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Priyodip P, Balaji S. Characterization of a putative metal-dependent PTP-like phosphatase from Lactobacillus helveticus 2126. Int Microbiol 2024; 27:37-47. [PMID: 37365352 PMCID: PMC10830716 DOI: 10.1007/s10123-023-00390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 04/01/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023]
Abstract
To date, there are very limited reports on sequence analysis and structure-based molecular modeling of phosphatases produced by probiotic bacteria. Therefore, a novel protein tyrosine-like phosphatase was characterized from L. helveticus 2126 in this study. The purified bacterial phosphatase was subjected to mass spectrometric analysis, and the identity of constructed sequence was analyzed using peptide mass fingerprint. The 3-D structure of protein was elucidated using homology modeling, while its stability was assessed using Ramachandran plot, VERIFY 3D, and PROCHECK. The bacterium produced an extracellular phosphatase of zone diameter 15 ± 0.8 mm on screening medium within 24 h of incubation. This bacterial phosphatase was highly specific towards sodium phytate as it yielded the lowest Km value of 299.50 ± 4.95 μM compared to other phosphorylated substrates. The activity was effectively stimulated in the presence of zinc, magnesium, and manganese ions thereby showing its PTP-like behavior. The phosphatase showed a molecular mass of 43 kDa, and the corresponding M/Z ratio data yielded 46% query coverage to Bacillus subtilis (3QY7). This showed a 61.1% sequence similarity to Ligilactobacillus ruminis (WP_046923835.1). The final sequence construct based on these bacteria showed a conserved motif "HCHILPGIDD" in their active site. In addition, homology modeling showed a distorted Tim barrel structure with a trinuclear metal center. The final model after energy minimization showed 90.9% of the residues in the favorable region of Ramachandran's plot. This structural information can be used in genetic engineering for improving the overall stability and catalytic efficiency of probiotic bacterial phosphatases.
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Affiliation(s)
- Paul Priyodip
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India
| | - Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, -576104, Manipal, Karnataka, India.
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2
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Omori KK, Drucker CT, Okumura TLS, Carl NB, Dinn BT, Ly D, Sacapano KN, Tajii A, Owens CP. The structure of a Lactobacillus helveticus chlorogenic acid esterase and the dynamics of its insertion domain provide insights into substrate binding. FEBS Lett 2023; 597:2946-2962. [PMID: 37698360 DOI: 10.1002/1873-3468.14731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/31/2023] [Accepted: 08/20/2023] [Indexed: 09/13/2023]
Abstract
Chlorogenic acid esterases (ChlEs) are a useful class of enzymes that hydrolyze chlorogenic acid (CGA) into caffeic and quinic acids. ChlEs can break down CGA in foods to improve their sensory properties and release caffeic acid in the digestive system to improve the absorption of bioactive compounds. This work presents the structure, molecular dynamics, and biochemical characterization of a ChlE from Lactobacillus helveticus (Lh). Molecular dynamics simulations suggest that substrate access to the active site of LhChlE is modulated by two hairpin loops above the active site. Docking simulations and mutational analysis suggest that two residues within the loops, Gln145 and Lys164 , are important for CGA binding. Lys164 provides a slight substrate preference for CGA, whereas Gln145 is required for efficient turnover. This work is the first to examine the dynamics of a bacterial ChlE and provides insights on substrate binding preference and turnover in this type of enzyme.
