An efficient random mutagenesis technique using anE.coli mutator strain

Random mutagenesis of a cloned gene remains a central method to understand many aspects of the gene products' function and structure. Having the ability to introduce a limited number of changes within a gene in a controlled fashion allows one to evaluate single changes and study the effect these variants have on the gene of interest. The in vivo random mutagenesis strategy described in this article, using anE. coli host, is a convenient method to introduce a limited number of mutations in a controlled manner.     

Improvement of the activity of arylmalonate decarboxylase by random mutagenesis

Arylmalonate decarboxylase (EC 4.1.1.76) catalyzes enantioselective decarboxylation of α-aryl-α-methylmalonates to give optically pure α-arylpropionates. Recently, we have succeeded in creating a double mutant enzyme that gave opposite enantionmer as the product. Unfortunately, however, the activity of the mutant decreased far lower than that of the native enzyme. Thus, we performed the directed evolution of the mutant via the random mutagenesis method employing the mutator strain Escherichia coli XL1-Red. About 50,000 mutants were screened on color assay plate, and one mutant with higher activity was obtained. Gene analysis of this mutant indicated that the obtained enzyme had an S36N mutation in addition to its original G74C/C188S mutations. The activity of the triple mutant enzyme was tenfold higher than that of the starting doubly mutated enzyme.     

细菌耐受噬菌体感染的分子机制研究进展

噬菌体是能感染细菌的病毒。为了抵抗噬菌体的感染,细菌进化出多种抵抗噬菌体感染的机制,这些机制的阐析极大地促进了基因编辑领域的发展,同时也为噬菌体治疗的开展奠定了基础。本文就细菌针对噬菌体感染的各个环节所进行的抵抗及其分子机制进行了简要综述,同时讨论了这些防御系统的存在对细菌自身的影响,分析了当前细菌耐受噬菌体机制研究存在的局限性,并对未来研究进行了展望。     

Removal of antibiotic resistance of live vaccine strain Escherichia coli MM-3 and evaluation of the immunogenicity of the new strain

MM-3 was a live vaccine strain candidate for protecting neonatal piglets from diarrhea.Designed in the 1980s,a high degree of protection from colibacillosis was afforded to piglets in a challengestudy and field trials.However MM-3 had a drawback of carrying the antibiotic resistance gene (chloramphenicolacetyltransferase gene,cat).The introduction of a host-plasmid balanced lethal system into the vaccine wasa good idea to solve the problem.The λ-Red recombination system was adopted in this study to realize thereplacement of cat by aspartate-semialdehyde dehydrogenase gene (asd) in the plasmid pMM085.The newplasmid named pMMASD was introduced into an Escherichia coli strain χ6097 and Salmonella typhimuriumχ4072 where the asd gene had been knocked out in their chromosomes.Cultured in an Erlenmeyer flask,expression levels of two antigens K88ac fimbriae and heat-labile enterotoxin B subunit (LTB) in cell lysatewere similar among MM-3,χ4072(pMMASD) and χ6097(pMMASD).However,χ4072(pMMASD) possessedthe more effective secretion mechanism to transport LTB enterotoxin into culture liquid.The relatively higherstability of pMMASD in Salmonella typhimurium χ4072 than that of pMM085 in MM-3 was determined bothin vitro in the absence of selective pressure,and in vivo following oral inoculation.Oral immunization ofBALB/c mice with χ4072(pMMASD) or χ6097(pMMASD) was sufficient to elicit IgA responses in mucosaltissues as well as systemic IgG antibody responses to the K88 fimbriae,while MM-3 failed to elicit specificantibody responses to K88 fimbriae in mucosal tissues.Among three live strains,only χ4072(pMMASD)could develop strong humoral responses against LTB enterotoxin.The results suggest that χ4072(pMMASD)is expected to be a promising live vaccine strain.     

Potential of AbiS as defence mechanism determined by conductivity measurement

AIM: To compare pH and conductivity used in the determination of growth in reconstituted skim milk (RSM), to determine whether the presence of one or two plasmids in Lactococcus lactis had any influence on growth, and whether AbiS improved bacteriophages resistance of L. lactis. METHODS AND RESULTS: Conductivity and pH were used to determine growth in RSM. A small increase in the generation time was found with increasing number of plasmids, while their size was unimportant. The introduction of a plasmid-encoding AbiS did only enhance the level of phage resistance significant when other plasmids encoding either AbiS1 or the restriction modification system LlaBIII was present. CONCLUSIONS: The earliest detection of growth was observed by measuring pH, rather than conductance. The plasmid-encoded AbiS system has a potential to be used as a phage resistance mechanisms in L. lactis during milk fermentations, especially when combined with other anti-phage mechanisms. SIGNIFICANCE AND IMPACT OF THE STUDY: This study widened the knowledge about the influence of plasmid introduction on the growth rate of L. lactis, which is important for the construction of new strains. The level of protection against 936 groups of phages was only significant when the mechanism was present together with the RM system LlaBIII.     

