scholarly journals CRISPR/Cas9-Assisted Seamless Genome Editing in Lactobacillus plantarum and Its Application in N-Acetylglucosamine Production

2019 ◽  
Vol 85 (21) ◽  
Author(s):  
Ding Zhou ◽  
Zhennan Jiang ◽  
Qingxiao Pang ◽  
Yuan Zhu ◽  
Qian Wang ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Genome Editing ◽  
Lactobacillus Plantarum ◽  
Strain Engineering ◽  
Single Stranded Dna ◽  
Content Type ◽  
Recombination Efficiency ◽  
Double Stranded Dna ◽  
Exogenous Genes

ABSTRACT Lactobacillus plantarum is a potential starter and health-promoting probiotic bacterium. Effective, precise, and diverse genome editing of Lactobacillus plantarum without introducing exogenous genes or plasmids is of great importance. In this study, CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering was established in L. plantarum WCFS1 to seamlessly edit the genome, including gene knockouts, insertions, and point mutations. To optimize our editing method, phosphorothioate modification was used to improve the dsDNA insertion, and adenine-specific methyltransferase was used to improve the ssDNA recombination efficiency. These strategies were applied to engineer L. plantarum WCFS1 toward producing N-acetylglucosamine (GlcNAc). nagB was truncated to eliminate the reverse reaction of fructose-6-phosphate (F6P) to glucosamine 6-phosphate (GlcN-6P). Riboswitch replacement and point mutation in glmS1 were introduced to relieve feedback repression. The resulting strain produced 797.3 mg/liter GlcNAc without introducing exogenous genes or plasmids. This strategy may contribute to the available methods for precise and diverse genetic engineering in lactic acid bacteria and boost strain engineering for more applications. IMPORTANCE CRISPR/Cas9-assisted recombineering is restricted in lactic acid bacteria because of the lack of available antibiotics and vectors. In this study, a seamless genome editing method was carried out in Lactobacillus plantarum using CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering, and recombination efficiency was effectively improved by endogenous adenine-specific methyltransferase overexpression. L. plantarum WCFS1 produced 797.3 mg/liter N-acetylglucosamine (GlcNAc) through reinforcement of the GlcNAc pathway, without introducing exogenous genes or plasmids. This seamless editing strategy, combined with the potential exogenous GlcNAc-producing pathway, makes this strain an attractive candidate for industrial use in the future.

scholarly journals D-Alanyl-D-Alanine Ligase as a Broad-Host-Range Counterselection Marker in Vancomycin-Resistant Lactic Acid Bacteria

2018 ◽  
Vol 200 (13) ◽  
Author(s):  
Shenwei Zhang ◽  
Jee-Hwan Oh ◽  
Laura M. Alexander ◽  
Mustafa Özçam ◽  
Jan-Peter van Pijkeren
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Heterologous Expression ◽  
Genome Editing ◽  
Vancomycin Resistance ◽  
Dependent Manner ◽  
Content Type ◽  
Suicide Vector ◽  
Vancomycin Resistant ◽  
Dose Dependent

ABSTRACTThe peptidoglycan composition in lactic acid bacteria dictates vancomycin resistance. Vancomycin binds relatively poorly to peptidoglycan ending ind-alanyl-d-lactate and binds with high affinity to peptidoglycan ending ind-alanyl-d-alanine (d-Ala-d-Ala), which results in vancomycin resistance and sensitivity, respectively. The enzyme responsible for generating these peptidoglycan precursors is dipeptide ligase (Ddl). A single amino acid in the Ddl active site, phenylalanine or tyrosine, determines depsipeptide or dipeptide activity, respectively. Here, we established that heterologous expression of dipeptide ligase in vancomycin-resistant lactobacilli increases their sensitivity to vancomycin in a dose-dependent manner and overcomes the effects of the presence of a natived-Ala-d-Ala dipeptidase. We incorporated the dipeptide ligase gene on a suicide vector and demonstrated that it functions as a counterselection marker (CSM) in lactobacilli; vancomycin selection allows only those cells to grow in which the suicide vector has been lost. Subsequently, we developed a liquid-based approach to identify recombinants in only 5 days, which is approximately half the time required by conventional approaches. Phylogenetic analysis revealed that Ddl serves as a marker to predict vancomycin resistance and consequently indicated the broad applicability of the use of Ddl as a counterselection marker in the genusLactobacillus. Finally, our system represents the first “plug and play” counterselection system in lactic acid bacteria that does not require prior genome editing and/or synthetic medium.IMPORTANCEThe genusLactobacilluscontains more than 200 species, many of which are exploited in the food and biotechnology industries and in medicine. Prediction of intrinsic vancomycin resistance has thus far been limited to selectedLactobacillusspecies. Here, we show that heterologous expression of the enzyme Ddl (dipeptide ligase)—an essential enzyme involved in peptidoglycan synthesis—increases sensitivity to vancomycin in a dose-dependent manner. We exploited this to develop a counterselection marker for use in vancomycin-resistant lactobacilli, thereby expanding the poorly developed genome editing toolbox that is currently available for most strains. Also, we showed that Ddl is a phylogenetic marker that can be used to predict vancomycin resistance inLactobacillus; 81% ofLactobacillusspecies are intrinsically resistant to vancomycin, which makes our tool broadly applicable.

