Evolution: bacterial mutation in stationary phase

A recent study indicates that the genomic mutation rate of the gut bacterium Escherichia coli is substantially higher in nongrowing than growing cultures. These findings are important in the light of the ongoing controversy over the generality and robustness of stationary phase mutagenesis and its evolutionary implications.     

Plasmid cloning vectors that integrate site-specifically in Streptomyces spp

Cloning vectors based on the Streptomyces ambofaciens plasmid pSAM2 and the streptomycete phage phi C31 were developed for use in Streptomyces spp. These vectors replicate in Escherichia coli but integrate by site-specific recombination in Streptomyces spp. Both pSAM2-based and phi C31-based vectors transformed a number of different Streptomyces spp; however, the phi C31-based vectors consistently transformed at higher frequencies than pSAM2-based vectors. Southern analysis indicated that the phi C31-based vectors integrated at a unique site in the S. ambofaciens chromosome, while the pSAM2-based vectors gave complex patterns which could indicate structural instability or use of multiple loci. Both types of vectors utilize the apramycin (Am)-resistance gene which can be selected in E. coli and Streptomyces spp. with either Am or the commercially available antibiotic Geneticin (G418).     

Human adenovirus cloning vectors based on infectious bacterial plasmids

By making use of the fact that human adenovirus DNA circularizes in infected cells, and that circular forms of the viral genome are infectious, we have developed an improved adenovirus-based cloning system. A deletion mutant of adenovirus type 5 (Ad5) with deletions in early regions 1 (E1) and 3 (E3) was converted to a bacterial plasmid which can regenerate infectious virus following transfection into human 293 cells. A single XbaI recognition site in the deleted E3 region serves as a site for the insertion of foreign DNA. We have used this system to clone a number of genes into the Ad5 genome and describe the insertion of the neomycin/G418 resistance marker into Ad5 as an example.     

A Leishmania donovani gene that confers accelerated recovery from stationary phase growth arrest

We have isolated a gene, LdGF1, from the protozoan parasite Leishmania donovani. Overexpression of this gene confers a strong selective advantage in liquid culture after stationary phase growth arrest. We could show that recombinant L. donovani or Leishmania major, when overexpressing LdGF1, recover faster from a stationary phase growth arrest than control parasite strains. While no advantage of LdGF1 overexpression could be observed in log phase cultures or after a hydroxyurea-induced S-phase growth arrest, recovery from a cell cycle arrest due to serum deprivation was faster in LdGF1-overexpressing strains. This was found to be due to an accelerated release from a G₁ cell cycle arrest. By contrast, in a BALB/c mouse infection system, overexpression of LdGF1 in L. major resulted in reduced virulence. We conclude that increased levels of LdGF1 are beneficiary during recovery from G₁ cell cycle arrest, but pose a disadvantage inside a mammalian host. These results are discussed in the context of the observed loss of virulence during in vitro passage of Leishmania parasites.     

Mutations that activate the silent bgl operon of Escherichia coli confer a growth advantage in stationary phase

Wild-type strains of Escherichia coli are unable to utilize aromatic beta-glucosides such as arbutin and salicin because the major genetic system that encodes the functions for their catabolism, the bgl operon, is silent and uninducible. We show that strains that carry an activated bgl operon exhibit a growth advantage over the wild type in stationary phase in the presence of the rpoS819 allele that causes attenuated rpoS regulon expression. Our results indicate a possible evolutionary advantage in retaining the silent bgl operon by wild-type bacteria.     

Pyoverdin cheats fail to invade bacterial populations in stationary phase

Microbes engage in cooperative behaviours by producing and secreting public goods, the benefits of which are shared among cells, and are therefore susceptible to exploitation by nonproducing cheats. In nature, bacteria are not typically colonizing sterile, rich environments in contrast to laboratory experiments, which involve inoculating sterile culture with few bacterial cells that then race to fill the available niche. Here, we study the potential implications of this difference, using the production of pyoverdin, an iron‐scavenging siderophore that acts as a public good in the bacteria Pseudomonas aeruginosa. We show that (1) nonproducers are able to invade cultures of producers when added at the start of growth or during early exponential growth phase, but not during late exponential or stationary phase; (2) the producer strain does not produce pyoverdin in the late exponential and stationary phases and so is not paying the cost of cooperating during those phases. These results suggest that whether a nonproducing mutant can invade will depend upon when the mutation arises, as well as the population structure, and raise a potential difficulty with the use of antimicrobial treatment strategies that propose to exploit the invasive abilities of cheats.     