Improvement of phage defence in Lactococcus lactis by introduction of the plasmid encoded restriction and modification system LlaAI

AIMS: To study the ability of the plasmid-encoded restriction and modification (R/M) system LlaAI to function as a bacteriophage resistance mechanism in Lactococcus lactis during milk fermentations. METHODS AND RESULTS: Plasmid pAIcat4, carrying the R/M system LlaAI and a chloramphenicol resistance cassette, was introduced into the plasmid-free strain L. lactis MG1614 and the industrial strain L. lactis 964. By measuring changes in conductivity the influence of different phage on the growth was determined. CONCLUSIONS: The plasmid-encoded R/M system LlaAI significantly improves the bacteriophage resistance of L. lactis during milk fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: It is essential to determine the potential of a phage defence mechanism in L. lactis starter culture strains during growth in milk before steps are taken to improve starter cultures. This study shows that LlaAI is useful for improvement of starter cultures.     

Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment

Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.     

Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy

The atomic resolution structure of Pf1 coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution is compared to the structures previously determined by X-ray fiber and neutron diffraction, the structure of its membrane-bound form, and the structure of fd coat protein. These structural comparisons provide insights into several biological properties, differences between class I and class II filamentous bacteriophages, and the assembly process. The six N-terminal amino acid residues adopt an unusual "double hook" conformation on the outside of the bacteriophage particle. The solid-state NMR results indicate that at 30 degrees C, some of the coat protein subunits assume a single, fully structured conformation, and some have a few mobile residues that provide a break between two helical segments, in agreement with structural models from X-ray fiber and neutron diffraction, respectively. The atomic resolution structure determined by solid-state NMR for residues 7-14 and 18-46, which excludes the N-terminal double hook and the break between the helical segments, but encompasses more than 80% of the backbone including the distinct kink at residue 29, agrees with that determined by X-ray fiber diffraction with an RMSD value of 2.0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers.     

A self-transmissible plasmid of an enteropathogenic Escherichia coli strain codes for mannose-resistant haemagglutinin and for antibiotic resistance

Abstract Four enteropathogenic Escherichia coli strains were studied with respect to their antibiotic resistance characters, plasmid patterns, toxin production and haemagglutination properties. Two of these strains showed multiple antibiotic resistance characters, although all possessed several plasmids of varying sizes. One of the strains DD-41 showed the presence of a non-fimbrial cell-associated mannose-resistant haemagglutinin (MRHA) which was encoded by a 70 MDa plasmid. Conjugation experiments demonstrated that this MRHA-containing plasmid also coded for ampicillin and tetracycline resistance factors and was self-transmissible.     

Unlocking of the filamentous bacteriophage virion during infection is mediated by the C domain of pIII

Protein III (pIII) of filamentous phage is required for both the beginning and the end of the phage life cycle. The infection starts by binding of the N-terminal N2 and N1 domains to the primary and secondary host receptors, F pilus and TolA protein, respectively, whereas the life cycle terminates by the C-terminal domain-mediated release of the membrane-anchored virion from the cell. It has been assumed that the role of the C-terminal domain of pIII in the infection is that of a tether for the receptor-binding domains N1N2 to the main body of the virion. In a poorly understood process that follows receptor binding, the virion disassembles as its protein(s) become integrated into the host inner membrane, resulting in the phage genome entry into the bacterial cytoplasm. To begin revealing the mechanism of this process, we showed that tethering the functional N1N2 receptor-binding domain to the virion via termination-incompetent C domain abolishes infection. This infection defect cannot be complemented by in trans supply of the functional C domain. Therefore, the C domain of pIII acts in concert with the receptor-binding domains to mediate the post receptor binding events in the infection. Based on these findings, we propose a model in which binding of the N1 domain to the periplasmic portion of TolA, the secondary receptor, triggers in cis a conformational change in the C domain, and that this change opens or unlocks the pIII end of the virion, allowing the entry phase of infection to proceed. To our knowledge, this is the first virus that uses the same protein domain both for the insertion into and release from the host membrane.     

