) and RSF1010 belonging to the incompatibility group IncQ from Gram-negative bacteria were found to be present as autonomous structurally unchanged DNA molecules in B. methylicum transformants. With the exception of pZ6-1, all these plasmids were stably maintained in B. methylicum cells grown under non-selective conditions. When plasmid DNAs isolated from B. methylicum were used, the highest efficiency of transformation (10(5) transformants/micrograms DNA) was achieved.

Production of threonine by Brevibacterium flavum containing threonine biosynthesis genes from Escherichia coli.

Genes of the threonine operon of Escherichia coli were used for the construction of a Brevibacterium flavum strain excreting threonine. Using the shuttle vector pCEM300 and a newly constructed shuttle vector pEC71 (7.1 kb, Kmr/Nmr), various plasmids carrying E. coli thr genes were prepared. Mutants resistant to the threonine analog 2-amino-3-hydroxyvaleric acid (AHV) were isolated after the ethyl methanesulfonate treatment of B. flavum carrying these recombinant plasmids. A mutant of B. flavum CCM 351 carrying the cloned genes thrA and thrB accumulated 12 g/L of threonine after 48 h of cultivation.

Design of cAMP-CRP-activated promoters in Escherichia coli.

We have studied the deoP2 promoter of Escherichia coli to define features that are required for optimal activation by the complex of adenosine 3',5' monophosphate (cAMP) and the cAMP receptor protein (CRP). Systematic mutagenesis of deoP2 shows that the distance between the CRP site and the -10 hexamer is the crucial factor in determining whether the promoter is activated by cAMP-CRP. Based on these observations, we propose that cAMP-CRP-activated promoters can be created by correctly aligning a CRP target and a -10 hexamer. This idea has been successfully tested by converting both a CRP-independent promoter and a sequence resembling the consensus -10 hexamer to strongly cAMP-CRP-activated promoters.

Stabilization of a miniderivative of the broad-host-range IncW plasmid pSa by insertion of plasmid R1 parB region.

The plasmid vector pEM100 (13.5 kb) constructed from pGV1106, a miniderivative of the broad-host-range IncW pSa plasmid, and the pAM330 plasmid of Brevibacterium lactofermentum is not stably maintained in Escherichia coli host cells under nonselective growth conditions. By insertion of a 0.9 kb DNA fragment containing the parB locus (responsible for the maintenance of plasmid R1 in E. coli cells) to plasmid pEM100, plasmid pEM110 was prepared which is maintained in a population of E. coli cells growing without a selection pressure very stably.

Plasmid shuttle vector with two insertionally inactivable markers for coryneform bacteria.

A new shuttle vector pCEM500 replicating in Escherichia coli and in Brevibacterium flavum was constructed. It carries two antibiotic resistance determinants (Kmr/Gmr from plasmid pSa of Gram-negative bacteria and Smr/Spr from plasmid pCG4 of Corynebacterium glutamicum) which are efficiently expressed in both hosts and can be inactivated by insertion of DNA fragments into the unique restriction endonuclease sites located within them. This vector was found to be stably maintained in B. flavum and can be used for transfer of the cloned genes into this amino-acid-producing coryneform bacterium.

Convenience of plasmid R6K higher-copy-number deletion derivative for cloning of larger DNA fragments.

Vector properties of plasmid pNH602, a higher-copy-number deletion mutant of plasmid R6K, were tested by cloning the 6.5 Mg/mol BamHI pSa fragment carrying determinants of resistance to four antibiotics in the unique BamHI site of pNH602. The resulting in vitro constructed recombinant plasmid pNH606 was found to be stable, conjugative, multicopy (20 copies of pNH606 per E. coli chromosome were estimated) and to ensure the increased expression of different genes responsible for the antibiotic resistance. The pSa fragment inserted in the BamHI site of plasmid pNH602 (located in Tn2660) was proved to be transposable to other replicons. Recombinant plasmid pNH606 was analyzed using restriction enzymes BamHI and EcoRI and its physical and genetic map was constructed.