scholarly journals An Extracellular Serine/Threonine-Rich Protein from Lactobacillus plantarum NCIMB 8826 Is a Novel Aggregation-Promoting Factor with Affinity to Mucin

2013 ◽  
Vol 79 (19) ◽  
pp. 6059-6066 ◽  
Author(s):  
Arancha Hevia ◽  
Noelia Martínez ◽  
Víctor Ladero ◽  
Miguel A. Álvarez ◽  
Abelardo Margolles ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lactobacillus Plantarum ◽  
D1 Protein ◽  
Extracellular Proteins ◽  
Human Immune System ◽  
Content Type ◽  
Probiotic Lactic Acid Bacteria ◽  
Adhesion Role ◽  
Internal Fragment

ABSTRACTAutoaggregation in lactic acid bacteria is directly related to the production of certain extracellular proteins, notably, aggregation-promoting factors (APFs). Production of aggregation-promoting factors confers beneficial traits to probiotic-producing strains, contributing to their fitness for the intestinal environment. Furthermore, coaggregation with pathogens has been proposed to be a beneficial mechanism in probiotic lactic acid bacteria. This mechanism would limit attachment of the pathogen to the gut mucosa, favoring its removal by the human immune system. In the present paper, we have characterized a novel aggregation-promoting factor inLactobacillus plantarum. A mutant with a knockout of the D1 gene showed loss of its autoaggregative phenotype and a decreased ability to bind to mucin, indicating an adhesion role of this protein. In addition, heterologous production of the D1 protein or an internal fragment of the protein, characterized by its abundance in serine/threonine, strongly induced autoaggregation inLactococcus lactis. This result strongly suggested that this internal fragment is responsible for the bioactivity of D1 as an APF. To our knowledge, this is the first report on a gene coding for an aggregation-promoting factor inLb. plantarum.

scholarly journals Streamlined, recombinase-free genome editing with CRISPR-Cas9 inLactobacillus plantarumreveals barriers to efficient editing

2018 ◽  
Author(s):  
Ryan T. Leenay ◽  
Justin M. Vento ◽  
Malay Shah ◽  
Maria Elena Martino ◽  
François Leulier ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Genome Editing ◽  
Lactobacillus Plantarum ◽  
Point Mutation ◽  
Stop Codon ◽  
Different Strains ◽  
Unexpected Outcomes ◽  
Complete Deletion ◽  
Sequence Modification

ABSTRACTLactic-acid bacteria such asLactobacillus plantarumare commonly used for fermenting foods and as probiotics, where increasingly sophisticated genome-editing tools are currently being employed to elucidate and enhance these microbes’ beneficial properties. The most advanced tools to-date require heterologous single-stranded DNA recombinases to integrate short oligonucleotides followed by using CRISPR-Cas9 to eliminate cells harboring unedited sequences. Here, we show that encoding the recombineering template on a replicating plasmid allowed efficient genome editing with CRISPR-Cas9 in multipleL. plantarumstrains without a recombinase. This strategy accelerated the genome-editing pipeline and could efficiently introduce a stop codon inribB, silent mutations inackA, and a complete deletion oflacM. In contrast, oligo-mediated recombineering with CRISPR-Cas9 proved far less efficient in at least one instance. We also observed unexpected outcomes of our recombinase-free method, including an ~1.3-kb genomic deletion when targetingribBin one strain, and reversion of a point mutation in the recombineering template in another strain. Our method therefore can streamline targeted genome editing in different strains ofL. plantarum, although the best means of achieving efficient editing may vary based on the selected sequence modification, gene, and strain.

