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Lee Y, Kim N, Werlinger P, Suh DA, Lee H, Cho JH, Cheng J. Probiotic Characterization of Lactobacillus brevis MJM60390 and In Vivo Assessment of Its Antihyperuricemic Activity. J Med Food 2022; 25:367-380. [PMID: 35438552 DOI: 10.1089/jmf.2021.k.0171] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Uric acid is the final product of purine metabolism in human. The increase of serum uric acid is tightly related to the incidence of hyperuricemia and gout. Also, it has been reported that the intake of purine-rich foods like meat and seafood is associated with an increased risk of gout. Therefore, the reduction of purine absorption is one of therapeutic approaches to prevent hyperuricemia and gout. Currently, probiotics are being studied for the management of hyperuricemia and gout. In this study, we aimed to investigate the effect of Lactobacillus brevis MJM60390 on hyperuricemia induced by a high-purine diet and potassium oxonate in a mouse model. L. brevis MJM60390 among 24 lactic acid bacteria isolated from fermented foods showed the highest ability to assimilate inosine and guanosine in vitro and typical probiotic characteristics, like the absence of bioamine production, D-lactate production, hemolytic activity, as well as tolerance to simulated orogastrointestinal conditions and adherence to Caco-2 cells. In an in vivo animal study, the uric acid level in serum was significantly reduced to a normal level after oral administration of L. brevis MJM60390 for 2 weeks. The activity of xanthine oxidase catalyzing the formation of uric acid was also inhibited by 30%. Interestingly, damage to the glomerulus, Bowman's capsule, and tubules in the hyperuricemia model were reversed by supplementation with this strain. Fecal microbiome analysis revealed that L. brevis MJM60390 supplementation enhanced the relative abundance of the Rikenellaceae family, which produces the short-chain fatty acid butyrate and helps to maintain good gut condition. Therefore, these results demonstrated that L. brevis MJM60390 can be a probiotic candidate to prevent hyperuricemia.
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Affiliation(s)
- Youjin Lee
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Neagawooridwimeu Kim
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Pia Werlinger
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Dong-A Suh
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Hanki Lee
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Joo-Hyung Cho
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea
| | - Jinhua Cheng
- Graduate School of Interdisciplinary Program of Biomodulation, and Myongji University, Yongin-si, Gyeonggi-Do, Korea.,Myongji Bioefficacy Research Center, Myongji University, Yongin-si, Gyeonggi-Do, Korea
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52
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Sharma P, Singh SP. Identification and profiling of microbial community from industrial sludge. Arch Microbiol 2022; 204:234. [PMID: 35362813 DOI: 10.1007/s00203-022-02831-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/05/2022] [Accepted: 03/06/2022] [Indexed: 02/03/2023]
Abstract
The purpose of this study is to identify microbial communities in pulp and paper industry sludge and their metagenomic profiling on the basis of; phylum, class, order, family, genus and species level. Results revealed that the dominant phyla in 16S rRNA Illumina Miseq analysis inside sludge were Anaerolinea, Pseudomonas, Clostridia, Bacteriodia, Gammaproteobacteria, Spirochetia, Deltaproteobacteria, Spirochaetaceae, Prolixibacteraceae and some unknown microbial strains are also dominant. Metagenomics is a molecular biology-based technology that uses bioinformatics to evaluate huge gene sequences extracted from environmental samples to assess the composition and function of microbiota. The results of metabarcoding of the V3-V4 16S rRNA regions acquired from paired-end Illumina MiSeq sequencing were used to analyze bacterial communities and structure. The present work demonstrates the potential approach to sludge treatment in the open environment via the naturally adapted microorganism, which could be an essential addition to the disposal site. In summary, these investigations indicate that the indigenous microbial community is an acceptable bioresource for remediation or detoxification following secondary treatment. This research aims at understanding the structure of microbial communities and their diversity (%) in highly contaminated sludge to perform in situ bioremediation.
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Affiliation(s)
- Pooja Sharma
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, 226 025, Uttar Pradesh, India.
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, Dayanand Anglo-Vedic (PG) College, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208 001, India.
