Stress responses and replication of plasmids in bacterial cells

Plasmids, DNA (or rarely RNA) molecules which replicate in cells autonomously (independently of chromosomes) as non-essential genetic elements, play important roles for microbes grown under specific environmental conditions as well as in scientific laboratories and in biotechnology. For example, bacterial plasmids are excellent models in studies on regulation of DNA replication, and their derivatives are the most commonly used vectors in genetic engineering. Detailed mechanisms of replication initiation, which is the crucial process for efficient maintenance of plasmids in cells, have been elucidated for several plasmids. However, to understand plasmid biology, it is necessary to understand regulation of plasmid DNA replication in response to different environmental conditions in which host cells exist. Knowledge of such regulatory processes is also very important for those who use plasmids as expression vectors to produce large amounts of recombinant proteins. Variable conditions in large-scale fermentations must influence replication of plasmid DNA in cells, thus affecting the efficiency of recombinant gene expression significantly. Contrary to extensively investigated biochemistry of plasmid replication, molecular mechanisms of regulation of plasmid DNA replication in response to various environmental stress conditions are relatively poorly understood. There are, however, recently published studies that add significant data to our knowledge on relations between cellular stress responses and control of plasmid DNA replication. In this review we focus on plasmids derived from bacteriophage lambda that are among the best investigated replicons. Nevertheless, recent results of studies on other plasmids are also discussed shortly.     

Intracellular retention of hepatitis B virus surface proteins reduces interleukin-2 augmentation after genetic immunizations

We have previously shown that hepatitis B virus (HBV) surface antigens (HBsAgs) are highly immunogenic after genetic immunization. Compared to the secreted middle HBV surface proteins (MHBs) or small HBV surface proteins (SHBs), the nonsecreted large HBV surface protein (LHBs), however, induced significantly weaker humoral and cellular immune responses that could not be augmented by genetic coimmunizations with cytokine expression plasmids. In order to understand the mechanisms underlying this phenomenon, we examined the effect of coimmunizations with an interleukin-2 (IL-2) DNA expression plasmid on the immunogenicity at the B- and T-cell level of nonsecreted wild-type LHBs, a secreted mutant LHBs, wild-type SHBs, and a nonsecreted mutant SHBs. Coimmunizations of mice with plasmids encoding wild-type SHBs or the secreted mutant LHBs and IL-2 increased anti-HBs responses, helper T-cell proliferative activity and cytotoxic T-lymphocyte killing. By contrast, coimmunizations of plasmids encoding wild-type LHBs or nonsecreted mutant SHBs and IL-2 had no significant effects on immune responses. Interestingly, mice immunized with cytokine expression plasmids 14 days after the injection of the wild-type LHBs plasmid showed augmented immune responses compared to animals simultaneously injected with both expression constructs. Anti-HBs responses in mice injected with plasmids encoding secreted forms of HBsAgs were detectable about 10 days earlier than those in mice immunized with plasmids encoding nonsecreted forms of HBsAgs. Based on these observations, we conclude that cytokines produced by DNA plasmids at the initial site of antigen presentation cannot augment LHBs specific immune responses because LHBs is not produced at high enough levels or is not accessible for uptake by antigen-presenting cells.     

The 120 kilodalton outer membrane protein (rOmp B) of Rickettsia rickettsii is encoded by an unusually long open reading frame: evidence for protein processing from a large precursor

A Rickettsia rickettsii outer surface membrane protein (rOmp B), of an apparent molecular mass of 120 kilodaltons, is a major surface antigen of the Rickettsiae that displays genus, species, and sub-species specific antigenic determinants. The 5' portion of this gene was found to be unstable in plasmids, but was stably cloned in a lambda vector. The nucleotide sequence of the 5' terminus has been determined, thus completing the DNA sequence of the entire gene. Genetic analysis revealed an unusually large open reading frame with the capacity to encode a product much larger than the mature protein. A 32 kilodalton peptide from purified rickettsiae was isolated and the amino terminus was sequenced, which revealed that the peptide is encoded by the 3' portion of this large open reading frame. This suggests a role for post-translational processing of rOmp B from a large precursor molecule.     

