Immobilization of genetically engineered cells: a new strategy for higher stability

In Vitro Gut Modeling as a Tool for Adaptive Evolutionary Engineering of Lactiplantibacillus plantarum

Research and marketing of probiotics demand holistic strain improvement considering both the biotic and abiotic gut environment. Here, we aim to establish the continuous in vitro colonic fermentation model PolyFermS as a tool for adaptive evolutionary engineering. Immobilized fecal microbiota from adult donors were steadily cultivated up to 72 days in PolyFermS reactors, providing a long-term compositional and functional stable ecosystem akin to the donor’s gut. Inoculation of the gut microbiota with immobilized or planktonic Lactiplantibacillus plantarum NZ3400, a derivative of the probiotic model strain WCFS1, led to successful colonization. Whole-genome sequencing of 45 recovered strains revealed mutations in 16 genes involved in signaling, metabolism, transport, and cell surface. Remarkably, mutations in LP_RS14990, LP_RS15205, and intergenic region LP_RS05100<LP_RS05095 were found in recovered strains from different adaptation experiments. Combined addition of the reference strain NZ3400 and each of those mutants to the gut microbiota resulted in increased abundance of the corresponding mutant in PolyFermS microbiota after 10 days, showing the beneficial nature of these mutations. Our data show that the PolyFermS system is a suitable technology to generate adapted mutants for colonization under colonic conditions. Analysis thereof will provide knowledge about factors involved in gut microbiota colonization and persistence.

IMPORTANCE Improvement of bacterial strains in regard to specific abiotic environmental factors is broadly used to enhance strain characteristics for processing and product quality. However, there is currently no multidimensional probiotic strain improvement approach for both abiotic and biotic factors of a colon microbiota. The continuous PolyFermS fermentation model allows stable and reproducible continuous cultivation of colonic microbiota and provides conditions akin to the host gut with high control and easy sampling. This study investigated the suitability of PolyFermS for adaptive evolutionary engineering of a probiotic model organism for lactobacilli, Lactiplantibacillus plantarum, to an adult human colonic microbiota. The application of PolyFermS controlled gut microbiota environment led to adaptive evolution of L. plantarum strains for enhanced gut colonization characteristics. This novel tool for strain improvement can be used to reveal relevant factors involved in gut microbiota colonization and develop adapted probiotic strains with improved functionality in the gut.

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor

Cultivation in a bioreactor of immobilized deep-sea hydrothermal microbial community was tested in order to assess the stability and reactivity of this new system. A community composed of eight hydrothermal strains was entrapped in a polymer matrix that was used to inoculate a continuous culture in a gas-lift bioreactor. The continuous culture was performed for 41 days at successively 60°C, 55°C, 60°C, 85°C and 60°C, at pH 6.5, in anaerobic condition and constant dilution rate. Oxic stress and pH variations were tested at the beginning of the incubation. Despite these detrimental conditions, three strains including two strict anaerobes were maintained in the bioreactor. High cell concentrations (3 × 10(8) cells mL(-1)) and high ATP contents were measured in both liquid fractions and beads. Cloning-sequencing and qPCR revealed that Bacillus sp. dominated at the early stage, and was later replaced by Thermotoga maritima and Thermococcus sp. Acetate, formate and propionate concentrations varied simultaneously in the liquid fractions. These results demonstrate that these immobilized cells were reactive to culture conditions. They were protected inside the beads during the stress period and released in the liquid fraction when conditions were more favorable. This confirms the advantage of immobilization that highlights the resilience capacity of certain hydrothermal microorganisms after a stress period.