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Hamada T, Hisatome I, Wakimizu T, Kato M, Gotou T, Koga A, Endo Y, Taniguchi SI, Yamamoto K, Ninomiya H, Tsuboi H, Yamaguchi M, Yamada N, Kano H, Asami Y. Lactobacillus gasseri PA-3 reduces serum uric acid levels in patients with marginal hyperuricemia. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:361-369. [PMID: 35227163 DOI: 10.1080/15257770.2022.2039702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 01/22/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Several studies have reported that Lactobacillus gasseri PA-3 reduces the level of serum uric acid (SUA) in patients with hyperuricemia. However, it remains unknown how PA-3 affects uric acid metabolism. In the present study, we examined effects of PA-3-containing yoghurt on uric acid metabolism in patients with marginal hyperuricemia. Sixteen patients with SUA > 357 μmol/L (marginal hyperuricemia) were enrolled. PA-3-containing yoghurt was administered for 8 weeks. Uric acid metabolism was evaluated just before and 8 weeks after the administration and at 4 weeks after the administration ended (post-administration). SUA levels after the administration were significantly lower than that before the administration and remained low at post-administration. Urinary uric acid concentration (Uur) after the administration were significantly lower than that before the administration. However, post-administration Uur levels were comparable to those before the administration. Therefore, PA-3-containing yoghurt significantly reduced the levels of SUA and Uur in patients with marginal hyperuricemia.
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Affiliation(s)
- Toshihiro Hamada
- Faculty of Medicine, Department of Community-Based Family Medicine, Tottori University, Yonago, Japan
| | - Ichiro Hisatome
- Department of Cardiology, Yonago Medical Center, Yonago, Japan
| | - Takayuki Wakimizu
- Department of Genetic Medicine and Regenerative Therapeutics, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
| | - Masahiko Kato
- Division of School of Health Science, Department of Pathobiological Science and Technology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Tamotsu Gotou
- Department of Pediatric Emergency and Intensive Care Medicine, Department of Emergency and Intensive Care Medicine, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Atsuro Koga
- Advanced Medicine & Translational Research Center, Organization for Research Initiative and Promotion, Tottori University, Yonago, Japan
| | - Yusuke Endo
- Advanced Medicine & Translational Research Center, Organization for Research Initiative and Promotion, Tottori University, Yonago, Japan
| | - Shin-Ichi Taniguchi
- Faculty of Medicine, Department of Community-Based Family Medicine, Tottori University, Yonago, Japan
| | - Kazuhiro Yamamoto
- Department of Cardiovascular Medicine, and Endocrinology and Metabolism, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Haruaki Ninomiya
- Department of Biological Regulation, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hiroshi Tsuboi
- Food Microbiology and Function Research Laboratories, Meiji Co., Ltd, Tokyo, Japan
| | - Makoto Yamaguchi
- Food Microbiology and Function Research Laboratories, Meiji Co., Ltd, Tokyo, Japan
| | - Naruomi Yamada
- Food Microbiology and Function Research Laboratories, Meiji Co., Ltd, Tokyo, Japan
| | - Hiroshi Kano
- Food Microbiology and Function Research Laboratories, Meiji Co., Ltd, Tokyo, Japan
| | - Yukio Asami
- Food Microbiology and Function Research Laboratories, Meiji Co., Ltd, Tokyo, Japan
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Qian Y, Li Y, Xu T, Zhao H, Zeng M, Liu Z. Dissecting of the AI-2/LuxS Mediated Growth Characteristics and Bacteriostatic Ability of Lactiplantibacillus plantarum SS-128 by Integration of Transcriptomics and Metabolomics. Foods 2022; 11:foods11050638. [PMID: 35267271 PMCID: PMC8909743 DOI: 10.3390/foods11050638] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 12/13/2022] Open
Abstract
Lactiplantibacillus plantarum could regulate certain physiological functions through the AI-2/LuxS-mediated quorum sensing (QS) system. To explore the regulation mechanism on the growth characteristics and bacteriostatic ability of L. plantarum SS-128, a luxS mutant was constructed by a two-step homologous recombination. Compared with ΔluxS/SS-128, the metabolites of SS-128 had stronger bacteriostatic ability. The combined analysis of transcriptomics and metabolomics data showed that SS-128 exhibited higher pyruvate metabolic efficiency and energy input, followed by higher LDH level and metabolite overflow compared to ΔluxS/SS-128, resulting in stronger bacteriostatic ability. The absence of luxS induces a regulatory pathway that burdens the cysteine cycle by quantitatively drawing off central metabolic intermediaries. To accommodate this mutations, ΔluxS/SS-128 exhibited lower metabolite overflow and abnormal proliferation. These results demonstrate that the growth characteristic and metabolism of L. plantarum SS-128 are mediated by the AI-2/LuxS QS system, which is a positive regulator involved in food safety. It would be helpful to investigate more bio-preservation control potential of L. plantarum, especially when applied in food industrial biotechnology.