Phylogenetic position of Rickettsia tsutsugamushi and the relationship among its antigenic variants by analyses of 16S rRNA gene sequences

Abstract The 16S rRNA gene sequences of Rickettsia tsutsugamushi and Rickettsia sibirica were determined by PCR and DNA sequencing. Phylogenetic analysis revealed that R. sibirica is positioned in a cluster of the genus Rickettsia with a similarity value of 98.1–99.6%, whereas R. tsutsugamushi is located apart from the cluster with a similarity value of 90.2–90.6%. This evidence suggests that R. tsutsugamushi should be excluded taxonomically from the genus Rickettsia . The phylogenetic classification of six antigenic variants in R. tsutsugamushi moderately reflected their antigenic relationship known in closely and distantly related strains.     

Some lessons from Rickettsia genomics

Sequencing of the Rickettsia conorii genome and its comparison with its closest sequenced pathogenic relative, i.e., Rickettsia prowazekii, provided powerful insights into the evolution of these microbial pathogens. However, advances in our knowledge of rickettsial diseases are still hindered by the difficulty of working with strict intracellular bacteria and their hosts. Information gained from comparing the genomes of closely related organisms will shed new light on proteins susceptible to be targeted in specific diagnostic assays, by new antimicrobial drugs, and that could be employed in the generation of future rickettsial vaccines. In this review we present a detailed comparison of the metabolic pathways of these bacteria as well as the polymorphisms of their membrane proteins, transporters and putative virulence factors. Environmental adaptation of Rickettsia is also discussed.     

On the origin of intracellular compartmentation and organized metabolic systems

The history of the development of the ideas and research of organized metabolic systems during last three decades is shortly reviewed. The cell cytoplasm is crowded with solutes, soluble macromolecules such as enzymes, nucleic acids, structural proteins and membranes. The high protein density within the large compartments of the cells predominantly determines the major characteristics of cellular environment such as viscosity, diffusion and inhomogeneity. The fact that the solvent viscosity of cytoplasm is not substantially different from the water is explained by intracellular structural heterogeneity: the intrinsic macromolecular density is relatively low within the interstitial voids in the cell because many soluble enzymes are apparently integral parts of the insoluble cytomatrix and are not distributed homogeneously. The molecular crowding and sieving restrict the mobility of very large solutes, binding severely restrict the mobility of smaller solutes. One of consequence of molecular crowding and hindered diffusion is the need to compartmentalize metabolic pathway to overcome diffusive barriers. Although the movement of small molecules is slowed down in the cytoplasm, the metabolism can successfully proceed and even be facilitated by metabolite channeling which directly transfers the intermediate from one enzyme to an adjacent enzyme without the need of free aqueous-phase diffusion. The enhanced probability for intermediates to be transferred from one active site to the other by sequential enzymes requires stable or transient interactions of the relevant enzymes, which associate physically in non-dissociable, static multienzyme complexes--metabolones, particles containing enzymes of a part or whole metabolic systems. Therefore, within the living cell the metabolism depends on the structural organization of enzymes forming microcompartments. Since cells contain many compartments and microenvironments, the measurement of the concentration of metabolites in whole cells or tissues gives an average cellular concentration and not that which is actually sensed by the active site of a specific enzyme. Thus, the microcompartmentation could provide a mechanism which can control metabolic pathways. Independently and in parallel to the developments described above, the ideas of compartmentation came into existence from the necessity to explain important physiological phenomena, in particular in heart research and in cardiac electrophysiology. These phenomena demonstrated the physiological importance of the biophysical and biochemical mechanisms described in this review.     

Evolution of cytomotive filaments: the cytoskeleton from prokaryotes to eukaryotes

The basic features of the active filaments that use nucleotide hydrolysis to organise the cytoplasm are remarkably similar in the majority of all cells and are either actin-like or tubulin-like. Nearly all prokaryotic cells contain at least one form of FtsZ, the prokaryotic homologue of tubulin and some bacterial plasmids use tubulin-like TubZ for segregation. The other main family of active filaments, assembled from actin-like proteins, occurs in a wide range of bacterial species as well as in all eukaryotes. Some bacterial plasmids also use ParM, another actin-like protein. Higher-order filament structures vary from simple to complex depending on the cellular application. Equally, filament-associated proteins vary greatly between species and it is not possible currently to trace their evolution from prokaryotes to eukaryotes. This lack of similarity except in the three-dimensional structures and longitudinal interactions between the filament subunits hints that the most basic cellular function of the filaments is to act as linear motors driven by assembly dynamics and/or bending and hence we term these filament systems 'cytomotive'. The principle of cytomotive filaments seems to have been invented independently for actin- and tubulin-like proteins. Prokaryotes appear to have a third class of cytomotive filaments, typically associated with surfaces such as membranes or DNA: Walker A cytoskeletal ATPases (WACA). A possible evolutionary relationship of WACAs with eukaryotic septins is discussed.     

