Predictions for oxygen supply control to enhance population stability of engineered production strains

The simultaneous growth and product formation in a microbial culture is an important feature of several laboratory, industrial, and environmental bioprocesses. Metabolic burden associated with product formation in these bioprocesses may lead to growth advantage of a nonproducing mutant leading to a loss of the producing population over time. A simple population dynamics model demonstrates the extreme sensitivity of population stability to the engineered productivity of a strain. Here we use flux balance analysis to estimate the effects of the metabolic burden associated with product secretion on optimal growth rates. Comparing the optimal growth rates of the producing and nonproducing strains under a given processing condition allows us to predict the population stability. In order to increase stability of an engineered strain, we determine processing conditions that simultaneously maximize the growth rate of the producing population while minimizing the growth rate of a nonproducing population. Using valine, tryptophan, and lysine production as specific examples, we demonstrate that although an appropriate choice of oxygenation may increase culture longevity more than twofold, total production as governed by economic criterion can be increased by several orders of magnitude. Choice of optimal nutrient and oxygen supply rates to enhance stability is important both for strain screening as well as for culture of engineered strains. Appropriate design of the culture environment can thus be used to enhance the productivity of bioprocesses that use engineered production strains. (c) 1994 John Wiley & Sons, Inc.     

Effect of growth conditions on production of rhamnose-containing cell wall and capsular polysaccharides by strains of Lactobacillus casei subsp. rhamnosus.

Strains of Lactobacillus casei subsp. rhamnosus possessing two cell wall polysaccharides, a hexosamine-containing H-polysaccharide and a rhamnose-containing R-polysaccharide, were examined for the effect of growth conditions on the production of these two components. In strain NCTC 6375, R- and H-polysaccharides accounted for an estimated 44 and 20%, respectively, of the cell wall for organisms grown in batch culture with glucose as the carbohydrate source. Growth on fructose-containing media reduced the amount of R-polysaccharide by approximately 50% without affecting the amount of H-polysaccharide. Subculture of fructose-grown organisms in glucose restored the original proportions of the two polysaccharides. Galactose- and sucrose-grown cells behaved similarly to glucose-grown cells with respect to polysaccharide production, whereas growth in rhamnose or ribose showed values close to those for fructose-grown cells. Continuous culture of strain NCTC 6375 for more than 100 generations showed a gradual and irreversible reduction of the R-polysaccharide to less than 5% of the cell wall and an increase of the H-polysaccharide to 40% of the cell wall. Other type culture strains of L. casei subsp. rhamnosus, NCIB 7473 and ATCC 7469, behaved similarly in batch and continuous culture. In contrast, strains of L. casei subsp. rhamnosus isolated at the Institute of Dental Research showed phenotypic stability with respect to the relative proportions of R- and H-polysaccharides in both batch and continuous culture. Changes in polysaccharide composition of type culture strains were also mirrored in changes in the immunogenicity of the two components and resistance to the rate of enzymic lysis of whole organisms. For L. casei subsp. rhamnosus strain NCTC 10302 the R-polysaccharide is present entirely as capsular material. The amount of R-polysaccharide produced was also markedly dependent on the carbohydrate component of the medium in batch culture and both dilution rate and nature of the limiting carbohydrate in continuous culture, varying over a 10-fold range, whereas the cell wall H-polysaccharide remained constant.     

金鱼草花粉管亚原生质体的分离及在培养中的行为

应用酶法从金鱼草花粉管中分离出大量的亚原生质体。这种亚原生质体培养在 D_2液体培养基中,不论是有核的或是无核的都能再生厚的细胞壁和生长出花粉管状的管状结构。这些管状结构除了它们的顶端区外也沉积厚的细胞壁。随着管状结构的生长,内含物逐渐移向管状结构的顶端。当生长停止后,内含物可能完全被耗尽;有时管状结构的顶端破裂,内含物释放至培养液中。无核和有核亚原生质体同样显示有正常花粉管的基因表达的特性,即在培养中有类似花粉管生长的行为。这一事实表明在萌发的花粉管中有预先合成的 mRNA 的存在。     

Monoxenic and axenic cultivation of carrier and patient strains of Entamoeba histolytica.

