Streptococcus thermophilus, an emerging and promising tool for heterologous expression: Advantages and future trends

Active induction: a promising strategy for enhancing the bioactivity of lactic acid bacteria

Lactic acid bacteria (LAB), as key probiotic, play crucial roles in maintaining human health. However, their survival and functionality in diverse habitats depend on their ability to sense and respond to environmental stresses. Notably, active induction has emerged as a promising strategy for regulating the biological activity of LAB, potentially enhancing their health benefits. Therefore, this review summarizes the beneficial effects of active induction, including acid, bile, oxidation, ethanol, heat, cold, and radiation induction on the functional activities of LAB. In addition, omics methods, in silico analysis, and gene editing technologies have greatly facilitated the profound exploration of the stress regulatory network in LAB, thereby aiding the identification of active components and stress adaptors. Through these advancements, LAB provide health benefits by regulating stress-related genes and proteins, as well as inducing bioactive metabolite production. As a result, they could enhance stress tolerance, cross-protection, intestinal colonization, adhesion properties, and provide antialcohol and liver protection in vitro or in vivo. This study highlights the potential of active induction strategies in enhancing the functional role of LAB in food applications.

Use of Rgg quorum-sensing machinery to create an innovative recombinant protein expression system in Streptococcus thermophilus

Streptococcus thermophilus holds promise as a chassis for producing and secreting heterologous proteins. Used for thousands of years to ferment milk, this species has generally recognized as safe (GRAS) status in the USA and qualified presumption of safety (QPS) status in Europe. In addition, it can be easily genetically modified thanks to its natural competence, and it secretes very few endogenous proteins, which means less downstream processing is needed to purify target proteins, reducing costs. Extracellular degradation of heterologous proteins can be eliminated by introducing mutations that inactivate the genes encoding the bacterium's three major surface proteases. Here, we constructed an inducible expression system that utilizes a peptide pheromone (SHP1358) and a transcriptional regulator (Rgg1358) involved in quorum-sensing regulation. We explored the functionality of a complete version of the system, in which the inducer is produced by the bacterium itself, by synthesizing a luciferase reporter protein. This complete version was assessed with bacteria grown in a chemically defined medium but also in vivo, in the faeces of germ-free mice. We also tested an incomplete version, in which the inducer had to be added to the culture medium, by synthesizing luciferase and a secreted form of elafin, a human protein with therapeutic properties. Our results show that, in our system, protein production can be modulated by employing different concentrations of the SHP1358 inducer or other SHPs with closed amino acid sequences. We also constructed a genetic background in which all system leakiness was eliminated. In conclusion, with this new inducible expression system, we have added to the set of tools currently used to produce secreted proteins in S. thermophilus, whose myriad applications include the delivery of therapeutic peptides or proteins.

Repurposing endogenous type II CRISPR-Cas9 system for genome editing in Streptococcus thermophilus

Streptococcus thermophilus has been extensively used in industrial milk fermentation. However, lack of efficient genetic manipulation approaches greatly hampered the industrial application of this species. Here, we repurposed the endogenous CRISPR1 and CRISPR3 systems, both belong to type II-A CRISPR-Cas9, by delivering a self-targeting CRISPR array with DNA repair template into S. thermophilus LMD-9. We achieved 785-bp deletion in lacZ gene by repurposing CRISPR1 and CRISPR3 systems with efficiencies of 35% and 59%, respectively, when 1-kb DNA repair template was provided. While providing with 1.5-kb repair template, the editing efficiency for deletion in lacZ gene reached 90% using CRISPR3 systems. Diverse editing outcomes encompassing a stop code insertion and single nucleotide variation within lacZ, as well as a 234-bp DNA fragment insertion upstream of ster_0903, were generated with high efficiencies of 75%-100% using the CRISPR3 system. Harnessing the customized endogenous CRISPR3 system to target six genes of eps gene cluster, we obtained six single-gene knockout mutants with efficiencies of 29%-80%, and proved that the epsA, epsE, and epsG were the key genes affecting exopolysaccharides biosynthesis in S. thermophilus LMD-9. Altogether, repurposing the native type II-A CRISPR-Cas9 can be served as a toolkit for precise genome engineering in S. thermophilus for biotechnological applications.