Plasmid cloning vectors that can be nicked at a unique site

Summary We describe ColE1-type plasmids, with relaxed DNA replication, based on pMB9, and carrying the Cm^R determinant of R1, in addition to the Tc^R determinant of pMB9. One of the plasmids, pPH207, has unique sites for EcoRI, HindIII, BamI, SalI and Hpal. Insertion of foreign DNA into all but the last of these inactivates cither the Cm^R or the Tc^R determinant.The original Cm^R Tc^R plasmid (pCM2) contains a copy of IS1 which produces deletions to left and to right. Most of these inactivate either the Cm^R or the Tc^R determinant. An internal 280 bp deletion of IS1 DNA in pPH207 greatly reduces the frequency at which deletions are observed.The main feature of these plasmids is a site that is cleaved by some preparations of EcoRI in only one strand of the DNA duplex (the EcoRIⁿ site). This site facilitates strand separation of sequences inserted at the HindIII, BamI and SalI sites of the Tc^R gene, and also of any inserted at the true EcoRI site by a method that destroys that site. Since the oricntation of the EcoRIⁿ site is known, the orientation of sequences inserted at the neighbouring sites can be easily determined.Plasmid pPH207 is not mobilised by a Hfr, but its mobilisation is promoted by ColE1. It is therefore Mob ^- bom ⁺. Experiments with minicells show that it directs the copious synthesis of chloramphenicol transacetylase.     

Transition phenomena in bacterial growth between logarithmic and stationary phases

Summary A method to calculate the age distribution of the cells in the transition phase starting from that of the cells in logarithmic phase is described. It is clarified that two transition phenomena (decrease in the growth rate of cell number and partial synchronization) in the transition phase come, mathematically, from the fact that da_g/dt > 0 (a_g = generation time).The cell age at which septum becomes observable is estimated from the age distribution of the cells and the ratio of septated cells at each time in the transition phase. The result suggests that the cell age at which septum synthesis starts increases in the transition phase and that the mode of septum synthesis changes during that phase.     

Comparison of definitions of the lag phase and the exponential phase in bacterial growth

M.H. ZWIETERING, F.M. ROMBOUTS AND K. VAN 'T RIET. 1992. Different definitions of the lag time and of the duration of the exponential phase can be used to calculate these quantities from growth models. The conventional definitions were compared with newly proposed definitions. It appeared to be possible to derive values for the lag time and the duration of the exponential phase from the growth models, and differences between the various definitions could be quantified. All the different values can be calculated from the growth parameters μ _m , and a. Therefore, it appeared to be unnecessary to use complicated mathematical equations: simple equations were adequate. For the Gompertz model the conventional definition of the lag time did not differ appreciably from the newly proposed definition. The end-point of the exponential phase and thus the duration of the exponential phase differed considerably for the two definitions. For the logistic model the two definitions lead to considerable differences for all quantities. It is recommended that the conventional definition is used for calculating the lag time. For the duration of the exponential phase it is recommended that the new definition is used. The value can be calculated, however, directly from the conventional growth parameters.     

Comparison of definitions of the lag phase and the exponential phase in bacterial growth.

Different definitions for the lag time and of the duration of the exponential phase can be used to calculate these quantities from growth models. The conventional definitions were compared with newly proposed definitions. It appeared to be possible to derive values for the lag time and the duration of the exponential phase from the growth models and differences between the various definitions could be quantified. All the different values can be calculated from the growth parameters microm, lambda and alpha. Therefore, it appeared to be unnecessary to use complicated mathematical equations; simple equations were adequate. For the Gompertz model the conventional definition of the lag time did not differ appreciably from the newly proposed definition. The end-point of the exponential phase and thus the duration of the exponential phase differed considerably for the two definitions. For the logistic model the two definitions lead to considerable differences for all quantities. It is recommended that the conventional definition is used for calculating the lag time. For the duration of the exponential phase it is recommended that the new definition is used. The value can be calculated, however, directly from the conventional growth parameters.     