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Affiliation(s)
- Kellie K Omori
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Charles T Drucker
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Tracie L S Okumura
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Nathaniel B Carl
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Brianna T Dinn
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Destiny Ly
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Kylie N Sacapano
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Allie Tajii
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Cedric P Owens
- Department of Chemistry and Biochemistry, Schmid College of Science and Technology, Chapman University, Orange, CA, USA
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3
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Wang X, Ma K, Zhang C, Ji F, Chen L, Zhang X, Mahsa GC, Azarpazhooh E, Ajami M, Rui X, Li W. The interaction among Kluyveromyces marxianus G-Y4, Lacticaseibacillus paracasei GL1, and Lactobacillus helveticus SNA12 and signaling molecule AI-2 participate in the formation of biofilm. Food Microbiol 2023; 116:104369. [PMID: 37689420 DOI: 10.1016/j.fm.2023.104369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 08/08/2023] [Accepted: 08/24/2023] [Indexed: 09/11/2023]
Abstract
In this study, two strains of lactic acid bacteria (Lacticaseibacillus paracasei GL1 and Lactobacillus helveticus SNA12) and one yeast strain of Kluyveromyces marxianus G-Y4 (G-Y4) isolated from Tibetan kefir grains were co-cultured. It was found that the addition of G-Y4 could not only promote the growth of lactic acid bacteria, but also increase the release of metabolites (lactic acid, ethanol, and amino nitrogen). Furthermore, the addition of live cells and cell-free fermentation supernatant (CFS) of G-Y4 could increase the ability of biofilm formation. Morever, the surface characteristics results showed that the addition of G-Y4 live cells could enhance the aggregation ability and hydrophobicity of LAB. Meanwhile, adding live cells and CFS of G-Y4 could promote the release of signaling molecule AI-2 and enhance the expression of the LuxS gene related to biofilm formation. In addition, Fourier-transform infrared spectroscopy and chemical composition analysis were used to investigate the composition of the biofilm, and the results indicated that the biofilm was mainly composed of a small amount of protein but it was rich in polysaccharides including glucose, galactose, and mannose with different ratios. Finally, the formation of biofilm could delay the decline of the number of viable bacteria in storage fermented milk.
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Affiliation(s)
- Xiaomeng Wang
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China; College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, 266404, PR China
| | - Kai Ma
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Changliang Zhang
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Feng Ji
- Jiangsu New-Bio Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China; Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu, 214400, PR China
| | - Lili Chen
- Xinyi Ziyuantian Biotechnology Development Co., Ltd, Xinyi, Jiangsu, 221400, PR China
| | - Xueliang Zhang
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Ghahvechi Chaeipeima Mahsa
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Elham Azarpazhooh
- Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Iran
| | - Marjan Ajami
- National Nutrition and Food Technology Research Institute, School of Nutrition Sciences and Food Technology, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Xin Rui
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Wei Li
- Sanya Institute of Nanjing Agricultural University, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China.
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Kido Y, Maeno S, Tanno H, Kichise Y, Shiwa Y, Endo A. Niche-specific adaptation of Lactobacillus helveticus strains isolated from malt whisky and dairy fermentations. Microb Genom 2021; 7:000560. [PMID: 33900907 PMCID: PMC8208680 DOI: 10.1099/mgen.0.000560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/15/2021] [Indexed: 01/24/2023] Open
Abstract
Lactobacillus helveticus is a well characterized lactobacillus for dairy fermentations that is also found in malt whisky fermentations. The two environments contain considerable differences related to microbial growth, including the presence of different growth inhibitors and nutrients. The present study characterized L. helveticus strains originating from dairy fermentations (called milk strains hereafter) and malt whisky fermentations (called whisky strains hereafter) by in vitro phenotypic tests and comparative genomics. The whisky strains can tolerate ethanol more than the milk strains, whereas the milk strains can tolerate lysozyme and lactoferrin more than the whisky strains. Several plant-origin carbohydrates, including cellobiose, maltose, sucrose, fructooligosaccharide and salicin, were generally metabolized only by the whisky strains, whereas milk-derived carbohydrates, i.e. lactose and galactose, were metabolized only by the milk strains. Milk fermentation properties also distinguished the two groups. The general genomic characteristics, including genomic size, number of coding sequences and average nucleotide identity values, differentiated the two groups. The observed differences in carbohydrate metabolic properties between the two groups correlated with the presence of intact specific enzymes in glycoside hydrolase (GH) families GH1, GH4, GH13, GH32 and GH65. Several GHs in the milk strains were inactive due to the presence of stop codon(s) in genes encoding the GHs, and the inactivation patterns of the genes encoding specific enzymes assigned to GH1 in the milk strains suggested a possible diversification manner of L. helveticus strains. The present study has demonstrated how L. helveticus strains have adapted to their habitats.