scholarly journals Bioluminescence Imaging Study of Spatial and Temporal Persistence of Lactobacillus plantarum and Lactococcus lactis in Living Mice

2012 ◽  
Vol 79 (4) ◽  
pp. 1086-1094 ◽  
Author(s):  
Catherine Daniel ◽  
Sabine Poiret ◽  
Véronique Dennin ◽  
Denise Boutillier ◽  
Bruno Pot
Keyword(s):  
Lactic Acid ◽  
Gastrointestinal Tract ◽  
Lactic Acid Bacteria ◽  
Lactobacillus Plantarum ◽  
Lactococcus Lactis ◽  
Bioluminescence Imaging ◽  
Ex Vivo ◽  
Mammalian Host ◽  
Content Type

ABSTRACTLactic acid bacteria, especially lactobacilli, are common inhabitants of the gastrointestinal tract of mammals, for which they have received considerable attention due to their putative health-promoting properties. In this study, we describe the development and application of luciferase-expressingLactobacillus plantarumandLactococcus lactisstrains for noninvasivein vivomonitoring in the digestive tract of mice. We report for the first time the functionalin vitroexpression inLactobacillus plantarumNCIMB8826 and inLactococcus lactisMG1363 of the click beetle luciferase (CBluc), as well asGaussiaand bacterial luciferases, using a combination of vectors, promoters, and codon-optimized genes. We demonstrate that a CBluc construction is the best-performing luciferase system for the noninvasivein vivodetection of lactic acid bacteria after oral administration. The persistence and viability of both strains was studied by bioluminescence imaging in anesthetized mice and in mouse feces.In vivobioluminescence imaging confirmed that after a single or multiple oral administrations,L. lactishas shorter survival times in the mouse gastrointestinal tract thanL. plantarum, and it also revealed the precise gut compartments where both strains persisted. The application of luciferase-labeled bacteria has significant potential to allow thein vivoandex vivostudy of the interactions of lactic acid bacteria with their mammalian host.

scholarly journals Immunogenic Properties of Lactobacillus plantarum Producing Surface-Displayed Mycobacterium tuberculosis Antigens

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
Katarzyna Kuczkowska ◽  
Charlotte R. Kleiveland ◽  
Rajna Minic ◽  
Lars F. Moen ◽  
Lise Øverland ◽  
...  
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Immune Responses ◽  
Lactobacillus Plantarum ◽  
Antigen Delivery ◽  
Bacille Calmette Guerin ◽  
Content Type ◽  
Fusion Antigen

ABSTRACT Tuberculosis (TB) remains among the most deadly diseases in the world. The only available vaccine against tuberculosis is the bacille Calmette-Guérin (BCG) vaccine, which does not ensure full protection in adults. There is a global urgency for the development of an effective vaccine for preventing disease transmission, and it requires novel approaches. We are exploring the use of lactic acid bacteria (LAB) as a vector for antigen delivery to mucosal sites. Here, we demonstrate the successful expression and surface display of a Mycobacterium tuberculosis fusion antigen (comprising Ag85B and ESAT-6, referred to as AgE6) on Lactobacillus plantarum. The AgE6 fusion antigen was targeted to the bacterial surface using two different anchors, a lipoprotein anchor directing the protein to the cell membrane and a covalent cell wall anchor. AgE6-producing L. plantarum strains using each of the two anchors induced antigen-specific proliferative responses in lymphocytes purified from TB-positive donors. Similarly, both strains induced immune responses in mice after nasal or oral immunization. The impact of the anchoring strategies was reflected in dissimilarities in the immune responses generated by the two L. plantarum strains in vivo. The present study comprises an initial step toward the development of L. plantarum as a vector for M. tuberculosis antigen delivery. IMPORTANCE This work presents the development of Lactobacillus plantarum as a candidate mucosal vaccine against tuberculosis. Tuberculosis remains one of the top infectious diseases worldwide, and the only available vaccine, bacille Calmette-Guérin (BCG), fails to protect adults and adolescents. Direct antigen delivery to mucosal sites is a promising strategy in tuberculosis vaccine development, and lactic acid bacteria potentially provide easy, safe, and low-cost delivery vehicles for mucosal immunization. We have engineered L. plantarum strains to produce a Mycobacterium tuberculosis fusion antigen and to anchor this antigen to the bacterial cell wall or to the cell membrane. The recombinant strains elicited proliferative antigen-specific T-cell responses in white blood cells from tuberculosis-positive humans and induced specific immune responses after nasal and oral administrations in mice.