Secretion cloning vectors in Escherichia coli

The DNA fragment coding for the signal peptide of the OmpA protein, a major outer membrane protein of Escherichia coli, has been inserted into the high-level expression vectors, pIN-III. A foreign DNA fragment can be cloned in any one of the three reading frames at the unique EcoRI, HindIII or BamHI sites immediately after the ompA signal peptide coding sequence. The cloned foreign gene is under the control of both the lpp promoter and the lac promoter-operator. The expression of the gene is regulated by the lac repressor produced by the same vectors. Using the pIN-III-ompA vector, the DNA fragment coding for only the mature portion of beta-lactamase was inserted into the EcoRI site. Upon induction of gene expression, beta-lactamase was secreted into the periplasmic space. The ompA signal peptide was correctly removed resulting in the production of beta-lactamase with four extra amino acid residues (Gly-Ile-Pro-Gly) at its amino terminus due to the linker sequence in the vector. After a 3-h induction, beta-lactamase was accumulated to 20% of total cellular protein without any detectable accumulation of pro-beta-lactamase. Using oligonucleotide-directed site-specific mutagenesis, we have also removed the linker sequence and upon induction of gene expression, beta-lactamase with the authentic NH2-terminal sequence was produced, in even larger amounts than the beta-lactamase with the linker sequence.     

Proteomic analysis of lactose-starved Lactobacillus casei during stationary growth phase

Aims:  Starvation stress is a condition that nonstarter lactic acid bacteria (NSLAB) normally encounter. This study was aimed to investigate starvation-induced proteins in Lactobacillus casei during stationary growth phase.
Methods and Results:  The impact of carbohydrate starvation on L. casei GCRL163 was investigated using two different media (a modified de Man, Rogosa and Sharpe broth and a semi-defined medium). Cells were grown in the presence of excess lactose (1%) or starvation (0%) and differences in the patterns of one-dimensional sodum dodecyl sulfate–polyacrylamide gel electrophoresis and two-dimensional electrophoresis of the cytosolic protein fractions were investigated. Differentially regulated proteins were identified by MALDI-TOF/TOF mass spectrometry. Many differentially regulated proteins were enzymes of various metabolic pathways involved in carbohydrate metabolism to yield energy. Differences in protein expression were also observed in the two culture conditions tested in this experiment.
Conclusion:  Numerous glycolytic enzymes were differentially regulated under lactose starvation. The differential expression of these glycolytic enzymes suggests a potential survival strategy under harsh growth conditions (i.e. lactose starvation).
Significance and Impact of the Study:  This paper reports improved understanding of stress responses and survival mechanism of NSLAB under lactose-depleted cheese-ripening condition. This knowledge of how NSLAB bacteria adapt to lactose starvation could be applied to predict the performances of bacteria in other industrial applications.     

RNA synthesis during the stationary growth phase in the Bacillus subtilis Cgr4 mutant

RNA synthesis was studied in Bacillus subtilis Cgr4 grown in the mineral sporulation medium enriched with glucose up to 2% and amino acids up to 1%. To study mRNA synthesis, a method of transfer of the 3H-uridine pulse-labeled culture to the supernatant of physiologically identical, not labeled culture, followed by further incubation was used, the amount of 3H-uridine in the supernatant as well as in cells being measured. RNA was also analysed electrophoretically and distribution of the label among the fractions was determined. It is shown that mRNA synthesized in the logarithmic phase degrades up to 12% on the 2nd hour of growth during 10 min; the mRNA in the stationary phase is stable on the 7th hour of growth; no degradation is observed in the course of 2-3 hours. The beginning of degradation coincides in time with secondary induction of the synthesis of serine proteases and with the onset of sharp decrease in incorporation of 3H-uridine in RNA as well as with induction of spore morphogenesis. On the basis of electrophoretical analysis of pulse-labeled RNA, it was demonstrated that, prior to the transfer, labeled uridine was included and preserved in RNA fraction for 2-3 hours after the transfer, this fraction corresponding in mobility with mRNA in polyacrylamide gel. The following conclusion may be drawn: stable mRNAs are synthesized in the stationary phase and may be used for the translation of extracellular serine protease.     