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Affiliation(s)
- Yoshihiko Kido
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Shintaro Maeno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Hiroki Tanno
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
| | - Yuko Kichise
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Akihito Endo
- Department of Food, Aroma and Cosmetic Chemistry, Tokyo University of Agriculture, Hokkaido 099-2493, Japan
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5
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Zago M, Massimiliano L, Bonvini B, Penna G, Giraffa G, Rescigno M. Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses. PLoS One 2021; 16:e0245903. [PMID: 33493208 PMCID: PMC7833162 DOI: 10.1371/journal.pone.0245903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/09/2021] [Indexed: 12/26/2022] Open
Abstract
Lactobacillus helveticus carries many properties such as the ability to survive gastrointestinal transit, modulate the host immune response, accumulate biopeptides in milk, and adhere to the epithelial cells that could contribute to improving host health. In this study, the applicability as functional cultures of four L. helveticus strains isolated from Italian hard cheeses was investigated. A preliminary strain characterization showed that the ability to produce folate was generally low while antioxidant, proteolytic, peptidase, and β-galactosidase activities resulted high, although very variable, between strains. When stimulated moDCs were incubated in the presence of live cells, a dose-dependent release of both the pro-inflammatory cytokine IL-12p70 and the anti-inflammatory cytokine IL-10, was shown for all the four strains. In the presence of cell-free culture supernatants (postbiotics), a dose-dependent, decrease of IL-12p70 and an increase of IL-10 was generally observed. The immunomodulatory effect took place also in Caciotta-like cheese made with strains SIM12 and SIS16 as bifunctional (i.e., immunomodulant and acidifying) starter cultures, thus confirming tests in culture media. Given that the growth of bacteria in the cheese was not necessary (they were killed by pasteurization), the results indicated that some constituents of non-viable bacteria had immunomodulatory properties. This study adds additional evidence for the positive role of L. helveticus on human health and suggests cheese as a suitable food for delivering candidate strains and modulating their anti-inflammatory properties.
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Affiliation(s)
- Miriam Zago
- CREA Research Centre for Animal Production and Aquaculture (CREA-ZA), Lodi, Italy
| | - Lucia Massimiliano
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Barbara Bonvini
- CREA Research Centre for Animal Production and Aquaculture (CREA-ZA), Lodi, Italy
| | - Giuseppe Penna
- Mucosal Immunology and Microbiota Unit, Humanitas Clinical and Research Center, IRCCS, Rozzano (Mi), Italy
| | - Giorgio Giraffa
- CREA Research Centre for Animal Production and Aquaculture (CREA-ZA), Lodi, Italy
- * E-mail:
| | - Maria Rescigno
- Mucosal Immunology and Microbiota Unit, Humanitas Clinical and Research Center, IRCCS, Rozzano (Mi), Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (Mi), Italy
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Zhong Z, Hu R, Zhao J, Liu W, Kwok LY, Sun Z, Zhang H, Chen Y. Acetate kinase and peptidases are associated with the proteolytic activity of Lactobacillus helveticus isolated from fermented food. Food Microbiol 2020; 94:103651. [PMID: 33279076 DOI: 10.1016/j.fm.2020.103651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 11/18/2022]
Abstract
Lactobacillus (L.) helveticus is widely used in food industry due to its high proteolytic activity. However, such activity varies greatly between isolates, and the determining factors regulating the strength of proteolytic activity in L. helveticus are unclear. This study sequenced the genomes of 60 fermented food-originated L. helveticus and systemically examined the proteolytic activity-determining factors. Our analyses found that the strength of proteolytic activity in L. helveticus was independent of the isolation source, geographic location, phylogenetic closeness between isolates, and distribution of cell envelope proteinases (CEPs). Genome-wide association study (GWAS) identified two genes, the acetate kinase (ackA) and a hypothetical protein, and 15 single nucleotide polymorphisms (SNPs) that were associated with the strength of the proteolytic activity. Further investigating the functions of these gene components revealed that ackA and two cysteine peptidases coding genes (pepC and srtA) rather than the highly heterogeneous and intraspecific CEPs were linked to the level of proteolytic activity. Moreover, the sequence type (ST) defined by SNP analysis revealed a total of ten STs, and significantly weaker proteolytic activity was observed among isolates of ST2. This study provides practical information for future selection of L. helveticus of strong proteolytic activity.