The intricate symbiotic relationship between lactic acid bacterial starters in the milk fermentation ecosystem

Fermentation is one of the most effective methods of food preservation. Since ancient times, food has been fermented using lactic acid bacteria (LAB). Fermented milk is a very intricate fermentation ecosystem, and the microbial metabolism of fermented milk largely determines its metabolic properties. The two most frequently used dairy starter strains are Streptococcus thermophilus (S. thermophilus) and Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus). To enhance both the culture growth rate and the flavor and quality of the fermented milk, it has long been customary to combine S. thermophilus and L. bulgaricus in milk fermentation due to their mutually beneficial and symbiotic relationship. On the one hand, the symbiotic relationship is reflected by the nutrient co-dependence of the two microbes at the metabolic level. On the other hand, more complex interaction mechanisms, such as quorum sensing between cells, are involved. This review summarizes the application of LAB in fermented dairy products and discusses the symbiotic mechanisms and interactions of milk LAB starter strains from the perspective of nutrient supply and intra- and interspecific quorum sensing. This review provides updated information and knowledge on microbial interactions in a fermented milk ecosystem.

Development of a Tetracycline-Inducible System for Conditional Gene Expression in Lactococcus lactis and Streptococcus thermophilus

Inducible gene expression systems are invaluable tools for the functional characterization of genes and in the construction of protein overexpression hosts. Controllable expression is especially important for the study of essential and toxic genes or genes where the level of expression tightly influences their cellular effect. Here, we implemented the well-characterized tetracycline-inducible expression system in two industrially important lactic acid bacteria, Lactococcus lactis and Streptococcus thermophilus. Using a fluorescent reporter gene, we show that optimization of the repression level is necessary for efficient induction using anhydrotetracycline in both organisms. Random mutagenesis in the ribosome binding site of the tetracycline repressor TetR in Lactococcus lactis indicated that altering the expression levels of TetR was necessary for efficient inducible expression of the reporter gene. Through this approach, we achieved plasmid-based, inducer-responsive, and tight gene expression in Lactococcus lactis. We then verified the functionality of the optimized inducible expression system in Streptococcus thermophilus following its chromosomal integration using a markerless mutagenesis approach and a novel DNA fragment assembly tool presented herein. This inducible expression system holds several advantages over other described systems in lactic acid bacteria, although more efficient techniques for genetic engineering are still needed to realize these advantages in industrially relevant species, such as S. thermophilus. Our work expands the molecular toolbox of these bacteria, which can accelerate future physiological studies. IMPORTANCE Lactococcus lactis and Streptococcus thermophilus are two industrially important lactic acid bacteria globally used in dairy fermentations and, therefore, are of considerable commercial interest to the food industry. Moreover, due to their general history of safe usage, these microorganisms are increasingly being explored as hosts for the production of heterologous proteins and various chemicals. Development of molecular tools in the form of inducible expression systems and mutagenesis techniques facilitates their in-depth physiological characterization as well as their exploitation in biotechnological applications.