Using the rate of respiration to monitor events in the infection of Escherichia coli cultures by bacteriophage T4

The growing interest in applications of bacteriophages creates a need for improvements in the production processes. Continuous monitoring of the phage production is an essential aspect of any control strategy and, at present, there is no completely satisfactory option. The approach presented here uses IR‐spectrometry to continuously measure the rate of respiration (CO₂ released) of Escherichia coli infected by phage T4 at various multiplicities of infection (MOI). Within the trends in these data, or in other aspects of the rate of respiration, it was possible to reliably and reproducibly identify five features that reflected specific events in the infection process. These included two events in the host cell apparent growth rate and events in the magnitude of the host cell density, in the measurement of OD₆₀₀ or in the specific rate of respiration. All of these correlations were within 95% confidence showing that they are suitable for the monitoring and control of E. coli populations infected by phage T4. This method is reliable, cheap, and can be operated in‐line and in real time. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Site-specific recombination events mediated by the DNA invertase Cin of bacteriophage P1 during transformation

Abstract Bacteriophage P1 encodes the site-specific recombinase Cin which promotes inversion of the C segment, thus controlling the P1 host range. Cin can also mediate inefficient inversion between the normal crossover site cixL and a quasi-crossover site cixQ 1 in inverted orientation. Inversion between cixL and cixQ 1 occurs more frequently in a short period of time after transformation with a plasmid carrying the cin gene, cixL and cixQ 1 than in an established transformant of the plasmid. This is also the case for Cin-mediated deletion on a plasmid containing the cin gene and directly repeated cix sites.     

Aerobactin uptake system, ColV production, and drug resistance encoded by a plasmid from an urinary tract infection Escherichia coli strain of human origin

A study of Escherichia coli strains isolated from patients suffering from urinary tract infections in Ljubljana, Yugoslavia, revealed a plasmid encoding the aerobactin iron uptake system, ColV production, and drug resistance. The plasmid is conjugative and at least 85 kilobases in length.     

Factors encoded by and affecting the holding stability of yeast plasmid pSR1

Summary A 2 m DNA-like plasmid, pSR1, isolated from a strain of Zygosaccharomyces rouxii has three coding frames, P, S and R. Insertional inactivation of R completely abolished the intramolecular recombination, and the defect was complemented by an intact R frame on a coexistent plasmid molecule. The P and S regions were also transactive and important, but not essential, for the stable maintenance of the plasmid molecules. Insertional disruption of the P frame suggested that it produces a protein factor. Similar insertional disruption of the S frame affected the plasmid stability in Z. rouxii and Saccharomyces cerevisiae hosts differently, depending on whether the inserted DNA fragment was a short 8 bp SalI linker or a long (2.2 kb) DNA fragment. Results strongly suggested that the S region encodes two factors, one RNA and the other a protein, and that the S protein is compatible with a sprecific hostfactor in Z. rouxii, but not in S. cerevisiae. In addition, a cis-acting locus, Z, was found at a site in the plasmid molecule where no distinct open reading frames were located. No long direct repeats or inverted repeats were observed in the Z region, such as are found in the REP3 locus of 2 m DNA.     

Loss of secreted hemolysin activity in the mutant strain Hsb. 1 is due to a lesion in a plasmid copy number locus

Further studies have been carried out on mutation hsb which was previously suggested to block hemolysin secretion (Mu?oa et al., 1988, FEMS Microbiol. Lett. 56: 167-172). We show that the reported reduction in the extracellular hemolytic activity of mutant Hsb. 1 is due to lower hemolysin synthesis and that this is itself a consequence of a decrease in plasmid copy number. We suggest that the hsb is identical to the pcnB lesion located at minute 3.6 of the chromosome.     

Molecular modeling of the human multidrug resistance protein 1 (MRP1/ABCC1)

Multidrug resistance protein 1 (MRP1/ABCC1) is a 190 kDa member of the ATP-binding cassette (ABC) superfamily of transmembrane transporters that is clinically relevant for its ability to confer multidrug resistance by actively effluxing anticancer drugs. Knowledge of the atomic structure of MRP1 is needed to elucidate its transport mechanism, but only low resolution structural data are currently available. Consequently, comparative modeling has been used to generate models of human MRP1 based on the crystal structure of the ABC transporter Sav1866 from Staphylococcus aureus. In these Sav1866-based models, the arrangement of transmembrane helices differs strikingly from earlier models of MRP1 based on the structure of the bacterial lipid transporter MsbA, both with respect to packing of the twelve helices and their interactions with the nucleotide binding domains. The functional importance of Tyr³²⁴ in transmembrane helix 6 predicted to project into the substrate translocation pathway was investigated.     