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Affiliation(s)
| | | | | | | | | | - Zunying Liu
- Correspondence: ; Tel./Fax: +86-532-8203-2400
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Wang S, Shao T, Li J, Zhao J, Dong Z. A survey of fermentation parameters, bacterial community compositions and their metabolic pathways during the ensiling of sorghum. J Appl Microbiol 2022; 132:3563-3577. [DOI: 10.1111/jam.15484] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro‐Grassland Science Nanjing Agricultural University Nanjing China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro‐Grassland Science Nanjing Agricultural University Nanjing China
| | - Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro‐Grassland Science Nanjing Agricultural University Nanjing China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro‐Grassland Science Nanjing Agricultural University Nanjing China
| | - Zhihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro‐Grassland Science Nanjing Agricultural University Nanjing China
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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58
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Key reaction components affect the kinetics and performance robustness of cell-free protein synthesis reactions. Comput Struct Biotechnol J 2022; 20:218-229. [PMID: 35024094 PMCID: PMC8718664 DOI: 10.1016/j.csbj.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022] Open
Abstract
Novel cell-free protein synthesis reaction buffer improves performance by 400%. Enhanced performance is maintained across the synthesis of different proteins. Protein synthesis performance is robust across different cell lysate batches and E. coli strains. Buffer components affect aspects of reaction kinetics in differing ways.
Cell-free protein synthesis (CFPS) reactions have grown in popularity with particular interest in applications such as gene construct prototyping, biosensor technologies and the production of proteins with novel chemistry. Work has frequently focussed on optimising CFPS protocols for improving protein yield, reducing cost, or developing streamlined production protocols. Here we describe a statistical Design of Experiments analysis of 20 components of a popular CFPS reaction buffer. We simultaneously identify factors and factor interactions that impact on protein yield, rate of reaction, lag time and reaction longevity. This systematic experimental approach enables the creation of a statistical model capturing multiple behaviours of CFPS reactions in response to components and their interactions. We show that a novel reaction buffer outperforms the reference reaction by 400% and importantly reduces failures in CFPS across batches of cell lysates, strains of E. coli, and in the synthesis of different proteins. Detailed and quantitative understanding of how reaction components affect kinetic responses and robustness is imperative for future deployment of cell-free technologies.
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Key Words
- 3-PGA, 3-phosphoglyceric acid
- ATP, adenosine triphosphate
- Automation
- CFE, cell-free extract
- CFPS, cell-free protein synthesis
- CTP, cytidine triphosphate
- Cell-free protein synthesis (CFPS)
- CoA, coenzyme A
- DSD, Definitive Screening Design
- DTT, dithiothreitol
- Design of Experiments (DoE)
- DoE, Design of Experiments
- FEU, fluorescein equivalent units
- G-6-P, glucose-6-phosphate
- GTP, guanosine triphosphate
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- K-glutamate, potassium glutamate
- LB, lysogeny broth
- Mg, magnesium glutamate
- NAD, nicotinamide adenine dinucleotide
- NTP, nucleoside triphosphate
- OFAT, one-factor-at-a-time
- PEG-8000, polyethylene glycol 8000
- PEP, phosphoenolpyruvate
- RFU, relative fluorescence units
- RSM, Response Surface Model
- Robustness
- Statistical engineering
- UTP, uridine triphosphate
- X-gal, 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside
- cAMP, cyclic adenosine monophosphate
- eGFP, enhanced green fluorescent protein
- tRNA, transfer ribonucleic acid
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Effect of Coix Seed Extracts on Growth and Metabolism of Limosilactobacillus reuteri. Foods 2022; 11:foods11020187. [PMID: 35053919 PMCID: PMC8774368 DOI: 10.3390/foods11020187] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 12/20/2022] Open
Abstract
Coix seed (Coix lachryma-jobi L.) is an important nourishing food and traditional Chinese medicine. The role of their bioactive constituents in physiology and pharmacology has received considerable scientific attention. However, very little is known about the role of coix seed bioactive components in the growth of Limosilactobacillus reuteri (L. reuteri). This study aimed to evaluate the effects of coix seed extract (CSE) on the growth, acidifying activity, and metabolism of L. reuteri. The results showed that CSE can increase the growth and acidifying activity of L. reuteri compared with the control group. During the stationary phase, the viable bacteria in the medium supplemented with coix seed oil (CSO, 13.72 Log10 CFU/mL), coix polysaccharide (CPO, 12.24 Log10 CFU/mL), and coix protein (CPR, 11.91 Log10 CFU/mL) were significantly higher (p < 0.05) than the control group (MRS, 9.16 Log10 CFU/mL). CSE also enhanced the biosynthesis of lactic acid and acetic acid of L. reuteri. Untargeted metabolomics results indicated that the carbohydrate metabolism, amino acid metabolism, and nucleotide metabolism activities of L. reuteri were increased after adding CSE. Furthermore, CSE increased the accumulation of bioactive metabolites, such as phenyl lactic acid, vitamins, and biotin. Overall, CSE may have prebiotic potential and can be used to culture L. reuteri with high viable bacteria.