The effect of glutathione biosynthesis of Streptococcus thermophilus ST-1 on cocultured Lactobacillus delbrueckii ssp. bulgaricus ATCC11842

Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus are the main species used for yogurt preparation. Glutathione (GSH) can be synthesized by S. thermophilus and plays a crucial role in combating environmental stress. However, the effect of GSH biosynthesis by S. thermophilus on cocultured L. delbrueckii ssp. bulgaricus is still unknown. In this study, a mutant S. thermophilus ΔgshF was constructed by deleting the GSH synthase. The wild strain S. thermophilus ST-1 and ΔgshF mutants were cocultured with L. delbrueckii ssp. bulgaricus ATCC11842 by using Transwell chambers (Guangzhou Shuopu Biotechnology Co., Ltd.), respectively. It was proven that the GSH synthesized by S. thermophilus ST-1 could be absorbed and used by L. delbrueckii ssp. bulgaricus ATCC11842, and promote growth ability and stress tolerance of L. delbrueckii ssp. bulgaricus ATCC11842. The biomass of L. delbrueckii ssp. bulgaricus ATCC11842 cocultured with S. thermophilus ST-1 or ΔgshF (adding exogenous GSH) increased by 1.8 and 1.4 times compared with the biomass of L. delbrueckii ssp. bulgaricus ATCC11842 cocultured with S. thermophilus ΔgshF. Meanwhile, after H₂O₂ and low-temperature treatments, the bacterial viability of L. delbrueckii ssp. bulgaricus cocultured with S. thermophilus ΔgshF, with or without GSH, was decreased by 41 and 15% compared with that of L. delbrueckii ssp. bulgaricus cocultured with S. thermophilus ST-1. Furthermore, transcriptome analysis showed that the expression levels of genes involved in purine nucleotide and pyrimidine nucleotide metabolism in L. delbrueckii ssp. bulgaricus ATCC11842 were at least 3 times increased when cocultured with S. thermophilus (fold change > 3.0). Moreover, compared with the mutant strain ΔgshF, the wild-type strain ST-1 could shorten the fermented curd time by 5.3 hours during yogurt preparation. These results indicated that the GSH synthesized by S. thermophilus during cocultivation effectively enhanced the activity of L. delbrueckii ssp. bulgaricus and significantly improved the quality of fermented milk.

A food-grade vector for Streptococcus thermophilus based on the α-complementation of β-galactosidase

Streptococcus thermophilus is a common yogurt starter that consumes lactose as its primary carbon source. The enzyme β-galactosidase is essential for the lactose metabolism and the growth of this species. Streptococcus thermophilus appears to be a promising cell factory. Food-grade vectors have advantages in heterologous protein expression. This study aimed to determine whether the β-galactosidase of S. thermophilus has the α-complementary characteristic and to develop a novel food-grade vector based on this phenomenon. The N-terminal 7 to 36 AA residues of the β-galactosidase in S. thermophilus were deleted. The obtained mutant S. thermophilus Δα lost β-galactosidase activity and growth ability in the lactose medium. Subsequently, plasmids expressing α-fragments with different lengths of 1 to 36 (Sα1), 1 to 53 (Sα2), and 1 to 88 (Sα3) AA were constructed and transformed into S. thermophilus Δα. Recombinant S. thermophilus Δα expressing Sα2 or Sα3 recovered the ability to grow in the lactose medium, and their β-galactosidase activity accounted for 24.5% or 11.5% of the wild strain, respectively. These results indicated that the α-complementation system of β-galactosidase existed in S. thermophilus. Based on the characteristic, a food-grade vector pSEα was constructed. Except for Sα2, vector pSEα expressed the α-donor derived from E. coli β-galactosidase. This facilitated the construction of recombinant plasmids in E. coli DH5α and thus improved the transformation efficiency of S. thermophilus. Green fluorescent protein as a reporter protein could be highly expressed in S. thermophilus using this vector. As a result, pSEα is an efficient and safe vector for S. thermophilus with potential food applications.