DNA metabolism and genetic diversity in Trypanosomes

Trypanosomes are protozoan parasites that cause major diseases in humans and other animals. Trypanosoma brucei and Trypanosoma cruzi are the etiologic agents of African and American Trypanosomiasis, respectively. In spite of large amounts of information regarding various aspects of their biology, including the essentially complete sequences of their genomes, studies directed towards an understanding of mechanisms related to DNA metabolism have been very limited. Recent reports, however, describing genes involved with DNA recombination and repair in T. brucei and T. cruzi, indicated the importance of these processes in the generation of genetic variability, which is crucial to the success of these parasites. Here, we review these data and discuss how the DNA repair and recombination machineries may contribute to strikingly different strategies evolved by the two Trypanosomes to create genetic variability that is needed for survival in their hosts. In T. brucei, two genetic components are critical to the success of antigenic variation, a strategy that allows the parasite to evade the host immune system by periodically changing the expression of a group of variant surface glycoproteins (VSGs). One component is a mechanism that provides for the exclusive expression of a single VSG at any one time, and the second is a large repository of antigenically distinct VSGs. Work from various groups showing the importance of recombination reactions in T. brucei, primarily to move a silent VSG into an active VSG expression site, is discussed. T. cruzi does not use the strategy of antigenic variation for host immune evasion but counts on the extreme heterogeneity of their population for parasite adaptation to different hosts. We discuss recent evidence indicating the existence of major differences in the levels of genomic heterogeneity among T. cruzi strains, and suggest that metabolic changes in the mismatch repair pathway could be an important source of antigenic diversity found within the T. cruzi population.     

Epitope mapping of antigenic determinants of hepatitis C virus proteins by phage display

Study of individual hepatitis C (HCV) proteins could help to find a molecular structure and conformation, localization of antigenic and immunogenic determinants, to reveal of protective epitopes. It is necessary for practical medicine - development of diagnostic test-systems, vaccines and therapeutics. Linear and conformation dependent epitopes of HCV proteins was localized in this work and immunogenic properties of phage displayed peptides screened on monoclonal antibodies to HCV proteins have been investigated. Eleven epitopes of four HCV proteins have been studied. Three epitopes was found as linear, two epitopes were dependent on secondary structure of proteins and one epitope was dependent on tertiary structure of NS3 protein. Aminoacid sequences of other determinants have been determined and the distinct localization of these determinants will be continued after discovering of tertiary structure of HCV proteins. It was shown, that phage mimotope 3f4 is immunogenic and could induce specific hu- moral immune response to NS5A HCV protein. The data obtained could be useful for improving of HCV diagnostic test-systems, studying of amino acid substitutions and its influence on antigenic properties of the HCV proteins. The results could help to study an immune response in patients infected with different genotypes of HCV. Phage displayed peptides mimicking the antigenic epitopes of HCV proteins could be applied to development of HCV vaccine.     

Membrane Transport in Primitive Cells

Although model protocellular membranes consisting of monoacyl lipids are similar to membranes composed of contemporary diacyl lipids, they differ in at least one important aspect. Model protocellular membranes allow for the passage of polar solutes and thus can potentially support cell-to functions without the aid of transport machinery. The ability to transport polar molecules likely stems from increased lipid dynamics. Selectively permeable vesicle membranes composed of monoacyl lipids allow for many lifelike processes to emerge from a remarkably small set of molecules.Lipid bilayer membranes are an integral component of living cells, providing a permeability barrier that is essential for nutrient transport and energy production. It is reasonable to assume that a similar boundary structure would be required for the origin of cellular life (Szostak et al. 2001). Even though bilayer membranes are a cellular necessity, they also pose a significant obstacle to early cellular functions, the most obvious being that the permeability barrier would inhibit chemical exchange with the environment. Such an exchange is important not only for acquiring nutrient substrates for primitive metabolic processes, but also for the release of inhibitory side-products.Contemporary cells circumvent the permeability problem by incorporating complex transmembrane protein machinery that provides specific transport capabilities. It is unlikely that Earth’s first cells assembled bilayer membranes together with specific membrane protein transporters. Rather, intermediate evolutionary steps must have existed in which simple lipid molecules provided many of the characteristics of contemporary membranes without relying on advanced protein machinery. What seems to have been necessary was the appearance of a simple membrane system capable of retaining and releasing specific molecules. In short, a protocell needed to be selectively permeable.     