Protein production using recombinant yeast in an immobilized-cell-film airlift bioreactor

A recombinant Saccharomyces cerevisiae C468/pGAC9 (ATCC 20690), which expresses Aspergillus awamori glucoamylase gene under the control of the yeast enolase I (ENO1) promoter and secretes glucoamylase into the extracellular medium, was used as a model system to investigate the effect of cell immobilization on bioreactor culture performance. Free suspension cultures in stirred-tank and airlift bioreactors confirmed inherent genetic instability of the recombinant yeast. An immobilized-cell-film airlift bioreactor was developed by employing cotton cloth sheets to immobilize the yeast cells by attachment. Enhanced enzyme productivity and production stability in the immobilized-cell system were observed. Experimental data indicated that the immobilized cells maintained a higher proportion of plasmid-bearing cells for longer periods under continuous operation. The higher plasmid maintenance with immobilized cells is possibly due to reduced specific growth rate and increased plasmid copy number. Double-selection pressure was used to select and maintain the recombinant yeast. The selected strain showed better production performance than the original strain. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 241-251, 1997.

Encapsulation of recombinant E. coli expressing cyclopentanone monooxygenase in polyelectrolyte complex capsules for Baeyer-Villiger biooxidation of 8-oxabicyclo[3.2.1]oct-6-en-3-one

Recombinant Escherichia coli cells, over-expressing cyclopentanone monooxygenase activity, were immobilized in polyelectrolyte complex capsules, made of sodium alginate, cellulose sulfate, poly(methylene-co-guanidine), CaCl(2) and NaCl. More than 90% of the cell viability was preserved during the encapsulation process. Moreover, the initial enzyme activity was fully maintained within encapsulated cells while it halved in free cells. Both encapsulated and free cells reached the end point of the Baeyer-Villiger biooxidation of 8-oxabicyclo[3.2.1]oct-6-en-3-one to 4,9-dioxabicyclo[4.2.1]non-7-en-3-one at the same time (48 h). Similarly, the enantiomeric excess above 94% was identical for encapsulated and free cells.

Continuous nisin production with bioengineered Lactococcus lactis strains

Nisin production in continuous cultures of bioengineered Lactococcus lactis strains that incorporate additional immunity and regulation genes was studied. Highest nisin activities were observed at 0.2 h(-1) dilution rate and 12.5 g l(-1) fructose concentration for all strains. Recombinant strains were able to produce greater amounts of nisin at dilution rates below 0.3 h(-1) compared to the control strain. However, this significant difference disappeared at dilution rates of 0.4 and 0.5 h(-1). For the strains LL27, LAC338, LAC339, and LAC340, optimum conditions for nisin production were determined to be at 0.29, 0.26, 0.27, and 0.27 h(-1) dilution rates and 11.95, 12.01, 11.63, and 12.50 g l(-1) fructose concentrations, respectively. The highest nisin productivity, 496 IU ml(-1) h(-1), was achieved with LAC339. The results of this study suggest that low dilution rates stabilize the high specific nisin productivity of the bioengineered strains in continuous fermentation. Moreover, response surface methodology analysis showed that regulation genes yielded high nisin productivity at wide ranges of dilution rates and fructose concentrations.

Potential of biofilm-based biofuel production

Biofilm technology has been extensively applied to wastewater treatment, but its potential application in biofuel production has not been explored. Current technologies of converting lignocellulose materials to biofuel are hampered by costly processing steps in pretreatment, saccharification, and product recovery. Biofilms may have a potential to improve efficiency of these processes. Advantages of biofilms include concentration of cell-associated hydrolytic enzymes at the biofilm-substrate interface to increase reaction rates, a layered microbial structure in which multiple species may sequentially convert complex substrates and coferment hexose and pentose as hydrolysates diffuse outward, and the possibility of fungal-bacterial symbioses that allow simultaneous delignification and saccharification. More importantly, the confined microenvironment within a biofilm selectively rewards cells with better phenotypes conferred from intercellular gene or signal exchange, a process which is absent in suspended cultures. The immobilized property of biofilm, especially when affixed to a membrane, simplifies the separation of biofuel from its producer and promotes retention of biomass for continued reaction in the fermenter. Highly consolidated bioprocessing, including delignification, saccharification, fermentation, and separation in a single reactor, may be possible through the application of biofilm technology. To date, solid-state fermentation is the only biofuel process to which the advantages of biofilms have been applied, even though it has received limited attention and improvements. The transfer of biofilm technology from environmental engineering has the potential to spur great innovations in the optimization of biofuel production.