All of five strains of Entamoeba histolytica, isolated from symptomatic cases of amoebiasis, could be adapted to axenic growth on the TP-S-1 medium of Diamond (1968). Four axenic strains were started from amoeba-Crithidia cultures; one could be axenized directly after isolation from a case of cutaneous amoebiasis. Attempts to monoxenize, resp. axenize strains, isolated from Dutch, asymptomatic carriers, were less successful. Only three out of ten strains could be submitted to bacteria-free growth. These three strains, however, originated probably from a recent case of intestinal amoebiasis. The results, suggesting that highly virulent strains can be easier cultivated bacteria-free than those with low or no virulence, are further discussed. The yield of axenic amoebae per tube fluctuates largely depending on many factors such as the strain, the number of transfers (i.e. degree of establishment), the quality of Panmede liver digest and serum in the TP-S-1 medium, and the care of manipulating the cultures. For optimal growth, a more acid medium was required in an amoeba-Crithidia culture than in an axenic culture. Multinucleated, giant amoebae were frequently observed in axenic cultures.     

Activation of the cryptic PhnE permease promotes rapid adaptive evolution in a population of Escherichia coli K-12 starved for phosphate

Escherichia coli K-12 suffers acetic acid stress during prolonged incubation in glucose minimal medium containing a limiting concentration of inorganic phosphate (0.1 mM P(i)), which decreases the number of viable cells from 6 × 10(8) to ≤10 CFU/ml between days 6 and 14 of incubation. Here we show that following two serial transfers into P(i)-limiting medium, evolved mutants survived prolonged incubation (≈10(7) CFU/ml on day 14 of incubation). The evolved strains that overtook the populations were generally PhnE(+), whereas the ancestral K-12 strain carries an inactive phnE allele, which prevents the transport of phosphonates. The switching in phnE occurred with a high frequency as a result of the deletion of an 8-bp repeated sequence. In a mixed culture starved for P(i) that contained the K-12 ancestral strain in majority, evolved strains grew through PhnE-dependent scavenging of probably organic phosphate esters (not phosphonates or P(i)) released by E. coli K-12 between days 1 and 3, before acetic acid excreted by E. coli K-12 reached toxic levels. The growth yield of phnE(+) strains in mixed culture was dramatically enhanced by mutations that affect glucose metabolism, such as an rpoS mutation inactivating the alternative sigma factor RpoS. The long-term viability of evolved populations was generally higher when the ancestral strain carried an inactive rather than an active phnE allele, which indicates that cross-feeding of phosphorylated products as a result of the phnE polymorphism may be essential for the spread of mutants which eventually help populations to survive under P(i) starvation conditions.     

红托竹荪菌种快速分离培养基优化

通过对红托竹荪快速分离培养基优化,提高红托竹荪菌种分离与评价效率。采用响应面分析法,以菌种生长速度为响应值拟合二次多元回归方程,确定培养基配方;测定优化培养基与PDA对照培养基菌丝生长速度和菌丝直径,以菌丝形态、锁状联合和菌落形态等指标评价优化培养基;测定优化培养基与PDA培养基培养菌丝在木屑培养基中菌丝生长速度,验证应用效果。通过试验,筛选出快速分离培养基配方为葡萄糖20.71 g/L、全麦粉8.36 g/L、玉米粉8.07 g/L、琼脂粉18.00 g/L、木屑水1.06 L。快速分离培养基与PDA培养基对比,培养的菌落直径平均增加66.25%,快速分离培养基菌丝日平均生长速度增加33.33%,木屑培养基菌丝日平均生长速度增加44.22%。由于优化培养基中含有淀粉、纤维素等有效成分,其刺激了菌种分泌淀粉酶、纤维素酶等,维持了胞外酶系的完整性。还可根据菌丝培养基过程形成的透明圈大小判定菌种胞外酶产生能力,达到快速评价菌种质量,保障菌种质量的目的。     

Isolation and Cultural Behavior of Pollen Tube Subprotoplasts in,Antirrhinum majus L.

Large numbers of subprotoplasts were isolated enzymatically from pollen tubes of Antirrhinum majus L. When these subI)rotoplasts, either nucleate or enucleate, were cultured in D2 liquid eulture medium, each formed a thick cell wall and germinated a pollen tube like strueture which also deposited a thick wall, except at the tip of the tube. Tube growth was accomparied by a continuous movement of the mass of cell inelusion in this tube to the tip. Rupture of the naked tip oeeurred within one to six days releasing the mass of cell inelusion in the tube into the culture medium. The faet that both nucleate and enneleate subprotoplasts show the same cultural behavior eharaeteristie of the gene expression of a normal pollen tube demonstrates the presence of presynthesized mRNA in the germinated tubes.     