Three Distinct Proteases Are Responsible for Overall Cell Surface Proteolysis in Streptococcus thermophilus

The lactic acid bacterium Streptococcus thermophilus was believed to display only two distinct proteases at the cell surface, namely, the cell envelope protease PrtS and the housekeeping protease HtrA. Using peptidomics, we demonstrate here the existence of an additional active cell surface protease, which shares significant homology with the SepM protease of Streptococcus mutans. Although all three proteases-PrtS, HtrA, and SepM-are involved in the turnover of surface proteins, they demonstrate distinct substrate specificities. In particular, SepM cleaves proteins involved in cell wall metabolism and cell elongation, and its inactivation has consequences for cell morphology. When all three proteases are inactivated, the residual cell-surface proteolysis of S. thermophilus is approximately 5% of that of the wild-type strain. IMPORTANCE Streptococcus thermophilus is a lactic acid bacterium used widely as a starter in the dairy industry. Due to its "generally recognized as safe" status and its weak cell surface proteolytic activity, it is also considered a potential bacterial vector for heterologous protein production. Our identification of a new cell surface protease made it possible to construct a mutant strain with a 95% reduction in surface proteolysis, which could be useful in numerous biotechnological applications.

Genetic tools for the development of recombinant lactic acid bacteria

Lactic acid bacteria (LAB) are a phylogenetically diverse group with the ability to convert soluble carbohydrates into lactic acid. Many LAB have a long history of safe use in fermented foods and are recognized as food-grade microorganisms. LAB are also natural inhabitants of the human intestinal tract and have beneficial effects on health. Considering these properties, LAB have potential applications as biotherapeutic vehicles to delivery cytokines, antigens and other medicinal molecules. In this review, we summarize the development of, and advances in, genome manipulation techniques for engineering LAB and the expected future development of such genetic tools. These methods are crucial for us to maximize the value of LAB. We also discuss applications of the genome-editing tools in enhancing probiotic characteristics and therapeutic functionalities of LAB.

Suppressive effects of Streptococcus thermophilus KLDS 3.1003 on some foodborne pathogens revealed through in vitro, in vivo and genomic insights

Foodborne diseases (FBDs) remain a persistent global challenge and recent research efforts suggest that lactic acid bacteria (LAB) strains can contribute towards their prevention and treatment. This study investigates the genetic properties of Streptococcus thermophilus KLDS 3.1003 as a potential probiotic and health-promoting LAB strain as well as its in vitro and in vivo activities against two foodborne pathogens. In vitro, its antimicrobial activities and tolerance levels in simulated bile salts and acids were determined. The cytotoxic effects of the LAB strain in RAW264.7 cells were also evaluated. For in vivo evaluation, 24 BALB/c mice were orally administered control and trial diets for 14 days. Genomic analyses of this strain's bacteriocin configuration, stress response system and multidrug resistance genes were annotated to validate in vitro and in vivo results. In vitro antimicrobial results show that the cells and CFS of S. thermophilus KLDS 3.1003 could inhibit both pathogens with the former being more effective (P < 0.05). In addition, its cell-free supernatant (CFS) could inhibit the growth of both pathogens, with catalase treatment having the highest effect against it. More so, after 3 h of incubation, survivability levels of S. thermophilus KLDS 3.1003 were significantly high (P < 0.05). LPS-induced RAW264.7 cell activities were also significantly reduced by 108-109 CFU mL-1 of S. thermophilus KLDS. In vivo, significant weight losses were inhibited in the TSTEC group compared to the TSTSA group (P < 0.05). Moreover, pathogen-disrupted blood biochemical parameters like HDL, LDL, TP, TG, AST, ALT and some minerals were restored in the respective prevention groups (TSTEC and TSTSA). Genomic analyses showed that S. thermophilus KLDS 3.1003 has bacteriocin-coding peptides, which accounts for its antimicrobial abilities in vitro and in vivo. S. thermophilus KLDS 3.1003 is also endowed with intact genes for acid tolerance, salt-resistance, cold and heat shock responses and antioxidant activities, which are required to promote activities against the selected foodborne pathogens. This study showed that S. thermophilus KLDS 3.1003 has the genomic capacity to inhibit foodborne pathogens' growth in vitro and in vivo, thus qualifying it as a potential probiotic, antimicrobial and bio-therapeutic candidate.

