A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures

The dairy fermentation industry relies on the activity of lactic acid bacteria in robust starter cultures to accomplish milk acidification. Maintenance of the composition of these starter cultures, whether defined or undefined, is essential to ensure consistent and high-quality fermentation end products. To date, limited information exists regarding the microbial composition of undefined starter culture systems. Here, we describe a culture-based analysis combined with a metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, we describe a qPCR-based genotype detection assay, which is capable of discerning nine distinct lactococcal genotypes to characterize these undefined starter cultures, and which can be applied to monitor compositional changes in an undefined starter culture during a fermentation.

IMPORTANCE

This study reports on the development of a combined culture-based analysis and metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, a novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes (based on lactococcal cell wall polysaccharide biosynthesis gene clusters), was used to monitor compositional changes in an undefined starter culture following phage attack. These analytical approaches facilitate a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important QC aspect due to the increasing demand for consistent and high-quality dairy products.

Development of a milk-based medium for the selection of urease-defective mutants of Streptococcus thermophilus

Streptococcus thermophilus strains are used in fermented dairy products for their capacity to metabolize lactose into lactic acid. The rate of lactic acid production in milk is of major economic importance, as rapid acidification prevents growth of undesirable microorganisms. It is also of paramount significance for aroma, texture and flavor of the end product. Besides achieving customer satisfaction, improvement of production rate and operational costs incite industrials into selecting fast acidifying strains. Another important trait of S. thermophilus influencing acidification is the urease, which catabolizes urea into ammonia and has a detrimental effect on acidification. Unfortunately, most of the S. thermophilus strains possess the urease, and the urease-negative ones are necessary for industrial applications. Urease activity is a widely distributed activity in S. thermophilus species, and urease-negative strains are rare. The later are however interesting from an industrial point of view, as they may give faster acidification in dairy applications, because lactic acid is not buffered by urea-derived ammonia. Nowadays, the efforts to improve the characteristics of strains for industrial applications are based on natural strategies such as random mutagenesis. This implies the need of a screening method that is efficient in terms of time and success. In this context, the aim of this study was the development of a new medium that allows selection of urease-defective mutants based on S. thermophilus colony morphology. Discrimination capacity of the new medium was verified using previously characterized urease-negative recombinant strains. The new milk-based medium, applied to industrial S. thermophilus strains subjected to UV mutagenesis, allowed the selection of 3 mutants, partially or completely defective in urease activity. Genetic characterization of urease-defective mutants highlighted the presence of nonsense or missense mutations in the ureA, ureC and ureG genes, thus supporting their phenotype. Evaluation of milk acidification revealed increased performance for one out of three urease-defective mutants compared to wild-type strains.

Optimizing HIV-1 protease production in Escherichia coli as fusion protein

Background

Human immunodeficiency virus (HIV) is the etiological agent in AIDS and related diseases. The aspartyl protease encoded by the 5' portion of the pol gene is responsible for proteolytic processing of the gag-pol polyprotein precursor to yield the mature capsid protein and the reverse transcriptase and integrase enzymes. The HIV protease (HIV-1Pr) is considered an attractive target for designing inhibitors which could be used to tackle AIDS and therefore it is still the object of a number of investigations.

Results

A recombinant human immunodeficiency virus type 1 protease (HIV-1Pr) was overexpressed in Escherichia coli cells as a fusion protein with bacterial periplasmic protein dithiol oxidase (DsbA) or glutathione S-transferase (GST), also containing a six-histidine tag sequence. Protein expression was optimized by designing a suitable HIV-1Pr cDNA (for E. coli expression and to avoid autoproteolysis) and by screening six different E. coli strains and five growth media. The best expression yields were achieved in E. coli BL21-Codon Plus(DE3)-RIL host and in TB or M9 medium to which 1% (w/v) glucose was added to minimize basal expression. Among the different parameters assayed, the presence of a buffer system (based on phosphate salts) and a growth temperature of 37°C after adding IPTG played the main role in enhancing protease expression (up to 10 mg of chimeric DsbA:HIV-1Pr/L fermentation broth). GST:HIVPr was in part (50%) produced as soluble protein while the overexpressed DsbA:HIV-1Pr chimeric protein largely accumulated in inclusion bodies as unprocessed fusion protein. A simple refolding procedure was developed on HiTrap Chelating column that yielded a refolded DsbA:HIV-1Pr with a > 80% recovery. Finally, enterokinase digestion of resolubilized DsbA:HIV-1Pr gave more than 2 mg of HIV-1Pr per liter of fermentation broth with a purity ≤ 80%, while PreScission protease cleavage of soluble GST:HIVPr yielded ~ 0.15 mg of pure HIV-1Pr per liter.

Conclusions

By using this optimized expression and purification procedure fairly large amounts of good-quality HIV-1Pr recombinant enzyme can be produced at the lab-scale and thus used for further biochemical studies.

Production of recombinant cholesterol oxidase containing covalently bound FAD in Escherichia coli

Background

Cholesterol oxidase is an alcohol dehydrogenase/oxidase flavoprotein that catalyzes the dehydrogenation of C(3)-OH of cholesterol. It has two major biotechnological applications, i.e. in the determination of serum (and food) cholesterol levels and as biocatalyst providing valuable intermediates for industrial steroid drug production. Cholesterol oxidases of type I are those containing the FAD cofactor tightly but not covalently bound to the protein moiety, whereas type II members contain covalently bound FAD. This is the first report on the over-expression in Escherichia coli of type II cholesterol oxidase from Brevibacterium sterolicum (BCO).

Results

Design of the plasmid construct encoding the mature BCO, optimization of medium composition and identification of the best cultivation/induction conditions for growing and expressing the active protein in recombinant E. coli cells, concurred to achieve a valuable improvement: BCO volumetric productivity was increased from ~500 up to ~25000 U/L and its crude extract specific activity from 0.5 up to 7.0 U/mg protein. Interestingly, under optimal expression conditions, nearly 55% of the soluble recombinant BCO is produced as covalently FAD bound form, whereas the protein containing non-covalently bound FAD is preferentially accumulated in insoluble inclusion bodies.

Conclusions

Comparison of our results with those published on non-covalent (type I) COs expressed in recombinant form (either in E. coli or Streptomyces spp.), shows that the fully active type II BCO can be produced in E. coli at valuable expression levels. The improved over-production of the FAD-bound cholesterol oxidase will support its development as a novel biotool to be exploited in biotechnological applications.