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Bai J, Franco M, Ding Z, Hao L, Ke W, Wang M, Xie D, Li Z, Zhang Y, Ai L, Guo X. Effect of Bacillus amyloliquefaciens and Bacillus subtilis on fermentation, dynamics of bacterial community and their functional shifts of whole-plant corn silage. J Anim Sci Biotechnol 2022; 13:7. [PMID: 34991716 PMCID: PMC8739699 DOI: 10.1186/s40104-021-00649-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background Bacillus amyloliquefaciens (BA) and Bacillus subtilis (BS) are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals. However, few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling. If the BA and BS inoculants have positive effects on silages, then they could not only improve fermentation characteristics, but also deliver BA or BS viable cells to ruminants, which would play its probiotic effect. Therefore, the objectives of this study were to investigate the effects of BA and BS on the fermentation, chemical characteristics, bacterial community and their metabolic pathway of whole-plant corn silage. Results Freshly chopped whole-plant corn was inoculated without or with BA and BS, respectively, and ensiled for 1, 3, 7, 14 and 60 d. Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control, and BA inoculation decreased acetic acid concentrations, whereas BS inoculation decreased fiber contents and increased crude protein (CP) content. Higher water-soluble carbohydrate contents and lower starch contents were observed in BA- and BS-inoculated silages compared with that in control. The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage, which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage. In addition, it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins, and decreased the relative abundances of drug resistance: antimicrobial pathways. We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study. There were no significant differences in bacterial community compositions among the three groups during ensiling. However, BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter. Conclusion Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.
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Affiliation(s)
- Jie Bai
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Marcia Franco
- Production systems, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - Zitong Ding
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Lin Hao
- School of Food Science and Engineering, Shanxi Agricultural University, Taigu, 030801, China
| | - Wencan Ke
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Musen Wang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Dongmei Xie
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Ziqian Li
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Yixin Zhang
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China
| | - Lin Ai
- China Animal Agriculture Association, Beijing, 100044, China
| | - Xusheng Guo
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Sciences, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China. .,Probiotics and Biological Feed Research Centre, Lanzhou University, Lanzhou, 730000, China.
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Wang S, Li J, Zhao J, Dong Z, Shao T. An investigation of fermentative profile, microbial numbers, bacterial community diversity and their predicted metabolic characteristics in Sudangrass ( Sorghum sudanense Stapf.) silages. Anim Biosci 2022; 35:1162-1173. [PMID: 34991212 PMCID: PMC9262718 DOI: 10.5713/ab.21.0326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022] Open
Abstract
Objective This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.
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Wang S, Li J, Zhao J, Dong Z, Dong D, Shao T. Dynamics of the bacterial communities and predicted functional profiles in wilted alfalfa silage. J Appl Microbiol 2021; 132:2613-2624. [PMID: 34923727 DOI: 10.1111/jam.15417] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/19/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022]
Abstract
AIMS To investigate the fermentation characteristics, bacterial community and predicted functional profiles during the ensiling of wilted alfalfa (Medicago sativa L.). METHODS AND RESULTS First-cutting alfalfa was harvested at the early bloom stage, wilted for 6 h, and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30 and 60 days of ensiling, respectively. The bacterial communities of wilted alfalfa and silages on day 3 and 60 were assessed through high throughput sequencing technology, and their functional characteristics were evaluated according to the Kyoto Encyclopedia of Genes and Genomes using Tax4Fun. After 60 days of ensiling, alfalfa silage showed a moderate fermentation quality, indicated by high lactic acid (56.7 g kg-1 dry matter [DM]) and acetic acid (39.4 g kg-1 DM) contents, and low concentrations of butyric acid (2.12 g kg-1 DM) and ammonia nitrogen (128 g kg-1 total nitrogen). Lactobacillus rapidly became predominant on day 3 and increased to 60.4% on day 60. Results of functional prediction analyses showed that the metabolism of amino acid, energy, cofactors and vitamins were reduced, while metabolism of nucleotide and carbohydrate were increased during ensiling. Fructokinase, 1-phosphofructokinase and pyruvate kinase played important roles in producing lactic acid. The production of acetic acid may be correlated with the enhancement of 6-phosphogluconate dehydrogenase and acetyl-CoA synthetase. CONCLUSIONS Knowledge regarding bacterial dynamics and their metabolic pathways during alfalfa ensiling is important for understanding the fermentation process and may contribute to the production of nutritious and stable alfalfa silage. SIGNIFICANCE AND IMPACT OF THE STUDY High throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses could provide a new and comprehensive insight into bacterial community dynamics and functional profiles to further improve the silage quality.