RNA polymerase binding sites on a plasmid R6K derivative with increased copy number.

The specific binding of Escherichia coli RNA polymerase molecules to the DNA of plasmid pNH602, a deletion derivative of R6K having an increased copy number, was detected by electron microscopy. Seven strong RNApol binding sites were found on pNH602 DNA linearized with BamHI or EcoRI restriction endonuclease. All of these specific sites occur in genetically defined regions of the pNH602 molecule. Two of them correspond with the recently reported transcription initiation sites within a region essential for plasmid R6K replication.

Glutamicin CBII, a bacteriocin-like substance produced by Corynebacterium glutamicum.

Corynebacterium glutamicum CBII, in the stationary phase of growth, was found to produce spontaneously a substance resembling bacteriocins by its bactericidal properties. This substance designated glutamicin CBII was observed to exhibit bactericidal activity against coryneform bacteria (12 species tested) but not against unrelated gram-positive (3) and gram-negative (3) bacteria, while its action on bacteria with no quite known relatedness to the coryneform group (14) was found to be variable. Glutamicin CBII was partially purified by precipitation with ammonium sulphate (70% saturation), selective heat precipitation and gel chromatography on Sephadex G-50. The antibacterial substance diffused through cellophane membrane with an approximate cut-off of 10,000 dalton and its sedimentation coefficient was determined to be 1.1 S by ultracentrifugation. Heating at 100 degrees C for 30 min had no effect on its activity. Glutamicin CBII was proved to be resistant to chloroform, trypsin, chymotrypsin, pronase, and subtilisin. According to its staining behaviour and 1H NMR spectra it probably represents a glycoprotein containing only a minor protein component.

An in vivo cointegrate of two plasmids from incompatibility group X.

Formation of a recombinant plasmid designated pNH603 was observed when two plasmids from incompatibility group X, the multicopy plasmid pNH602 (a higher-copy-number deletion derivative of R6K) and the oligocopy plasmid R485, coexisted in a single Escherichia coli cell. According to its size and its restriction endonuclease cleavage pattern, plasmid pNH603 is a true cointegrate of pNH602 and R485. An insertion-sequence-like element coming from plasmid R485 is supposed to mediate the fusion of both replicons. The pNH603 copy number (1-2 per chromosome) indicates that the mechanism of replication of the low-copy-number plasmid is dominant in this cointegrate. No dissociation of pNH603 to parental plasmids was observed even in E. coli K-12 recA+ cells. On the other hand, deletion derivatives of four size classes originate from pNH603 in both recA+ and recA hosts. A miniplasmid designated pNH604, a representative of the most frequent 7 Mg/mol size class, was found, in a low number of copies per host chromosome.

New bacteriophage-like particles in Corynebacterium glutamicum.

Three new phage-like particles (CG1, CG2, and CGK1) were isolated from Corynebacterium glutamicum CBII. Particles CG1 and CG2 are DNA phages with long, noncontractile tails, CGK1 is a killer particle according to electron microscopy. A heat-stable low-molecular-weight bacteriocidal substance affecting various coryneform bacteria was observed to be joined to the killer particle CGK1.

DNA-protein interactions during replication of genetic elements of bacteria.

Specific interactions of DNA with proteins are required for both the replication of deoxyribonucleic acid proper and its regulation. Genetic elements of bacteria, their extrachromosomal elements in particular, represent a suitable model system for studies of these processes at the molecular level. In addition to replication enzymes (DNA polymerases), a series of other protein factors (e.g. topoisomerases, DNA unwinding enzymes, and DNA binding proteins) are involved in the replication of the chromosomal, phage and plasmid DNA. Specific interactions of proteins with DNA are particularly important in the regulation of initiation of DNA synthesis. Association of DNAs with the cell membrane also plays an important role in their replication in bacteria.