Interaction of Bacteriophage Infection and Low Penicillin Concentrations on the Performance of Yogurt Cultures

Bacteriophage infection of a mixed-strain Streptococcus thermophilus culture, one strain of which is phage sensitive and the other phage resistant, may induce lysis of both strains. Experiments were carried out with three different phage-resistant strains. One such strain lysed in penicillin-free growth medium and another needed penicillin G (0.005 IU/ml) for lysis, while the third strain continued to grow in the presence of this concentration of antibiotic. Growth of the latter strain was inhibited when the medium contained a relatively high concentration of phage lysin. The different penicillin concentrations required to induce “lysis from without” of these phage-resistant strains correlated with their individual sensitivities to the antibiotic. The apparent relationship between the sensitivities of these strains to penicillin and to phage lysin could be explained by a difference in the degree of polymerization of the cell wall peptidoglycan.     

CRISPR/Cas9介导的高产谷胱甘肽原养型酵母工程菌的构建

谷胱甘肽(Glutathione,GSH)是具有多种生理功能的非蛋白质类巯基化合物,已广泛应用于药品、食品等行业,且市场需求量逐年增加。遗传工程育种是提高细胞内GSH含量的重要策略,但在遗传操作过程中使用到的营养缺陷型遗传标记可能会影响菌株的正常生长,且不利于高密度发酵的进行。为回复工程菌株的营养缺陷型,利用g RNA转录表达框和靶基因同源DNA片段直接共转化酵母细胞,由细胞内表达的Ⅱ型CRISPR/Cas9(Clustered regularly interspaced short palindromic repeats(CRISPR)-Cas9)介导的基因组编辑技术将营养缺陷型GSH工程菌株W303-1b/FGP回复为原养型菌株。结果显示,与营养缺陷型菌株相比,原养型菌株生长周期缩短,且可以利用简单的合成培养基进行培养,方便菌株的大规模培养。     

Fermentation performance of engineered and evolved xylose-fermenting Saccharomyces cerevisiae strains

Lignocellulose hydrolysate is an abundant substrate for bioethanol production. The ideal microorganism for such a fermentation process should combine rapid and efficient conversion of the available carbon sources to ethanol with high tolerance to ethanol and to inhibitory components in the hydrolysate. A particular biological problem are the pentoses, which are not naturally metabolized by the main industrial ethanol producer Saccharomyces cerevisiae. Several recombinant, mutated, and evolved xylose fermenting S. cerevisiae strains have been developed recently. We compare here the fermentation performance and robustness of eight recombinant strains and two evolved populations on glucose/xylose mixtures in defined and lignocellulose hydrolysate-containing medium. Generally, the polyploid industrial strains depleted xylose faster and were more resistant to the hydrolysate than the laboratory strains. The industrial strains accumulated, however, up to 30% more xylitol and therefore produced less ethanol than the haploid strains. The three most attractive strains were the mutated and selected, extremely rapid xylose consumer TMB3400, the evolved C5 strain with the highest achieved ethanol titer, and the engineered industrial F12 strain with by far the highest robustness to the lignocellulosic hydrolysate.     

Changes in the properties of Bacillus thuringiensis after prolonged culture in a rich medium

Aim:  To investigate the effect of repeated culture in a rich medium on certain genetic, metabolic, pathogenic and structural characteristics of fresh isolates of Bacillus thuringiensis.
Methods and Results:  Four strains of B. thuringiensis , which had been isolated in vegetative form from leaf surfaces, were grown for 500 generations in batch culture in a rich medium. One of the strains, S4g, differed from the parent in the following respects: greater cell width; changed plasmid profile; complete loss of ability to produce δ-endotoxins; loss of ability to produce β-exotoxin and disruption of vip 3 gene; radically different fatty acid composition; and altered metabolic activity. Two of the other evolved strains (S1g and S6g) showed differences in fatty acid profiles compared with the parents. Genetic finger-printing showed that there were also mutations in the cry genes of two of the evolved strains (S1g and S2g). The δ -endotoxins of strain S6g were significantly less toxic to the larvae of Pieris brassica compared with those of the parent and it also differed in the plasmid content.
Conclusion:  Radical and unpredictable changes can occur in fresh isolates of B. thuringiensis when subjected to growth in the laboratory.
Significance and Impact of the Study:  This is the first analysis of a Gram positive and biotechnologically significant bacterium after repeated laboratory culture. It is of great relevance to the biotechnological exploitation of B. thuringiensis that prolonged growth of environmental isolates on laboratory culture media can have profound effects on their structure, genome and virulence determinants.     