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Affiliation(s)
- Zhi Zhong
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Richa Hu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China.
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Kittibunchakul S, van Leeuwen SS, Dijkhuizen L, Haltrich D, Nguyen TH. Structural Comparison of Different Galacto-oligosaccharide Mixtures Formed by β-Galactosidases from Lactic Acid Bacteria and Bifidobacteria. J Agric Food Chem 2020; 68:4437-4446. [PMID: 32196339 PMCID: PMC7168588 DOI: 10.1021/acs.jafc.9b08156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/05/2020] [Accepted: 03/20/2020] [Indexed: 06/10/2023]
Abstract
The LacLM-type β-galactosidase from Lactobacillus helveticus DSM 20075 expressed in both Escherichia coli (EcoliBL21Lhβ-gal) and Lactobacillus plantarum (Lp609Lhβ-gal) was tested for their potential to form galacto-oligosaccharides (GOS) from lactose. The Lh-GOS mixture formed by β-galactosidase from L. helveticus, together with three GOS mixtures produced using β-galactosidases of both the LacLM and the LacZ type from other lactic acid bacteria, namely, L. reuteri (Lr-GOS), L. bulgaricus (Lb-GOS), and Streptococcus thermophilus (St-GOS), as well as two GOS mixtures (Br-GOS1 and Br-GOS2) produced using β-galactosidases (β-gal I and β-gal II) from Bifidobacterium breve, was analyzed and structurally compared with commercial GOS mixtures analyzed in previous work (Vivinal GOS, GOS I, GOS III, and GOS V) using high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD), high-performance size-exclusion chromatography with a refractive index (RI) detector (HPSEC-RI), and one-dimensional 1H NMR spectroscopy. β-Galactosidases from lactic acid bacteria and B. breve displayed a preference to form β-(1→6)- and β-(1→3)-linked GOS. The GOS mixtures produced by these enzymes consisted of mainly DP2 and DP3 oligosaccharides, accounting for ∼90% of all GOS components. GOS mixtures obtained with β-galactosidases from lactic acid bacteria and B. breve were quite similar to the commercial GOS III mixture in terms of product spectrum and showed a broader product spectrum than the commercial GOS V mixture. These GOS mixtures also contained a number of GOS components that were absent in the commercial Vivinal GOS (V-GOS).
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Affiliation(s)
- Suwapat Kittibunchakul
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
- Institute of Nutrition, Mahidol University, 999 Phutthamonthon 4 Road Salaya, Nakhon Pathom 73170, Thailand
| | - Sander S van Leeuwen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
- Laboratory Medicine, Cluster Human Nutrition & Health, University Medical Center Groningen (UMCG), Hanzeplein 1, NL-9713 GZ Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
- CarbExplore Research BV, Zernikepark 12, NL-9747 AN Groningen, The Netherlands
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Thu-Ha Nguyen
- Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
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Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH. Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system. BMC Microbiol 2019; 19:143. [PMID: 31238873 PMCID: PMC6593500 DOI: 10.1186/s12866-019-1500-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/31/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS Two NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.
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Affiliation(s)
- Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, CH-3003 Bern, Switzerland
| | - Jürg E. Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics, Schloss 1, CH-8820 Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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9
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Tang CD, Ding PJ, Shi HL, Jia YY, Zhou MZ, Yu HL, Xu JH, Yao LG, Kan YC. One-Pot Synthesis of Phenylglyoxylic Acid from Racemic Mandelic Acids via Cascade Biocatalysis. J Agric Food Chem 2019; 67:2946-2953. [PMID: 30807132 DOI: 10.1021/acs.jafc.8b07295] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phenylglyoxylic acid (PGA) are key building blocks and widely used to synthesize pharmaceutical intermediates or food additives. However, the existing synthetic methods for PGA generally involve toxic cyanide and complex processes. To explore an alternative method for PGA biosynthesis, we envisaged cascade biocatalysis for the one-pot synthesis of PGA from racemic mandelic acid. A novel mandelate racemase named ArMR showing higher expression level (216.9 U·mL-1 fermentation liquor) was cloned from Agrobacterium radiobacter and identified, and six recombinant Escherichia coli strains were engineered to coexpress three enzymes of mandelate racemase, d-mandelate dehydrogenase and l-lactate dehydrogenase, and transform racemic mandelic acid to PGA. Among them, the recombinant E. coli TCD 04, engineered to coexpress three enzymes of ArMR, LhDMDH, and LhLDH, can transform racemic mandelic acid (100 mM) to PGA with 98% conversion. Taken together, we provide a green approach for one-pot biosynthesis of PGA from racemic mandelic acid.