Physiological and morphological characteristics of stationary phase vibrio cells able to support phase growth

Growth of phase alpha 3a on stationary phase Vibrio cultures requires micro-aerophilic conditions and is inhibited by aeration. Since pre-conditioning of the bacteria by allowing them to stand for 24 h after shaking for 3 d is an important aspect of the stationary phase phage growth system, various physiological and morphological characteristics of the stationary phase cells during the transition from shaking to standing were investigated. Shaken stationary phase cells were less viable and more sensitive to ultraviolet irradiation and heat than standing stationary phase cells. During pre-conditioning the small, non-flagellated cells present in shaken stationary phase cultures underwent morphological changes and became large, flagellated rods which resembled exponential phase cells. The transition of stationary phase cells from shaking to standing was associated with a marked increase in total RNA synthesis but a rapid and large decrease in total protein synthesis. Intracellular concentrations of ATP in shaken stationary phase cells were 53% lower than those in standing stationary phase cells. Studies on leucine uptake indicated that its transport was inhibited by isoleucine and that the major part (90%) of the total leucine uptake was due to a shared system for uptake of both amino acids. Shaken stationary phase cells transported less leucine than standing stationary phase cells. Inhibition of phage growth in aerated stationary phase cultures was not due to the prevention of phase absorption by shaking. It is suggested that the observed differences between shaken and standing stationary phase cells could be due to aeration affecting the template specificity of the Vibrio RNA polymerase.     

Introduction to the biology of the bacterial stationary phase: mechanism of general response to stress

This review is devoted to the biology of stationary-phase bacteria, occurring in a specific physiological state at which they arrive in the process of complex response to various kinds of stresses accompanying the retardation and cessation of growth and reproduction. A general account of the problem is presented. Special emphasis is placed on one of the metabolic mechanisms involved in the formation of the physiological state of stationary-phase bacteria and performing primarily protective functions (the so-called general response of cells to stresses). The relationship between this and other regulatory mechanisms involved in the transition of bacteria to the stationary phase and the maintenance of this phase is discussed.     

Induction of entry into the stationary growth phase in Pseudomonas aeruginosa by N-acylhomoserine lactone

N-acylhomoserine lactone (AHSL, autoinducer) is capable of regulating a set of genes by sensing cell density and developing an intercellular communication in Pseudomonas aeruginosa. Addition of AHSL in the exponential growth phase, regardless of cell density, induces a repression of cell growth of P. aeruginosa, an expression of stationary phase specific factor σ^s in vivo and a morphological change into smaller spherical shape indistinguishable from that in the stationary phase. It is demonstrated that AHSL can trigger an entry of bacteria into stationary phase as a growth controlling signal.     

A broad-range of recombination cloning vectors in mycobacteria

The increased incidence of tuberculosis (TB) gave impetus for the increased interest in the study of mycobacterial genetics, which culminated in the publication of the full genome sequence of many mycobacterial strains. Since then, many genes and open reading frames of unknown function have been described and the expression of their encoded proteins is critical toward understanding the pathogenesis of TB and developing therapeutic and preventive strategies. Therefore there is an increased need for highly efficient methods for cloning of mycobacterial genes, as the limited cloning flexibility of current Escherichia coli–mycobacteria shuttle vectors remains a frequent impediment in genetic manipulation of mycobacteria. In order to overcome this limitation, we have converted representative extrachromosomal and integrative vectors into multiple destination mycobacterial vectors for one-step and restriction enzyme-free recombination cloning methodology that uses in vitro site-specific recombination. We provide several examples that highlight the potential of recombination cloning for gene expression in slow and fast-growing mycobacteria. Thus, a gene of interest can be transferred by simple recombination into our mycobacterial destination vectors, which serve a multitude of functional genomic studies.