Fermentation products, amino acid utilization, maintenance energies and growth yields for the fibrillar Streptococcus salivarius HB and a non-fibrillar mutant HB-B grown in continuous culture under glucose limitation

The fibrillar strain Streptococcus salivarius HB and a non-fibrillar mutant, strain HB-B, were grown in a defined medium under glucose limitation in a chemostat. Fermentation balances were produced for both strains in batch culture and at growth rates between 0.1/h and 1.1/h. In batch culture both strains fermented glucose to lactate, but in continuous culture glucose was fermented to formate, acetate and ethanol with increasing amounts of lactate as the growth rate was increased. Lactate never became the major fermentation product even at the highest growth rate. Amino acid analysis showed that only lysine was more than 50% utilized, while proline and tyrosine showed net production. The non-fibrillar strain HB-B showed, in general, a reduced utilization of amino acids compared with the fibrillar strain HB. Calculated growth yields and maintenance energies for the two strains showed that there was a reduction in the true growth yield and the maintenance energy coefficient of the non-fibrillar strain HB-B when compared with the fibrillar strain HB. The increase in the maintenance energy of the fibrillar strain HB (1.382 mmol/g/h) when compared with the non-fibrillar strain HB-B (0.546 mmol/g/h) of 153% is proposed to be the energy required for the maintenance of the fibrillar surface of the cell.     

Fermentation products, amino acid utilization, maintenance energies and growth yields for the fibrillar Streptococcus salivarius HB and a non-fibrillar mutant HB-B grown in continuous culture under glucose limitation

The fibrillar strain Streptococcus salivarius HB and a non-fibrillar mutant, strain HB-B, were grown in a defined medium under glucose limitation in a chemostat. Fermentation balances were produced for both strains in batch culture and at growth rates between 0.1/h and 1.1/h. In batch culture both strains fermented glucose to lactate, but in continuous culture glucose was fermented to formate, acetate and ethanol with increasing amounts of lactate as the growth rate was increased. Lactate never became the major fermentation product even at the highest growth rate. Amino acid analysis showed that only lysine was more than 50% utilized, while proline and tyrosine showed net production. The non-fibrillar strain HB-B showed, in general, a reduced utilization of amino acids compared with the fibrillar strain HB. Calculated growth yields and maintenance energies for the two strains showed that there was a reduction in the true growth yield and the maintenance energy coefficient of the non-fibrillar strain HB-B when compared with the fibrillar strain HB. The increase in the maintenance energy of the fibrillar strain HB (1.382 mmol/g/h) when compared with the non-fibrillar strain HB-B (0.546 mmol/g/h) of 153% is proposed to be the energy required for the maintenance of the fibrillar surface of the cell.     

l-Methionine, a Precursor of Trace Methane in Some Proteolytic Clostridia

The in vivo formation of methane and of several S-methyl volatile compounds from the terminal S-methyl group of l-methionine is reported for growing cultures of four Clostridium strains (C. hastiforme, C. histolyticum, C. subterminale, and Clostridium sp. strain DSM 1786). After growth in 5 ml of unamended medium, C. hastiforme formed the highest amount of methane (408 nmol per tube in the headspace). When the culture medium was amended with 100 mM l-[S-methyl-H(3)]methionine, the four strains formed [H(3)]methane (proportion in the methane peak, >85%) as well as methanethiol, dimethyl disulfide, dimethyl trisulfide, and S-methyl thioacetate labeled on the methyl moiety. Methanethiol is also a precursor of methane for Clostridium sp. strain DSM 1786. The trace methane formation observed for these four proteolytic, nonglucidolytic Clostridium strains can be of ecological interest, particularly in aquatic sediments and in the gastrointestinal tract of humans and animals. It can explain in part the trace methane formation which cannot be ascribed to methanogens sensu stricto.     

Identification of genome-scale metabolic network models using experimentally measured flux profiles

Genome-scale metabolic network models can be reconstructed for well-characterized organisms using genomic annotation and literature information. However, there are many instances in which model predictions of metabolic fluxes are not entirely consistent with experimental data, indicating that the reactions in the model do not match the active reactions in the in vivo system. We introduce a method for determining the active reactions in a genome-scale metabolic network based on a limited number of experimentally measured fluxes. This method, called optimal metabolic network identification (OMNI), allows efficient identification of the set of reactions that results in the best agreement between in silico predicted and experimentally measured flux distributions. We applied the method to intracellular flux data for evolved Escherichia coli mutant strains with lower than predicted growth rates in order to identify reactions that act as flux bottlenecks in these strains. The expression of the genes corresponding to these bottleneck reactions was often found to be downregulated in the evolved strains relative to the wild-type strain. We also demonstrate the ability of the OMNI method to diagnose problems in E. coli strains engineered for metabolite overproduction that have not reached their predicted production potential. The OMNI method applied to flux data for evolved strains can be used to provide insights into mechanisms that limit the ability of microbial strains to evolve towards their predicted optimal growth phenotypes. When applied to industrial production strains, the OMNI method can also be used to suggest metabolic engineering strategies to improve byproduct secretion. In addition to these applications, the method should prove to be useful in general for reconstructing metabolic networks of ill-characterized microbial organisms based on limited amounts of experimental data.     