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Affiliation(s)
- Cun-Duo Tang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Peng-Ju Ding
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Hong-Ling Shi
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Yuan-Yuan Jia
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Mao-Zhi Zhou
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Lun-Guang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
| | - Yun-Chao Kan
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North , Nanyang Normal University , 1638 Wolong Road , Nanyang , Henan 473061 , People's Republic of China
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10
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Senan S, Prajapati JB, Joshi CG. Whole-genome based validation of the adaptive properties of Indian origin probiotic Lactobacillus helveticus MTCC 5463. J Sci Food Agric 2015; 95:321-328. [PMID: 24798512 DOI: 10.1002/jsfa.6721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/24/2014] [Accepted: 04/26/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND The aim of the study was to mine the Lactobacillus helveticus MTCC 5463 genome for genetic determinants to validate its ability to adapt to gut transit stresses and translate functionality to the host. RESULTS In silico analysis of the 1 911 350 bp single chromosome of the strain predicted that it had excellent adaptive features like the multisubunit F0F1 ATPase, conjugated bile salt hyrolase, chaperones like hsp33, HtrA, GroEL, GroES, dnaK, grpE, starvation-inducible proteins and heavy-metal transporting ATPases. The genome revealed genes for adhesion and aggregation including exopolysaccharides, capsular polysaccharides sortase, elongation factor Tu, aggregation promoting proteins, fibronectin-binding proteins, S-layer and mucus-binding proteins. We could identify genes conferring physiological benefits like immunostimulation, cholesterol reduction, antibacterial and folate production. Thus, through trait and gene matching, the study established that the strain possessed the genetic arsenal required to adapt to the gut milieu. The predictions of functional genes further validate the experimental evidences of adaptation and probiosis. CONCLUSION This study provides insight into the feasibility of applying probiogenomics to identify genes that could function as pre-selection criteria for identification of potential probiotic strains.
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Affiliation(s)
- Suja Senan
- Department of Dairy Microbiology, Sheth MC College of Dairy Science, Anand Agricultural University, Anand, 388110, India
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11
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Stressler T, Eisele T, Schlayer M, Lutz-Wahl S, Fischer L. Characterization of the recombinant exopeptidases PepX and PepN from Lactobacillus helveticus ATCC 12046 important for food protein hydrolysis. PLoS One 2013; 8:e70055. [PMID: 23894590 PMCID: PMC3716637 DOI: 10.1371/journal.pone.0070055] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 06/15/2013] [Indexed: 11/18/2022] Open
Abstract
The proline-specific X-prolyl dipeptidyl aminopeptidase (PepX; EC 3.4.14.11) and the general aminopeptidase N (PepN; EC 3.4.11.2) from Lactobacillus helveticus ATCC 12046 were produced recombinantly in E. coli BL21(DE3) via bioreactor cultivation. The maximum enzymatic activity obtained for PepX was 800 µkat(H-Ala-Pro-pNA) L(-1), which is approx. 195-fold higher than values published previously. To the best of our knowledge, PepN was expressed in E. coli at high levels for the first time. The PepN activity reached 1,000 µkat(H-Ala-pNA) L(-1). After an automated chromatographic purification, both peptidases were biochemically and kinetically characterized in detail. Substrate inhibition of PepN and product inhibition of both PepX and PepN were discovered for the first time. An apo-enzyme of the Zn(2+)-dependent PepN was generated, which could be reactivated by several metal ions in the order of Co(2+)>Zn(2+)>Mn(2+)>Ca(2+)>Mg(2+). PepX and PepN exhibited a clear synergistic effect in casein hydrolysis studies. Here, the relative degree of hydrolysis (rDH) was increased by approx. 132%. Due to the remarkable temperature stability at 50°C and the complementary substrate specificities of both peptidases, a future application in food protein hydrolysis might be possible.