Persistence and spread of a chloramphenicol resistance-mediating plasmid in antigenic types of Escherichia coli, pathogenic for piglets

All chloramphenicol-resistant Escherichia coli strains isolated from piglets in the State veterinary Serum Laboratory, Copenhagen, in 1974-1975 harbored plasmids of IncFII group with largely the same resistance markers. Two strains from 1978 carried plasmids with similar characters. Restriction enzyme analysis of DNA from these plasmids with restriction endonucleases EcoRI, BglII, and PstI shows that the Cm plasmids are extremely closely related; but the patterns obtained (particularly from PstI digests) enable the classification of the plasmids into groups. These bear a strong relation to time and place of isolation so that plasmids isolated on the same farm belong to the same group even when their host strains are of different antigenic types. It is concluded that these plasmids have evolved from a single plasmid.     

Effects of plasmids on chromosome metabolism in bacteria

In addition to many other functions of the cell, many bacterial plasmids are involved in repair, mutagenesis, replication, and recombination of the host chromosome. Numerous studies performed with wild-type strains and various mutants suggest that plasmids participate in these processes through three basic routes: (i) contribution to cell's regulatory systems; (ii) introduction of new pathways operating either independently of the existing ones or affecting the efficiency of the latter; these new pathways may or may not be subject to cellular regulation; (iii) replacement of defective proteins by functionally similar plasmid products or compensation for missing proteins by either activating existing pathways or introducing plasmid-born bypass pathways. The differences among individual plasmids in their effects on DNA metabolism are governed by intimate mechanisms of the metabolic process, the genetic background of the host, and the genetic constitution of the plasmid. The corresponding plasmid genetic determinants and the products thereof remain, for the most part, unidentified. However, the available evidence indicates that plasmids can confer on the cell additional resources which extend its DNA metabolism potential, thereby promoting evolutionary transformations.     

In vitro excision of adeno-associated virus DNA from recombinant plasmids: isolation of an enzyme fraction from HeLa cells that cleaves DNA at poly(G) sequences.

When circular recombinant plasmids containing adeno-associated virus (AAV) DNA sequences are transfected into human cells, the AAV provirus is rescued. Using these circular AAV plasmids as substrates, we isolated an enzyme fraction from HeLa cell nuclear extracts that excises intact AAV DNA in vitro from vector DNA and produces linear DNA products. The recognition signal for the enzyme is a polypurine-polypyrimidine sequence which is at least 9 residues long and rich in G.C base pairs. Such sequences are present in AAV recombinant plasmids as part of the first 15 base pairs of the AAV terminal repeat and in some cases as the result of cloning the AAV genome by G.C tailing. The isolated enzyme fraction does not have significant endonucleolytic activity on single-stranded or double-stranded DNA. Plasmid DNA that is transfected into tissue culture cells is cleaved in vivo to produce a pattern of DNA fragments similar to that seen with purified enzyme in vitro. The activity has been called endo R for rescue, and its behavior suggests that it may have a role in recombination of cellular chromosomes.     

Membrane and metabolic requirements for tolerance induction of neonatal B cells

The metabolic requirements of tolerance induction of immature B cells has been analyzed through the use of various putative inhibitors. The study utilizes the splenic fragment assay in which tolerance induction of individual B cells can be examined. Concentrations of inhibitors were determined which, if removed after the first 18 hr of culture, before antigenic stimulation, had no inhibitory effects. Thus, by adding tolerogen in the presence or absence of inhibitor during the first 18 hr of culture, the effect of that inhibitor on tolerance could be assessed. By using this protocol, the data indicate that several metabolic functions of the cell are necessary for tolerance induction to occur, including RNA biosynthesis, DNA biosynthesis, and a methyltransferase reaction, because drugs that interfere with these metabolic processes also prevent tolerance induction. Our previous studies indicated that protein biosynthesis and energy generation are also required. However, drugs that interact with the cytoskeletal structure of the cell and inhibit surface immunoglobulin capping do not interfere with tolerance induction. Moreover, colchicine, which inhibits cell division, does not inhibit B cell tolerance. Collectively, the results provide compelling evidence that the mechanism of immature B cell tolerance involves an active process requiring several metabolic activities of the cell.     