Use and engineering aspects of immobilized cells in biotechnology

A short review of the research in the past two years (1990-1991) on immobilized whole cells, such as microbial, plant, and animal cells, is presented including a discussion from an engineering point of view. Recent works concerning the intraparticle mass transfer effect on immobilized microbial cells by the authors and their co-workers are also introduced. Finally, future prospects of the immobilized cell system will be discussed.

Plasmid stability in recombinant Saccharomyces cerevisiae

Because of many advantages, the yeast Saccharomyces cerevisiae is increasingly being employed for expression of recombinant proteins. Usually, hybrid plasmids (shuttle vectors) are employed as carriers to introduce the foreign DNA into the yeast host. Unfortunately, the transformed host often suffers from some kind of instability, tending to lose or alter the foreign plasmid. Construction of stable plasmids, and maintenance of stable expression during extended culture, are some of the major challenges facing commercial production of recombinant proteins. This review examines the factors that affect plasmid stability at the gene, cell, and engineering levels. Strategies for overcoming plasmid loss, and the models for predicting plasmid instability, are discussed. The focus is on S. cerevisiae, but where relevant, examples from the better studied Escherichia coli system are discussed. Compared to free suspension culture, immobilization of cells is particularly effective in improving plasmid retention, hence, immobilized systems are examined in some detail. Immobilized cell systems combine high cell concentrations with enhanced productivity of the recombinant product, thereby offering a potentially attractive production method, particularly when nonselective media are used. Understanding of the stabilizing mechanisms is a prerequisite to any substantial commercial exploitation and improvement of immobilized cell systems.

Development of bioreaction engineering

In addition to summarizing the early investigations in bioreaction engineering, the present short review covers the development of the field in the last 50 years. A brief overview of the progress of the fundamentals is presented in the first part of this article and the key issues of bioreaction engineering are advanced in its second part.

Continuous production of lacticin 3147 and nisin using cells immobilized in calcium alginate

Bacteriocinogenic strains, Lactococcus lactis subsp. lactis DPC 3147 and L. lactis DPC 496, producing lacticin 3147 and nisin, respectively, were immobilized in double-layered calcium alginate beads. These beads were inoculated into MRS broth at a ratio of 1:4 and continuously fermented for 180 h. Free cells were used to compare the effect of immobilization on bacteriocin production. After equilibrium was reached, a flow rate of 580 ml h(-1) was used in the immobilized cell (IC), and 240 ml h(-1) in free-cell (FC) bioreactors. Outgrowth from beads was observed after 18 h. Bacteriocin production peaked at 5120 AU ml(-1) in both IC and FC bioreactors. However, FC production declined after 80 h to 160 AU ml(-1) at the end of the fermentation. Results of this study indicate that immobilization offers the possibility of a more stable and long-term means of producing lacticin 3147 in laboratory media than with free cells.

Activity and stability of a recombinant plasmid-borne TCE degradative pathway in biofilm cultures

The activity and stability of the TCE degradative plasmid TOM31c in the transconjugant host Burkholderia cepacia 17616 was studied in selective and non-selective biofilm cultures. The activity of plasmid TOM31c in biofilm cultures was measured by both TCE degradative studies and the expression of the Tom pathway. Plasmid loss was measured using continuous flow, rotating annular biofilm reactors, and various analytical and microbiological techniques. The probability of plasmid loss in the biofilm cultures was determined using a non-steady-state biofilm plasmid loss model that was derived from a simple mass balance, incorporating results from biofilm growth and plasmid loss studies. The plasmid loss model also utilized Andrew's inhibition growth kinetics and a biofilm detachment term. Results from these biofilm studies were compared to similar studies performed on suspended cultures of Burkholderia cepacia 17616-TOM31c to determine if biofilm growth has a significant effect on either plasmid retention or Tom pathway expression (i.e., TCE degradation rates). Results show that the activity and expression of the Tom pathway measured in biofilm cultures was significantly less than that found in suspended cultures at comparable growth rates. The data obtained from these studies fit the plasmid loss model well, providing plasmid loss probability factors for biofilm cultures that were equivalent to those previously found for suspended cultures. The probability of plasmid loss in the B. cepacia 17616-TOM31c biofilm cultures was equivalent to those found in the suspended cultures. The results indicate that biofilm growth neither helps nor hinders plasmid stability. In both the suspended and the biofilm cultures, plasmid retention and expression could be maintained using selective growth substrates and/or an appropriate plasmid-selective antibiotic. Copyright 1998 John Wiley & Sons, Inc.