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Affiliation(s)
- Timo Stressler
- Department of Biotechnology, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Thomas Eisele
- Department of Biotechnology, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Michael Schlayer
- Department of Biotechnology, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Sabine Lutz-Wahl
- Department of Biotechnology, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
| | - Lutz Fischer
- Department of Biotechnology, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany
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12
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Callanan MJ, Ross RP, Beresford TP. Insertion sequence elements as mediators of strain diversity in Lactobacillus helveticus. Int J Food Microbiol 2007; 120:120-3. [PMID: 17628131 DOI: 10.1016/j.ijfoodmicro.2007.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 11/28/2006] [Indexed: 11/26/2022]
Abstract
Insertion sequence (IS) elements were found to be associated with the truncation of predicted cellobiose transport, acetaldehyde dehydrogenase and diacetyl reductase genes in the genome of Lactobacillus helveticus DPC 4571. The conservation of the IS elements in these different genomic locations among L. helveticus cheese isolates was determined by amplification with gene-specific and IS element-specific primers. The presence of two of the IS elements was found to follow a genotypic profile of the strains generated by randomly amplified polymorphic DNA (RAPD)-PCR and strains that clustered by RAPD-PCR tended to have the IS element in the same position. However, the IS element that interrupted the cellobiose transport gene was found to be common to all strains tested. This conserved genotype suggests the insertion event occurred early in the evolution of L. helveticus as a separate species.
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Affiliation(s)
- M J Callanan
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
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13
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Lee WJ, Banavara DS, Hughes JE, Christiansen JK, Steele JL, Broadbent JR, Rankin SA. Role of cystathionine beta-lyase in catabolism of amino acids to sulfur volatiles by genetic variants of Lactobacillus helveticus CNRZ 32. Appl Environ Microbiol 2007; 73:3034-9. [PMID: 17337535 PMCID: PMC1892856 DOI: 10.1128/aem.02290-06] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Catabolism of sulfur-containing amino acids plays an important role in the development of cheese flavor. During ripening, cystathionine beta-lyase (CBL) is believed to contribute to the formation of volatile sulfur compounds (VSCs) such as methanethiol and dimethyl disulfide. However, the role of CBL in the generation of VSCs from the catabolism of specific sulfur-containing amino acids is not well characterized. The objective of this study was to investigate the role of CBL in VSC formation by Lactobacillus helveticus CNRZ 32 using genetic variants of L. helveticus CNRZ 32 including the CBL-null mutant, complementation of the CBL-null mutant, and the CBL overexpression mutant. The formation of VSCs from methionine, cystathionine, and cysteine was determined in a model system using gas chromatography-mass spectrometry with solid-phase microextraction. With methionine as a substrate, CBL overexpression resulted in higher VSC production than that of wild-type L. helveticus CNRZ 32 or the CBL-null mutant. However, there were no differences in VSC production between the wild type and the CBL-null mutant. With cystathionine, methanethiol production was detected from the CBL overexpression variant and complementation of the CBL-null mutant, implying that CBL may be involved in the conversion of cystathionine to methanethiol. With cysteine, no differences in VSC formation were observed between the wild type and genetic variants, indicating that CBL does not contribute to the conversion of cysteine.