scholarly journals Optimization of the Bioactivation of Isoflavones in Soymilk by Lactic Acid Bacteria

Processes ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 963
Author(s):  
Jon Kepa Izaguirre ◽  
Leire Barañano ◽  
Sonia Castañón ◽  
Itziar Alkorta ◽  
Luis M. Quirós ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lactobacillus Plantarum ◽  
Inoculum Size ◽  
Process Time ◽  
Medical Applications ◽  
Bacterial Strains ◽  
Food Industries ◽  
Glucosidase Activity ◽  
Interesting Candidate

Soybeans and soy-based products contain isoflavones which can be used for nutraceutical and medical applications. In soybeans and in unfermented soy foods, isoflavones are normally present as glycosides. Isoflavone glycosides can be enzymatically converted to isoflavone aglycones, thus releasing the sugar molecule. The effective absorption of isoflavones in humans requires the bioconversion of isoflavone glycosides to isoflavone aglycones through the activity of the enzyme β-glucosidase. The objective was to assess the capacity of 42 bacterial strains (belonging to Lactobacillus, Streptococcus and Enterococcus) to produce β-glucosidase activity. The strain that showed the highest β-glucosidase activity (Lactobacillus plantarum 128/2) was then used for the optimization of the bioconversion of genistin and daidzin present in commercial soymilk to their aglycone forms genistein and daidzein. The contribution of process parameters (temperature, inoculum size, time) to the efficiency of such bioactivation was tested. Lactobacillus plantarum 128/2 was able to completely bioactivate soymilk isoflavones under the following conditions: 25 °C temperature, 2% inoculum size and 48 h process time. These results confirm the suitability of lactic acid bacteria for the bioactivation of isoflavones present in soymilk and provide an interesting candidate (L. plantarum 182/2) for food industries to perform this transformation.

scholarly journals An Efficient, Rapid, and Recyclable System for CRISPR-Mediated Genome Editing in Candida albicans

mSphere ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Namkha Nguyen ◽  
Morgan M. F. Quail ◽  
Aaron D. Hernday
Keyword(s):  
Candida Albicans ◽  
Genome Editing ◽  
Fungal Pathogen ◽  
Gene Knockout ◽  
Strain Engineering ◽  
Molecular Genetic Analysis ◽  
Content Type ◽  
Highly Efficient ◽  
Discovery Research ◽  
Gene Knockouts

ABSTRACT Candida albicans is the most common fungal pathogen of humans. Historically, molecular genetic analysis of this important pathogen has been hampered by the lack of stable plasmids or meiotic cell division, limited selectable markers, and inefficient methods for generating gene knockouts. The recent development of clustered regularly interspaced short palindromic repeat(s) (CRISPR)-based tools for use with C. albicans has opened the door to more efficient genome editing; however, previously reported systems have specific limitations. We report the development of an optimized CRISPR-based genome editing system for use with C. albicans. Our system is highly efficient, does not require molecular cloning, does not leave permanent markers in the genome, and supports rapid, precise genome editing in C. albicans. We also demonstrate the utility of our system for generating two independent homozygous gene knockouts in a single transformation and present a method for generating homozygous wild-type gene addbacks at the native locus. Furthermore, each step of our protocol is compatible with high-throughput strain engineering approaches, thus opening the door to the generation of a complete C. albicans gene knockout library. IMPORTANCE Candida albicans is the major fungal pathogen of humans and is the subject of intense biomedical and discovery research. Until recently, the pace of research in this field has been hampered by the lack of efficient methods for genome editing. We report the development of a highly efficient and flexible genome editing system for use with C. albicans. This system improves upon previously published C. albicans CRISPR systems and enables rapid, precise genome editing without the use of permanent markers. This new tool kit promises to expedite the pace of research on this important fungal pathogen.