Association between the Ro and La antigenic determinants: immunodiffusion analysis of human spleen extract

The Ro (SS-A) and La (SS-B) antigenic determinants appear to be related to one another because of the frequent coincidence of spontaneous anti-Ro and anti-La in the same autoimmune sera, and because of a tendency of the Ro and La immunoprecipitin lines in double immunodiffusion analysis to fuse. We have developed an enzyme immunodiffusion staining (EIS) procedure that permitted us to identify the specific antigenic determinants found in an immunoprecipitin line. By using this technique with human spleen extract, we showed that the Ro and La particles are found together as a complex, as well as individually. The EIS technique insured that our results were not confounded by lack of monospecificity of our autoantibody and antigenic reagents. Ro-La antigenic complexes exist at physiologic pH, and are dissociated by high ionic strength. They may be formed in vivo either intracellularly or extracellularly. Such Ro-La complexes could be immunogenic, and thereby might account for the frequent coincidence of the anti-La and anti-Ro autoantibody specificities.     

Intestinal absorption and metabolism of carotenoids: insights from cell culture

Cell culture models are useful for studying intestinal absorption and metabolism of carotenoids. The human intestinal cell line, Caco-2, has been the most widely used model for these studies. The PF11 and TC7 clones of Caco-2 exhibit beta-carotene-15,15'-oxygenase activity, a key enzyme in the conversion of carotenoids to vitamin A. Studies on the recent cloning of this enzyme are discussed. An in vitro cell culture system used to study intestinal absorption of carotenoids is presented. Under conditions mimicking the postprandial state, Caco-2 cells on membranes take up carotenoids and secrete them incorporated into chylomicrons. Both the cellular uptake and secretion of beta-carotene are saturable, concentration-dependent processes. The selective absorption of all-trans beta-carotene versus its cis isomers, the differential absorption of individual carotenoids, and the specific interactions between carotenoids during their absorption are discussed. The participation of a specific epithelial transporter in the intestinal absorption of carotenoids is proposed.     

Solid-phase immunoenzyme analysis of Coccidioides immitis antigens

A highly effective and specific solid-phase enzyme immunoassay system has been developed. The enzyme immunoassay is a highly sensitive technique for the detection and identification of C. immitis cellular and metabolic antigens. This technique is suitable for the study of strain differences in the antigenic composition of C. immitis, rendered harmless by different methods. The expediency of the preliminary sonification of cell suspensions of C. immitis, the causative agent of coccidioidomycosis, has been experimentally confirmed.     

Analysis of the Inc P-1 group plasmids R906 and R751 and their relationship to RP1

Three Inc-W group plasmids R388, Sa, and R7K have been studied by a variety of physical and genetic techniques. The data presented here permit the mapping of function onto the restriction enzyme maps of all three plasmids. When the physical and functional maps of these three plasmids are then compared they show a high degree of sequence conservation in the regions encoding replication and transfer functions but large differences in the regions which code for antibiotic resistance. In all three plasmids the DNA in and around the antibiotic resistance genes contains the majority of the restriction enzyme sites. The evolution of these three plasmids is discussed.     

Universal restriction endonucleases: designing novel cleavage specificities by combining adapter oligodeoxynucleotide and enzyme moieties

Class IIS restriction endonucleases cleave double-stranded (ds) DNA at precise distances from their recognition sequences. A method is proposed which utilizes this separation between the recognition site and the cut site to allow a class IIS enzyme, e.g., FokI, to cleave practically any predetermined sequence by combining the enzyme with a properly designed oligodeoxynucleotide adapter. Such an adapter is constructed from the constant recognition site domain (a hairpin containing the ds sequence, e.g., GGATG CCTAC for FokI) and a variable, single-stranded (ss) domain complementary to the ss sequence to be cleaved (at 9 and 13 nucleotides on the paired strands from the recognition sequence in the example of FokI). The ss sequence designated to be cleaved could be provided by ss phage DNA (e.g., M13), gapped ds plasmids, or supercoiled ds plasmids that were alkali denatured and rapidly neutralized. Combination of all three components, namely the class IIS enzyme, the ss DNA target sequence, and the complementing adapter, would result in target DNA cleavage at the specific predetermined site. The target ss DNA could be converted to the precisely cleaved ds DNA by DNA polymerase, utilizing the adapter oligodeoxynucleotide as primer. This novel procedure represents the first example of changing enzyme specificity by synthetic design. A practically unlimited assortment of new restriction specificities could be produced. The method should have many specific and general applications when its numerous ramifications are exploited.