Kinetics of continuous GM-CSF production by recombinant Saccharomyces cerevisiae in an airlift bioreactor

Continuous production of murine GM-CSF by recombinant Saccharomyces cerevisiae in an airlift bioreactor was studied at three different dilution rates. The reactor was initially fed with a selective medium to increase cell concentration, and then was fed with a rich, nonselective medium for GM-CSF production. Ethanol was used as the main carbon source to provoke GM-CSF expression. In continuous culture, GM-CSF production was maintained for over 150 h, even though the fraction of plasmid-carrying cells continuously dropped to lower than 20%. The stable GM-CSF production during the later phase of the continuous culture was attributed to increased specific cell productivity possibly resulting from an increase in the plasmid copy number in plasmid-carrying cells. This also indicated the possibility of natural selection of high-copy number cells in continuous culture. Plasmid stability was found to be growth rate (dilution rate) dependent; it increased with the dilution rate. Reactor productivity and specific productivity also increased with the dilution rate. A two-parameter kinetic equation was used to model the plasmid stability kinetics. The growth rate ratio between plasmid-carrying and plasmid-free cells increased from 0.996 to 0.998 while the segregational instability or the probability of plasmid loss from each cell division increased from 1.1% to 16% as the dilution rate decreased from 0.11 h-1 to 0.05 h-1. Oscillation of the dilution rate between 0.05 h-1 and 0.11 h-1 stabilized the plasmids and gave a higher productivity than that achieved without oscillation.

Pediocin 5 production and plasmid stability during continuous free and immobilized cell cultures of Pediococcus acidilactici UL5

Continuous production of pediocin 5 from Pediococcus acidilactici UL5 was investigated in MRS medium at different pH and dilution rates during continuous free cell (FC) and immobilized cell (IC) fermentations. Pediocin 5 activity from FC operated at a dilution rate of 0.31 h-1 largely increased from 128 to 2048 AU mL-1 as pH decreased from 7.0 to 5.0. Pediocin 5 activity in IC at a dilution rate of 0.93 h-1 was much less affected by pH, varying from 256 AU mL-1 at pH 7.0 to 512 AU mL-1 at pH 5.0. At the optimum pH 5.0, the dilution rate greatly influenced pediocin 5 activity both in FC and IC. Pediocin 5 production during continuous FC culture decreased with time for all dilution rates tested except 0.31 h-1 and average activity over 144 h cultures reached a maximal value of 4915 AU mL-1 at a dilution rate of 0.26 h-1. For IC, pediocin 5 production was stable with time and increased with the dilution rate from 256 to 1024 AU mL-1 in the range of 0.47-2.28 h-1. Three Listeria strains were tested for their ability to screen low bacteriocin-producing variants (Bac+v) of Bac+ cells in FC and IC cultures by using a modified deferred antagonism method. Ten to 28% of Bac+v cells appeared after 144 h of FC cultures at dilution rates in the range 0.09-0.42 h-1 and pH control set points of 5.0-7.0 while almost no Bac+v cell was detected during 192 h IC culture in the same pH range and for dilution rates varying from 0.47 to 2.28 h-1. The Bac+v cells isolated produced eight- to 64-fold less pediocin 5 than the Bac+ cells. Although electrophoresis analysis showed no apparent difference in the plasmid profiles of Bac+v and Bac+ cells, the Bac- mutant obtained by acriflavine treatment had lost the pMJ5 plasmid encoding for bacteriocin production. The decreased quantity of plasmid DNA in Bac+v cells suggests that the decreased pediocin 5 activity of Bac+v cells resulted from a decrease in plasmid copy number.