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Affiliation(s)
- Won-Jae Lee
- Division of Animal Science and Technology, Gyeongsang National University, Jinju, South Korea
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14
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Abstract
Microbial conversion of renewable raw materials to useful products is an important objective in industrial biotechnology. Pichia stipitis, a yeast that naturally ferments xylose, was genetically engineered for l-(+)-lactate production. We constructed a P. stipitis strain that expressed the l-lactate dehydrogenase (LDH) from Lactobacillus helveticus under the control of the P. stipitis fermentative ADH1 promoter. Xylose, glucose, or a mixture of the two sugars was used as the carbon source for lactate production. The constructed P. stipitis strain produced a higher level of lactate and a higher yield on xylose than on glucose. Lactate accumulated as the main product in xylose-containing medium, with 58 g/liter lactate produced from 100 g/liter xylose. Relatively efficient lactate production also occurred on glucose medium, with 41 g/liter lactate produced from 94 g/liter glucose. In the presence of both sugars, xylose and glucose were consumed simultaneously and converted predominantly to lactate. Lactate was produced at the expense of ethanol, whose production decreased to approximately 15 to 30% of the wild-type level on xylose-containing medium and to 70 to 80% of the wild-type level on glucose-containing medium. Thus, LDH competed efficiently with the ethanol pathway for pyruvate, even though the pathway from pyruvate to ethanol was intact. Our results show, for the first time, that lactate production from xylose by a yeast species is feasible and efficient. This is encouraging for further development of yeast-based bioprocesses to produce lactate from lignocellulosic raw material.
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Affiliation(s)
- Marja Ilmén
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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15
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Ricci G, Fortina MG. Characterization of Lactobacillus helveticus strains isolated from cheeses by distribution studies of insertion sequences. Int J Food Microbiol 2006; 112:112-9. [PMID: 16859795 DOI: 10.1016/j.ijfoodmicro.2006.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 02/08/2006] [Accepted: 05/27/2006] [Indexed: 11/22/2022]
Abstract
A collection of 38 Lactobacillus helveticus strains, isolated from a number of different artisan Italian cheeses, and 4 reference strains were studied with respect to the presence of insertion sequences and their distribution and abundance. The mobile genetic element ISLh1, that contains one open reading frame coding for a putative transposase of the IS982 family, was used for DNA fingerprinting, together with IS1201 and ISL2, previously isolated from L. helveticus. The number of insertion sequences per strain and the size of DNA restriction fragments containing them, was variable and allowed the discrimination at the strain-level. The genomic distribution of the three unrelated insertion sequences showed significant correlations and allowed the differentiation of the strains also with regard to the specific ecological niche of origin of the isolates. Consequently, insertion sequences comparison may be useful in determining the history of a group of strains known to be related because of identity and offers a further parameter for evaluating the population polymorphism in L. helveticus.
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Affiliation(s)
- Giovanni Ricci
- Department of Food Science and Microbiology - Industrial Microbiology Section, University of Milano, via Celoria 2, 20133 Milan, Italy
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16
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Abstract
AIMS To investigate the distribution and the level of diversity of extrachromosomal molecules in Lactobacillus helveticus strains in relation to their different ecological niches. METHODS AND RESULTS The plasmid profile of 22 Lact. helveticus strains, isolated from five different Italian cheeses, was determined. Among the tested strains, there was a variable presence of plasmids: eight plasmid-free strains and the remaining with several plasmids that could be differentiated on the basis of number and molecular weight. The profiles showed between one and five plasmid bands, which size ranged between 2.3 and 31 kb. Four of these plasmids were further analyzed by restriction digestion and compared with the plasmids from Lact. helveticus ATCC 15009(T). Analyses and comparison of their primary structures and hybridization experiments revealed the presence of different DNA homology groups. CONCLUSIONS This study indicates that within Lact. helveticus species, there is a high degree of variability in relation to the presence of plasmid molecules. Moreover, the structural diversity found among some of these plasmids allows to hypothesize the presence of different evolutionary lineages. SIGNIFICANCE AND IMPACT OF THE STUDY Studies on plasmid distribution and diversity should be considered as an essential component in a continuing effort to explore microbial diversity as well as to understand the real role of plasmids in the flow of genetic information in natural bacterial communities.