Whole Genomic analysis of a clinical isolate of Uropathogenic Escherichia coli strain of Sequence Type - 101 carrying the drug resistance NDM-7 in IncX3 plasmid

The emerging NDM-producing Enterobactereciae is a major threat to public health. The association of NDM-7 with sequence type 101 E.coli is identified in very few numbers. Therefore, it is of interest to analyse the whole genome sequence of NDM-producing uropathogenic E. coli XA31 that was found to carry numerous drug resistance genes of different antibiotic classes. The isolate E. coli belongs to ST-101 carrying blaNDM-7 coexisting with several resistance genes blaOXA-1, blaTEM1-A, blaCTX-M15, aac(6'')-Ib-cr, catB3, tetB. Resfinder predicts this and four other plasmid replicons were identified using the Plasfinder in the CGE platform. The high transferable IncX3 plasmid was found to carry the NDM-7 gene. Thus, we the report the combination of NDM-7-ST101-IncX3 in India. The combination of this epidemic clone with NDM-7 is highly required to develop an effective infection control strategy.     

Nuclear exopolyphosphatase of Saccharomyces cerevisiae is not encoded by the PPX1 gene encoding the major yeast exopolyphosphatase

Intact nuclei from a parental strain CRY and a PPX1-mutant CRX of Saccharomyces cerevisiae were isolated and found to be essentially free of cytoplasmic, mitochondrial and vacuolar marker enzymes. The protein-to-DNA ratios of the nuclei were 22 and 30 for CRY and CRX nuclei, respectively. An exopolyphosphatase (exopolyPase) with molecular mass of approximately 57 kDa and a pyrophosphatase (PPase) of approximately 41 kDa were detected in the parental strain CRY. Inactivation of PPX1 encoding a major exopolyPase (PPX1) in S. cerevisiae did not result in considerable changes in the content and properties of nuclear exopolyPase as compared to the parental strain of S. cerevisiae. Consequently, the nuclear exopolyPase was not encoded by PPX1. In the CRX strain, the exopolyPase was stimulated by bivalent metal cations. Co2+, the best activator, stimulated it by approximately 2.5-fold. The exopolyPase activity was nearly the same with polyphosphate (polyP) chain lengths ranging from 3 to 208 orthophosphate when measured with Mg2+. With Co 2+, the exopolyPase activity increased along with the increase in polymerization degree of the substrate.     

Chromosomal and plasmid encoded drug resistances of a <Emphasis Type="Italic">Klebsiella pneumoniae</Emphasis> UTI 2 strain isolated from urine of a post-operative patient

The multi drug resistance Klebsiella pneumoniae in urinary tract infection is a common clinical problem in developing country like India. Use of random antibiotics, resulting multi drug resistance development, creates difficulties for treatment. In our present study, we investigated a strain of Klebsiella pneumoniae UTI 2 with multiple drug resistance, which was isolated from urine of a post operative woman patient (50 years) suffering from urinary tract infection with high fever. This strain is resistant to 36 antibiotics and sensitive to cefotaxime (Ce) and imipenem (I). After curing of plasmids, we observed that, 55% of drug resistant loci of K. pneumoniae UTI 2 are chromosomal and 40% are plasmid encoded. The organism is sensitive to 5% of drugs tested, i.e. Ce and I. This study contributes to understand the drug resistance of Klebsiella pneumoniae, which will enable better clinical management of catheter-associated urinary tract infections, a major health problem.     

Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux

The large conjugative multidrug resistance (MDR) plasmid pOLA52 was sequenced and annotated. The plasmid encodes two phenotypes normally associated with the chromosomes of opportunistic pathogens, namely MDR via a resistance-nodulation-division (RND)-type efflux-pump (oqxAB), and the formation of type 3 fimbriae (mrkABCDF). The plasmid was found to be 51,602 bp long with 68 putative genes. About half of the plasmid constituted a conserved IncX1-type backbone with predicted regions for conjugation, replication and partitioning, as well as a toxin/antitoxin (TA) plasmid addiction system. The plasmid was also classified as IncX1 with incompatibility testing. The conjugal transfer and plasmid maintenance regions of pOLA52 therefore seem to represent IncX1 orthologues of the well-characterized IncX2 plasmid R6K. Sequence homology searches in GenBank also suggested a considerably higher prevalence of IncX1 group plasmids than IncX2. The 21 kb 'genetic load' region of pOLA52 was shown to consist of a mosaic, among other things a fragmented Tn3 transposon encoding ampicillin resistance. Most notably the oqxAB and mrkABCDF cassettes were contained within two composite transposons (Tn6010 and Tn6011) that seemed to originate from Klebsiella pneumoniae, thus demonstrating the capability of IncX1 plasmids of facilitating lateral transfer of gene cassettes between different Enterobacteriaceae.