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Affiliation(s)
- Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Dong Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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Wang S, Li J, Zhao J, Dong Z, Shao T. Effect of storage time on the fermentation quality, bacterial community structure and metabolic profiles of napiergrass (Pennisetum purpureum Schum.) silage. Arch Microbiol 2021; 204:22. [DOI: 10.1007/s00203-021-02658-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/23/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
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Nakamya MF, Ayoola MB, Shack LA, Swiatlo E, Nanduri B. The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome. Pathogens 2021; 10:pathogens10101322. [PMID: 34684271 PMCID: PMC8540371 DOI: 10.3390/pathogens10101322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infections due to Streptococcus pneumoniae, a commensal in the nasopharynx, still claim a significant number of lives worldwide. Genome plasticity, antibiotic resistance, and limited serotype coverage of the available polysaccharide-based conjugate vaccines confounds therapeutic interventions to limit the spread of this pathogen. Pathogenic mechanisms that allow successful adaption and persistence in the host could be potential innovative therapeutic targets. Polyamines are ubiquitous polycationic molecules that regulate many cellular processes. We previously reported that deletion of polyamine transport operon potABCD, which encodes a putrescine/spermidine transporter (ΔpotABCD), resulted in an unencapsulated attenuated phenotype. Here, we characterize the transcriptome, metabolome, and stress responses of polyamine transport-deficient S. pneumoniae. Compared with the wild-type strain, the expression of genes involved in oxidative stress responses and the nucleotide sugar metabolism was reduced, while expression of genes involved in the Leloir, tagatose, and pentose phosphate pathways was higher in ΔpotABCD. A metabolic shift towards the pentose phosphate pathway will limit the synthesis of precursors of capsule polysaccharides. Metabolomics results show reduced levels of glutathione and pyruvate in the mutant. Our results also show that the potABCD operon protects pneumococci against hydrogen peroxide and nitrosative stress. Our findings demonstrate the importance of polyamine transport in pneumococcal physiology that could impact in vivo fitness. Thus, polyamine transport in pneumococci represents a novel target for therapeutic interventions.
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Affiliation(s)
- Mary F. Nakamya
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.F.N.); (M.B.A.); (L.A.S.)
| | - Moses B. Ayoola
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.F.N.); (M.B.A.); (L.A.S.)
| | - Leslie A. Shack
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.F.N.); (M.B.A.); (L.A.S.)
| | - Edwin Swiatlo
- Section of Infectious Diseases, Southeast Louisiana Veterans Health Care System, New Orleans, LA 70112, USA;
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.F.N.); (M.B.A.); (L.A.S.)
- Correspondence: ; Tel.: +1-662-325-5859; Fax: +1-662-325-1031
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Xu Y, Curtis T, Dolfing J, Wu Y, Rittmann BE. N-acyl-homoserine-lactones signaling as a critical control point for phosphorus entrapment by multi-species microbial aggregates. WATER RESEARCH 2021; 204:117627. [PMID: 34509868 DOI: 10.1016/j.watres.2021.117627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Quorum sensing (QS) has been extensively studied in pure stains of microorganisms, but the ecological roles of QS in multi-species microbial aggregates are poorly understood due to the aggregates' heterogeneity and complexity, in particular the phosphorus (P) entrapment, a key aspect of element cycling. Using periphytic biofilm as a microbial-aggregate model, we addressed how QS signaling via N-acyl-homoserine-lactones (AHLs) regulated P entrapment. The most-abundant AHLs detected were C8-HSL, 3OC8-HSL, and C12-HSL, are the primary regulator of P entrapment in the periphytic biofilm. QS signaling-AHL is a beneficial molecule for bacterial growth in periphytic biofilm and the addition of these three AHLs optimized polyphosphate accumulating organisms (PAOs) community. Growth promotion was accompanied by up-regulation of pyrimidine, purine and energy metabolism. Both intra- and extra-cellular P entrapment were enhanced in the addition of AHLs. AHLs increased extracellular polymeric substances (EPS) production to drive extracellular P entrapment, via up-regulating amino acids biosynthesis and amino sugar/nucleotide sugar metabolism. Also, AHLs improved intracellular P entrapment potential by regulating genes involved in inorganic-P accumulation (ppk, ppx) and P uptake and transport (pit, pstSCAB). This proof-of-concept evidence about how QS signaling regulates P entrapment by microbial aggregates paves the way for managing QS to enhance P removal by microbial aggregates in aquatic environments.