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Affiliation(s)
- G Ricci
- Industrial Microbiology Section, Department of Food Science and Microbiology, University of Milan, Milan, Italy
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17
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Naser SM, Hagen KE, Vancanneyt M, Cleenwerck I, Swings J, Tompkins TA. Lactobacillus suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla-Jensen 1919) Bergey et al. 1925 (Approved Lists 1980). Int J Syst Evol Microbiol 2006; 56:355-360. [PMID: 16449439 DOI: 10.1099/ijs.0.64001-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain R0052, isolated from a North American dairy starter culture, was initially identified as Lactobacillus acidophilus based on phenotypic analyses. However, upon sequencing the 16S rRNA gene, it became clear that the isolate was very highly related to Lactobacillus suntoryeus, Lactobacillus helveticus and Lactobacillus gallinarum, as similarities ranging from 99·3 to 99·8 % were observed. As an initial screening test to investigate the relatedness of strain R0052 and reference strains of L. suntoryeus, L. helveticus and L. gallinarum, the partial sequences for the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), the translational elongation factor Tu (tuf), a surface-layer protein (slp) and the Hsp60 chaperonins (groEL) were determined and they revealed high relatedness between all of the strains. The determination of the 16S–23S rRNA internally transcribed spacer (ITS) sequences revealed 98·3–100 % similarity between L. suntoryeus and L. helveticus strains. SDS-PAGE of whole-cell proteins did not distinguish between these species. Fluorescent amplified fragment length polymorphism (FAFLP) could distinguish between these taxa, but they still constituted a single cluster within the L. acidophilus group. Finally, DNA–DNA hybridization experiments between strain R0052 and the type strains of L. helveticus and L. suntoryeus yielded reassociation values above 70 % and confirmed that these names are synonyms.
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Affiliation(s)
- Sabri M Naser
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Karen E Hagen
- Institut Rosell Inc., Research and Development, 6100 Royalmount Ave, Montreal, Quebec, Canada, H4P 2R2
| | - Marc Vancanneyt
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Ilse Cleenwerck
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Jean Swings
- BCCMTM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
- Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent 9000, Belgium
| | - Thomas A Tompkins
- Institut Rosell Inc., Research and Development, 6100 Royalmount Ave, Montreal, Quebec, Canada, H4P 2R2
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18
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Gatti M, Rossetti L, Fornasari ME, Lazzi C, Giraffa G, Neviani E. Heterogeneity of putative surface layer proteins in Lactobacillus helveticus. Appl Environ Microbiol 2005; 71:7582-8. [PMID: 16269809 PMCID: PMC1287734 DOI: 10.1128/aem.71.11.7582-7588.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The S-layer-encoding genes of 21 Lactobacillus helveticus strains were characterized. Phylogenetic analysis based on the identified S-layer genes revealed two main clusters, one which includes a sequence similar to that of the slpH1 gene of L. helveticus CNRZ 892 and a second cluster which includes genes similar to that of prtY. These results were further confirmed by Southern blot hybridization. This study demonstrates S-layer gene variability in the species L. helveticus.
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Affiliation(s)
- Monica Gatti
- Department of Genetic Anthropology Evolution, Parco Area delle Scienze 11A, University of Parma, 43100 Parma, Italy.
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19
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Cappa F, Cattivelli D, Cocconcelli PS. The uvrA gene is involved in oxidative and acid stress responses in Lactobacillus helveticus CNBL1156. Res Microbiol 2005; 156:1039-47. [PMID: 16125908 DOI: 10.1016/j.resmic.2005.06.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 06/01/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022]
Abstract
The uvrA gene of Lactobacillus helveticus CNBL1156 coding for subunit A of the excinuclease ABC complex involved in the nucleotide excision repair mechanism was identified. Analysis of the uvrA locus revealed the presence of three open reading frames, merR, sat and uvrA, which coded respectively for a MerR-like regulatory protein, a putative protein with homology to streptothricin acetyl transferase and for a UvrA protein. RNA analysis by northern blotting and RT-PCR showed that sat and uvrA were transcriptionally coupled. UvrA from L. helveticus contained the conserved domains of bacterial excinuclease A, as well as the two ATP binding sites and the zinc binding domains. The transcriptional activity of uvrA indicated that this gene was activated by exposure to UV radiation and oxidative stress. In addition, we observed that the expression of uvrA was inducible by pH; moreover, the role of UvrA in protection against stress was confirmed by acid adaptation experiments. Pretreatment of cells at pH 5 conferred resistance to H2O2, suggesting a specific adaptive response to pH-induced DNA damage. The results from this study indicate that UvrA contributes to acid and oxidative tolerance in L. helveticus, and suggest that it plays a role in survival at low pH under normal conditions.
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Affiliation(s)
- Fabrizio Cappa
- Istituto di Microbiologia, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy
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