Industrial production of heterologous proteins by fed-batch cultures of the yeast Saccharomyces cerevisiae

This review concerns the issues involved in the industrial development of fed-batch culture processes with Saccharomyces cerevisiae strains producing heterologous proteins. Most of process development considerations with fed-batch recombinant cultures are linked to the reliability and reproducibility of the process for manufacturing environments where quality assurance and quality control aspects are paramount. In this respect, the quality, safety and efficacy of complex biologically active molecules produced by recombinant techniques are strongly influenced by the genetic background of the host strain, genetic stability of the transformed strain and production process factors. An overview of the recent literature of these culture-related factors is coupled with our experience in yeast fed-batch process development for producing various therapeutic grade proteins. The discussion is based around three principal topics: genetics, microbial physiology and fed-batch process design. It includes the fundamental aspects of yeast strain physiology, the nature of the recombinant product, quality control aspects of the biological product, features of yeast expression vectors, expression and localization of recombinant products in transformed cells and fed-batch process considerations for the industrial production of Saccharomyces cerevisiae recombinant proteins. It is our purpose that this review will provide a comprehensive understanding of the fed-batch recombinant production processes and challenges commonly encountered during process development.

Improvement of plasmid stability of recombinant Bacillus-subtilis cells in continuous immobilized cultures

The immobilization of recombinant Bacillus subtilis in K-carrageenan gel beads has been performed in order to study the growth conditions inside the gel beads and to improve plasmid stability. Bacterial colonies showing high cell density were studied using scanning electron microscopy. A series of continuous cultures of free and immobilized B. subtilis MT119 (pHV1431, pIL252 and pIL252 Kpn) have been developed without selection pressure. In the free-cell systems, it was found that a loss of plasmid vectors occurred after a short period. In contrast, in the immobilized cell systems, plasmid-free segregants were not detected in any of the cases during the first 80 h of the culture.

Plasmid stability and ecological competence in recombinant cultures

The instability of cell cultures containing plasmid vectors is a major problem in the commercial exploitation of molecular cloning techniques. Plasmid stability is influenced by the nature of the host cell, the type of plasmid and/or environmental conditions. Plasmid encoded properties may confer a selective advantage on the host cell but can be an energy drain due to replication and expression. Stability of recombinant cultures ultimately may be determined by the cost to benefit ratio of plasmid carriage. The relative competition between plasmid containing and plasmid-free or indigenous populations can determine the degree of dominance of recombinant cultures. The use of inocula in biotechnological processes in which dynamic environmental conditions dominate may also result in instabilities resulting from the characteristics of the ecosystem. In such dynamic conditions plasmid stability is just one contribution to culture stability. Strategies to enhance plasmid stability, within such environments, based on manipulation of physiological state of host cells, must consider the responsiveness or plasticity of both cells and populations. The robustness of cells or the responses to stresses or transient environmental conditions can influence the levels of instability detected; for example, instability or mutation in the host genome may lead to enhanced plasmid stability. Competition among subpopulations arising from unstable copy number control may determine the levels of recombinant cells in open versus closed fermenter systems. Thus the ecological competence (ability to survive and compete) of recombinant cells in dynamic or transient environments is fundamental to the understanding of the ultimate dominance or survival of such recombinant cultures and may form the basis of a strategy to enhance or control stability either in fermenter systems or dynamic process environments. The creation of microniches in time and/or space can enhance plasmid stability. Transient operation based on defined environmental stresses or perturbations in fermenter systems or in heterogeneous or dynamic environments found in gel immobilized cultures have resulted in enhanced stability. Spatial organization resulting from immobilization has the additional advantage of regulated cell protection within defined microenvironments and controlled release, depending on the nature of the gel, from these microenvironments or microcosms. This regulation of ecological competence allied to the advantages of microbial cell growth in gel microenvironments combined with the spatial organization (or juxtapositioning of cells, selective agents, nutrients, protectants, etc.) possible through immobilization technology offers new strategies to enhance plasmid and culture stability.