scholarly journals Probiotic Potential of a Novel Vitamin B2-Overproducing Lactobacillus plantarum Strain, HY7715, Isolated from Kimchi

2021 ◽  
Vol 11 (13) ◽  
pp. 5765
Author(s):  
Joo-Yun Kim ◽  
Eun-Jung Choi ◽  
Jae-Ho Lee ◽  
Myeong-Seok Yoo ◽  
Keon Heo ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Lactobacillus Plantarum ◽  
Probiotic Strain ◽  
Optimal Growth ◽  
Control Group ◽  
High Survival ◽  
Vitamin B2 ◽  
Riboflavin Deficiency

Vitamin B2, also known as riboflavin, is essential for maintaining human health. The purpose of this study was to isolate novel lactic acid bacteria that overproduce vitamin B2 and to validate their potential as probiotics. In this study, Lactobacillus plantarum HY7715 (HY7715) was selected among lactic acid bacteria isolated from Kimchi. HY7715 showed a very high riboflavin-producing ability compared to the control strain due to the high expression of ribA, ribB, ribC, ribH, and ribG genes. HY7715 produced 34.5 ± 2.41 mg/L of riboflavin for 24 h without consuming riboflavin in the medium under optimal growth conditions. It was able to produce riboflavin in an in vitro model of the intestinal environment. In addition, when riboflavin deficiency was induced in mice through nutritional restriction, higher levels of riboflavin were detected in plasma and urine in the HY7715 administration group than in the control group. HY7715 showed high survival rate in simulated gastrointestinal conditions and had antibiotic resistance below the cutoff MIC value suggested by the European Food Safety Authority; moreover, it did not cause hemolysis. In conclusion, HY7715 could be considered a beneficial probiotic strain for human and animal applications, suggesting that it could be a new alternative to address riboflavin deficiency.

scholarly journals Core Fluxome and Metafluxome of Lactic Acid Bacteria under Simulated Cocoa Pulp Fermentation Conditions

2013 ◽  
Vol 79 (18) ◽  
pp. 5670-5681 ◽  
Author(s):  
Philipp Adler ◽  
Christoph Josef Bolten ◽  
Katrin Dohnt ◽  
Carl Erik Hansen ◽  
Christoph Wittmann
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Starter Cultures ◽  
Superior Performance ◽  
Gas Chromatography Mass Spectrometry ◽  
Glycolytic Flux ◽  
Content Type ◽  
Phosphoketolase Pathway ◽  
Labeling Approach ◽  
Cocoa Fermentation

ABSTRACTIn the present work, simulated cocoa fermentation was investigated at the level of metabolic pathway fluxes (fluxome) of lactic acid bacteria (LAB), which are typically found in the microbial consortium known to convert nutrients from the cocoa pulp into organic acids. A comprehensive13C labeling approach allowed to quantify carbon fluxes during simulated cocoa fermentation by (i) parallel13C studies with [13C6]glucose, [1,2-13C2]glucose, and [13C6]fructose, respectively, (ii) gas chromatography-mass spectrometry (GC/MS) analysis of secreted acetate and lactate, (iii) stoichiometric profiling, and (iv) isotopomer modeling for flux calculation. The study of several strains ofL. fermentumandL. plantarumrevealed major differences in their fluxes. TheL. fermentumstrains channeled only a small amount (4 to 6%) of fructose into central metabolism, i.e., the phosphoketolase pathway, whereas onlyL. fermentumNCC 575 used fructose to form mannitol. In contrast,L. plantarumstrains exhibited a high glycolytic flux. All strains differed in acetate flux, which originated from fractions of citrate (25 to 80%) and corresponding amounts of glucose and fructose. Subsequent, metafluxome studies with consortia of differentL. fermentumandL. plantarumstrains indicated a dominant (96%) contribution ofL. fermentumNCC 575 to the overall flux in the microbial community, a scenario that was not observed for the other strains. This highlights the idea that individual LAB strains vary in their metabolic contribution to the overall fermentation process and opens up new routes toward streamlined starter cultures.L. fermentumNCC 575 might be one candidate due to its superior performance in flux activity.

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