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Affiliation(s)
- Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Shuitianba Zigui, Yichang 443605, China; College of Resource and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Thomas Curtis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, UK
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Shuitianba Zigui, Yichang 443605, China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P. O. Box 875701, Tempe, AZ 85287-5701, USA
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Allen MM, Pike OA, Kenealey JD, Dunn ML. Metabolomics of acid whey derived from Greek yogurt. J Dairy Sci 2021; 104:11401-11412. [PMID: 34454763 DOI: 10.3168/jds.2021-20442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/16/2021] [Indexed: 11/19/2022]
Abstract
Acid whey, a byproduct of Greek yogurt production, has little commercial value due to its low protein content and is also environmentally harmful when disposed of as waste. However, as a product of microbial fermentation, acid whey could be a rich source of beneficial metabolites associated with fermented foods. This study increases understanding of acid whey composition by providing a complete metabolomic profile of acid whey. Commercial and laboratory-made Greek yogurts, prepared with 3 different bacterial culture combinations, were evaluated. Samples of uncultured milk and cultured whey from each batch were analyzed. Ultra-high-performance liquid chromatography-tandem mass spectrometry metabolomics were used to separate and identify 477 metabolites. Compared with uncultured controls, acid whey from fermented yogurt showed decreases in some metabolites and increases in others, presumably due to the effects of microbial metabolism. Additional metabolites appeared in yogurt whey but not in the uncultured control. Therefore, the effect of microbial fermentation is complex, leading to increases or decreases in potentially bioactive bovine metabolites while generating new microbial compounds that may be beneficial. Metabolite production was significantly affected by combinations of culturing organisms and production location. Differences between laboratory-made and commercial samples could be caused by different starting ingredients, environmental factors, or both.
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Affiliation(s)
- Muriel M Allen
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602
| | - Oscar A Pike
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602
| | - Jason D Kenealey
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602
| | - Michael L Dunn
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602.
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Zimmermann J, Hubel P, Pfannstiel J, Afzal M, Longin CFH, Hitzmann B, Götz H, Bischoff SC. Comprehensive proteome analysis of bread deciphering the allergenic potential of bread wheat, spelt and rye. J Proteomics 2021; 247:104318. [PMID: 34224905 DOI: 10.1016/j.jprot.2021.104318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/09/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES Cereal products like flour and bread are known to trigger diseases such as wheat allergy, celiac disease and non-celiac wheat sensitivity (NCWS). Some of these diseases are caused by allergenic proteins, the expression of which might vary depending on the grain type and manufacturing processes. Therefore, we examined the protein composition and abundance of potentially allergenic proteins in flours from bread wheat, spelt and rye, and corresponding breads. MATERIALS AND METHODS Using Nano-LC-ESI-MS/MS and label free quantification (LFQ) we analyzed the proteome of six different bread flours (wholegrain and superfine flours from rye, spelt and bread wheat) and 14 bread types (yeast and sourdough fermented breads from all flours and wheat breads plus/minus bread improver). Potentially allergenic proteins in flours and breads were functionally categorized using the Pfam database and relatively quantified by LFQ. RESULTS We could show that almost equal numbers of proteins can be identified in rye- and spelt samples compared to wheat samples using the Uniprot bread wheat protein database, indicating high sequence conservation between cereals. In total, 4424 proteins were identified in the 20 flour and bread samples. The average number of identified proteins in flour (2719 ± 243) was slightly higher than in bread (2283 ± 232; P < 0.001). In wheat- and spelt wholegrain flour higher protein numbers (wheat: 2891 ± 90; spelt: 2743 ± 140) were identified on average than in superfine flour (wheat: 2562 ± 79; P = 0.009; spelt: 2431 ± 140; P = 0.004). Neither the absolute number nor the abundance distribution of potentially allergenic proteins were dependent on the flour type or the fermentation process, but known allergenic proteins like gliadins showed higher relative abundance in spelt- and wheat samples, compared to rye samples. CONCLUSION We provide comprehensive proteome data for six flour types and related breads showing that the grain species have greater influence on proteome composition than milling and fermentation processes. Our data indicate that allergenic proteins are not selectively degraded during bread production and are more abundant in bread wheat and spelt compared to rye. SIGNIFICANCE Our proteomics study revealed that bread contains a number of potentially and proven allergenic proteins. Most likely allergenicity is not dependent on milling or conventional fermentation processes, but on the grain type. Relative abundance of allergenic proteins was higher in spelt- and wheat samples than in rye samples. Considering rye bread as better suited to atopic individuals predisposed to react to cereal allergens, clinical trials are warranted to verify this assumption.
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Affiliation(s)
- Julia Zimmermann
- Department of Nutritional Medicine/Prevention, University of Hohenheim, Fruwirthstrasse 12, Stuttgart 70593, Germany.
| | - Philipp Hubel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, August-von-Hartmann-Strasse 3, 70599 Stuttgart, Germany.
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Module, University of Hohenheim, August-von-Hartmann-Strasse 3, 70599 Stuttgart, Germany.
| | - Muhammad Afzal
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany.