Experimental evolution of a facultative thermophile from a mesophilic ancestor

Experimental evolution via continuous culture is a powerful approach to the alteration of complex phenotypes, such as optimal/maximal growth temperatures. The benefit of this approach is that phenotypic selection is tied to growth rate, allowing the production of optimized strains. Herein, we demonstrate the use of a recently described long-term culture apparatus called the Evolugator for the generation of a thermophilic descendant from a mesophilic ancestor (Escherichia coli MG1655). In addition, we used whole-genome sequencing of sequentially isolated strains throughout the thermal adaptation process to characterize the evolutionary history of the resultant genotype, identifying 31 genetic alterations that may contribute to thermotolerance, although some of these mutations may be adaptive for off-target environmental parameters, such as rich medium. We undertook preliminary phenotypic analysis of mutations identified in the glpF and fabA genes. Deletion of glpF in a mesophilic wild-type background conferred significantly improved growth rates in the 43-to-48°C temperature range and altered optimal growth temperature from 37°C to 43°C. In addition, transforming our evolved thermotolerant strain (EVG1064) with a wild-type allele of glpF reduced fitness at high temperatures. On the other hand, the mutation in fabA predictably increased the degree of saturation in membrane lipids, which is a known adaptation to elevated temperature. However, transforming EVG1064 with a wild-type fabA allele had only modest effects on fitness at intermediate temperatures. The Evolugator is fully automated and demonstrates the potential to accelerate the selection for complex traits by experimental evolution and significantly decrease development time for new industrial strains.     

Stability of plasmid-bearing microorganisms in batch and continuous cultures

The stability of five microbial strains bearing a domestic and/or exotic plasmid was investigated in continuous culture to obtain basic information on the fate of genetically engineered microorganisms released in the natural environment.The three strains with an exotic plasmid were constructed by the conjugal or mobilized transfer of conjugative plasmid R100-1 and non-conjugative plasmid RSF2124. Plasmid loss occurred only at the declining growth phase of batch culture of the transconjugants; the ratio of plasmid-free cells was 40–50% at the end of the culture, independent of the strains, whereas the plasmid in the native host cells was maintained at almost 100% of stability.In continuous culture of the transconjugant cells, the population ratio of plasmid-free cells at the pseudo-steady state was between 5–80% depending on the strain. The plasmid-bearing cells were not washed out of the continuous fermentor for 43 generations but maintained their quasi-stable concentration with some degree of oscillation. Simultaneous loss and retransfer of the plasmid from and to its host cells is suggested for the explanation.     

The growth of mycobacteria in liquid medium is influenced by the dimension of glass wall in contact with the medium

The growth of the type strain of Mycobacterium aurum was compared between flask and tube, both of which contained the same concentration of bacteria in synthetic media and had the same air-contact dimension but had different dimensions of the glass wall of vessels contacting the medium. Much better growth occurred in the flask, which had a smaller dimension of the glass wall contacting the medium, than in the tube, which had a larger dimension. The finding shows that the growth of bacteria is influenced by the dimension of the glass wall of vessels. It was considered that a high chance of the attack shock for bacteria given by the Brownian movement lowers the multiplication of bacteria.     

Experimental Evolution of a Trypanosome Parasite of Bumblebees and its Implications for Infection Success and Host Immune Response

Selection on basic growth properties of parasites may have many consequences for parasite traits, infection outcome, or host responses to infection. It is known that genotypes (strains) of the trypanosome parasite of bumblebees Crithidia bombi vary widely in their growth rates in their natural host, Bombus terrestris, as well as when cultured in medium. To test for changes in growth rates and their consequences, we here experimentally evolved six strains of C. bombi for fast and slow growth under controlled conditions in culture medium. Subsequently, we infected the evolved lines in live host and found that lines selected for slow growth attained higher infection intensity in the live bumblebee than those evolved for fast growth, whilst the immune response of the host was the same to both kinds of lines. These results fit the expectation that attenuation through rapid adaptation to a different environment, the culture medium, makes the parasite less successful in its next host. Selection for fast growth therefore does not necessarily lead to higher parasite success or more transmission. Hence, insect trypanosome pathogens can be attenuated by experimental evolution in the culture; this could inform important aspects of host-parasite evolution and perhaps vaccine development.