Immobilized cells in meat fermentation

The immobilization of microbial cells can contribute to fermented meat technology at two basic levels. First, the solid/semisolid nature (low available water) of the substrate restricts the mobility of cells and results in spatial organizations based on "natural immobilization" within the fermentation matrix. The microniches formed influence the fermentation biochemistry through mass transfer limitations and the subsequent development and activity of the microflora. This form of immobilization controls the nature of competition between subpopulations within the microflora and ultimately exerts an effect on the ecological competence (ability to survive and compete) of the various cultures present. Second, immobilized cell technology (ICT) can be used to enhance the ecological competence of starter cultures added to initiate the fermentation. Immobilization matrices such as alginate can provide microniches or microenvironments that protect the culture during freezing or lyophilization, during subsequent rehydration, and when in competition with indigenous microflora. The regulated release of cells from the microenvironments can also contribute to competitive ability. The regulation of both immobilization processes can result in enhanced fermentation activity.

Investigation of parameters affecting a fixed bed bioreactor process for recombinant cell lines

A BHK 21 cell line expressing a recombinant antibody was grown in a fixed bed reactor (FBR) system using a porous support made of Siran glass beads. The contribution of five process variables (bead and inoculum sizes; circulation and dilution rates; glutamine concentration of the feed) to the productivity of the process (defined as production rate, effluent product concentration or yield of product on medium supplied) was investigated using a partial factorial experimental design. Individually, none of the variables tested had a significant affect upon productivity. The combination of smaller bead and inoculum sizes, higher circulation and dilution rates, plus higher feed glutamine concentration gave a markedly higher productivity than any other combination of variable levels tested. This combination of variable levels suggested that better results should be obtained using a fluidized bed reactor system. However, comparison of the productivities of the two systems showed that the FBR gave the better results. This result can be explained in terms of the relationship of QsrAb to mu.

Direct determination of the cephalosporin transforming activity of immobilized cells with use of an enzyme thermistor. 1. Verification of the mathematical model

A simple method for the direct measurement of the catalytic properties of immobilized cells in the flow minicalorimeter, the enzyme thermistor (ET), is presented. A Trigonopsis variabilis strain with cephalosporin C-transforming activity was used as the model system. The yeast cells were immobilized either by crosslinking with a homobifunctional reagent or by entrapment in gels. The actual activity of the immobilized cells used in the ET was estimated by means of a stirred-batch reactor measurement in conjunction with HPLC analysis of substrate and products. Similar results were also obtained using D-amino acid oxidase (EC 1.4.3.3) isolated from T. variabilis cells and immobilized by gel entrapment. This calibration procedure was found to be appropriate for all biocatalyst systems used. The thermometric signal was proportional to the amount of biocatalyst immobilized in the ET minicolumn. It was shown that the rate of reaction catalyzed by T. variabilis entrapped in calcium pectate gel was limited by internal diffusion to an extent depending on the cell concentration in the biocatalyst particle. This approach offers a direct method for studying the kinetic properties of immobilized cells.

On the merits of viable-cell immobilisation

Many advantages have been claimed over the years for the use of immobilised cells, both as enzyme systems and as whole viable cell systems for complete fermentation reactions. However, few of the claims have been fully substantiated, and may not even be entirely justified. Most research is involved with single applications and the best that can be hoped for is some evidence that immobilised cells in each of these individual cases display some advantage over the equivalent free cell system. The purpose of this review is to assess the merits of viable cell immobilisation in the light of published literature and to elucidate the underlying mechanisms. Particular attention is paid to the generally unanticipated, but widely observed enhanced stability of immobilised cell fermentation processes.