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstrasse 21, 70599 Stuttgart, Germany.
| | - Bernd Hitzmann
- Department of Process Analytics and Cereal Science, University of Hohenheim, Garbenstraße, 23 70599 Stuttgart, Germany.
| | - Herbert Götz
- Department of Process Analytics and Cereal Science, University of Hohenheim, Garbenstraße, 23 70599 Stuttgart, Germany.
| | - Stephan C Bischoff
- Department of Nutritional Medicine/Prevention, University of Hohenheim, Fruwirthstrasse 12, Stuttgart 70593, Germany.
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Obesity-Related Gut Microbiota Aggravates Alveolar Bone Destruction in Experimental Periodontitis through Elevation of Uric Acid. mBio 2021; 12:e0077121. [PMID: 34061595 PMCID: PMC8262938 DOI: 10.1128/mbio.00771-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obesity is a risk factor for periodontal disease (PD). Initiation and progression of PD are modulated by complex interactions between oral dysbiosis and host responses. Although obesity is associated with increased susceptibility to bacterial infection, the detailed mechanisms that connect obesity and susceptibility to PD remain elusive. Using fecal microbiota transplantation and a ligature-induced PD model, we demonstrated that gut dysbiosis-associated metabolites from high-fat diet (HFD)-fed mice worsen alveolar bone destruction. Fecal metabolomics revealed elevated purine degradation pathway activity in HFD-fed mice, and recipient mice had elevated levels of serum uric acid upon PD induction. Furthermore, PD induction caused more severe bone destruction in hyperuricemic than normouricemic mice, and the worsened bone destruction was completely abrogated by allopurinol, a xanthine oxidase inhibitor. Thus, obesity increases the risk of PD by increasing production of uric acid mediated by gut dysbiosis.
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Bai J, Ding Z, Ke W, Xu D, Wang M, Huang W, Zhang Y, Liu F, Guo X. Different lactic acid bacteria and their combinations regulated the fermentation process of ensiled alfalfa: ensiling characteristics, dynamics of bacterial community and their functional shifts. Microb Biotechnol 2021; 14:1171-1182. [PMID: 33666350 PMCID: PMC8085944 DOI: 10.1111/1751-7915.13785] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 11/29/2022] Open
Abstract
The objectives of this study were to investigate the adaptation and competition of Lactobacillus plantarum, Pediococcus pentosaceus and Enterococcus faecalis inoculated in alfalfa silage alone or in combination on the fermentation quality, dynamics of bacterial community, and their functional shifts using single-molecule real-time (SMRT) sequencing technology. Before ensiling, alfalfa was inoculated with L. plantarum (Lp), P. pentosaceus (Pp), E. faecalis (Ef) or their combinations (LpPp, LpEf, LpPpEf) and sampled at 1, 3, 7, 14 and 60 days. After 60-days fermentation, the Lp-, Pp- and LpPp-inoculated silages had lower pH but greater concentrations of lactic acid were observed in Pp, LpEf and LpPpEf-inoculated silages. The inoculants altered the keystone taxa and the bacterial community dynamics in different manners, where L. plantarum, Weissella cibaria and L. pentosaceus dominated the bacterial communities after 14 days-fermentation in all treatments. The silages with better fermentation quality had simplified bacterial correlation structures. Moreover, different inoculants dramatically changed the carbohydrate, amino acid, energy, nucleotide and vitamin metabolism of bacterial communities during ensiling. Results of the current study indicate that effect of different inoculants on alfalfa silage fermentation was implemented by modulating the succession of bacterial community, their interactions and metabolic pathways as well during ensiling.
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Affiliation(s)
- Jie Bai
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- State Key Laboratory of Grassland Agro‐ecosystemsCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou730020China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Zitong Ding
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Wencan Ke
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Dongmei Xu
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Museng Wang
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Wenkang Huang
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Yixin Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Fang Liu
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
| | - Xusheng Guo
- State Key Laboratory of Grassland Agro‐ecosystemsSchool of Life SciencesLanzhou UniversityLanzhou730000China
- Probiotics and Biological Feed Research CentreLanzhou UniversityLanzhou730000China
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Okabe S, Shafdar AA, Kobayashi K, Zhang L, Oshiki M. Glycogen metabolism of the anammox bacterium "Candidatus Brocadia sinica". THE ISME JOURNAL 2021; 15:1287-1301. [PMID: 33288860 PMCID: PMC8115630 DOI: 10.1038/s41396-020-00850-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/03/2020] [Accepted: 11/18/2020] [Indexed: 01/19/2023]
Abstract
Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in "Ca. Brocadia sinica" growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)-1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that "Ca. B. sinica" synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.