In vitro Organic Acid Production and In Vivo Food Pathogen Suppression by Probiotic S. thermophilus and L. bulgaricus

Foodborne pathogens are a major source of morbidity and mortality worldwide. For this cause, exploring various effective ways of suppressing their spread is at the forefront of many research projects. The current study aims to investigate the in vitro organic acid production of S. thermophilus KLDS 3.1003 and L. bulgaricus KLDS 1.0207 strains, their in vivo suppression of and immuno-modulatory effects against E. coli ATCC 25922 and S. aureus ATCC 25923 pathogens. First, lactic and acetic acid production using three carbon sources – 1% glucose (control), 1% sucrose, and 1% fructo-oligosaccharides (FOS) – was determined by HPLC. For the in vivo section, a total of 40 BALB/c mice were purchased and divided into 10 treatment groups (control and nine treatments). Animals were given 1 week to acclimatize and then fed treatment diets for 14 days. Afterward, hematological (RBC, WBC, HB, PLT, Neutrophils, Eosinophils, Lymphocytes, and Monocytes) and histopathological analyses were carried out. All analyses were done in triplicate. Results show that lactic and acetic acid productions for both strains increased with supplementation and were highest after 1% FOS addition. Regardless of carbon source, L. bulgaricus KLDS 1.0207 produced higher (P < 0.05) amounts of lactic and acetic acids than S. thermophilus KLDS 3.1003. Also, generally better hematological parameters in probiotic groups than the control (P < 0.05) were observed. In some instances, mice in probiotic treatment groups had better immunity levels (lymphocytes, monocytes, neutrophils, eosinophils) than those in the control and pathogen groups. Histopathological studies showed that no anomalies were associated with S. thermophilus KLDS 3.1003 and L. bulgaricus KLDS 1.0207 administration. In conclusion, S. thermophilus KLDS 3.1003 and L. bulgaricus KLDS 1.0207 strains are not only probiotic candidates but can have therapeutic applications.

Optimized cultural conditions of functional yogurt for γ-aminobutyric acid augmentation using response surface methodology

Yogurt, a functional dairy food product, is an effective medium for delivering beneficial functional ingredients. One ingredient, γ-aminobutyric acid (GABA), has growing appeal in the development of functional foods for its potential in reducing the risk of diabetes, hypertension, and stress as a bioactive agent. However, the concentration of GABA in existing food products is remarkably low. We developed a functional yogurt rich in GABA using Streptococcus thermophilus fmb5. The GABA yield of yogurt was enhanced by optimization of culture conditions using single factor and response surface methods. The results showed that culture temperature, monosodium glutamate concentration, and culture time are the 3 main factors that affect GABA yield. The optimal culture conditions were determined as follows: 38.8°C for culture temperature, 20 g/L of monosodium glutamate, and 120 h of culture time. Under the above optimal conditions, the actual yield of GABA production was maximized at 9.66 g/L, which was 1.2 times or higher than that of from any single factor treatment. The GABA concentration, viable bacteria number, and water-holding capacity of GABA-rich yogurt were stable throughout the whole storage time. The results show that producing yogurt with Streptococcus thermophilus fmb5 and the optimized culture conditions will achieve high GABA concentrations that maximize health benefits to consumers.

Host recognition by lactic acid bacterial phages

Bacteriophage infection of lactic acid bacteria (LAB) is one of the most significant causes of inconsistencies in the manufacture of fermented foods, affecting production schedules and organoleptic properties of the final product. Consequently, LAB phages, and particularly those infecting Lactococcus lactis, have been the focus of intensive research efforts. During the past decade, multidisciplinary scientific approaches have uncovered molecular details on the exquisite process of how a lactococcal phage recognises and binds to its host. Such approaches have incorporated genomic/molecular analyses and their partnership with phage structural analysis and host cell wall biochemical studies are discussed in this review, which will also provide our views on future directions of this research field.