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Affiliation(s)
- Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
| | - Amrini Amalia Shafdar
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Kanae Kobayashi
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Lei Zhang
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North-13, West-8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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Zhu B, Green SP, Ge X, Puccio T, Nadhem H, Ge H, Bao L, Kitten T, Xu P. Genome-wide identification of Streptococcus sanguinis fitness genes in human serum and discovery of potential selective drug targets. Mol Microbiol 2021; 115:658-671. [PMID: 33084151 PMCID: PMC8055731 DOI: 10.1111/mmi.14629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/20/2020] [Accepted: 10/16/2020] [Indexed: 12/17/2022]
Abstract
Streptococcus sanguinis is a primary colonizer of teeth and is associated with oral health. When it enters the bloodstream, however, this bacterium may cause the serious illness infective endocarditis. The genes required for survival and proliferation in blood have not been identified. The products of these genes could provide a rich source of targets for endocarditis-specific antibiotics possessing greater efficacy for endocarditis, and also little or no activity against those bacteria that remain in the mouth. We previously created a comprehensive library of S. sanguinis mutants lacking every nonessential gene. We have now screened each member of this library for growth in human serum and discovered 178 mutants with significant abundance changes. The main biological functions disrupted in these mutants, including purine metabolism, were highlighted via network analysis. The components of an ECF-family transporter were required for growth in serum and were shown for the first time in any bacterium to be essential for endocarditis virulence. We also identified two mutants whose growth was reduced in serum but not in saliva. This strategy promises to enable selective targeting of bacteria based on their location in the body, in this instance, treating or preventing endocarditis while leaving the oral microbiome intact.
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Affiliation(s)
- Bin Zhu
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Shannon P. Green
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Xiuchun Ge
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Tanya Puccio
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Haider Nadhem
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Henry Ge
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Liang Bao
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
| | - Todd Kitten
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
| | - Ping Xu
- Philips Institute for Oral Health ResearchVirginia Commonwealth UniversityRichmondVAUSA
- Department of Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVAUSA
- Center for Biological Data ScienceVirginia Commonwealth UniversityRichmondVAUSA
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Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
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Martínez B, Rodríguez A, Kulakauskas S, Chapot-Chartier MP. Cell wall homeostasis in lactic acid bacteria: threats and defences. FEMS Microbiol Rev 2021; 44:538-564. [PMID: 32495833 PMCID: PMC7476776 DOI: 10.1093/femsre/fuaa021] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB.
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Affiliation(s)
- Beatriz Martínez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Ana Rodríguez
- DairySafe research group. Department of Technology and Biotechnology of Dairy Products. Instituto de Productos Lácteos de Asturias, IPLA-CSIC. Paseo Río Linares s/n. 33300 Villaviciosa, Spain
| | - Saulius Kulakauskas
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Nguyen S, Truong JQ, Bruning JB. Targeting Unconventional Pathways in Pursuit of Novel Antifungals. Front Mol Biosci 2021; 7:621366. [PMID: 33511160 PMCID: PMC7835888 DOI: 10.3389/fmolb.2020.621366] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 01/31/2023] Open
Abstract
The impact of invasive fungal infections on human health is a serious, but largely overlooked, public health issue. Commonly affecting the immunocompromised community, fungal infections are predominantly caused by species of Candida, Cryptococcus, and Aspergillus. Treatments are reliant on the aggressive use of pre-existing antifungal drug classes that target the fungal cell wall and membrane. Despite their frequent use, these drugs are subject to unfavorable drug-drug interactions, can cause undesirable side-effects and have compromised efficacy due to the emergence of antifungal resistance. Hence, there is a clear need to develop novel classes of antifungal drugs. A promising approach involves exploiting the metabolic needs of fungi by targeted interruption of essential metabolic pathways. This review highlights potential antifungal targets including enolase, a component of the enolase-plasminogen complex, and enzymes from the mannitol biosynthesis and purine nucleotide biosynthesis pathways. There has been increased interest in the enzymes that comprise these particular pathways and further investigation into their merits as antifungal targets and roles in fungal survival and virulence are warranted. Disruption of these vital processes by targeting unconventional pathways with small molecules or antibodies may serve as a promising approach to discovering novel classes of antifungals.
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Jia Q Truong
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
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75
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Mosier-Boss PA, Sorensen KC, George RD, Sims PC, Obraztsova A. Surface enhanced Raman scattering of bacteria using capped and uncapped silver nanoparticles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118742. [PMID: 32717522 DOI: 10.1016/j.saa.2020.118742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/01/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Surface enhanced Raman scattering (SERS) spectra of bacteria were obtained using citrate (capped) and borohydride (uncapped) generated silver nanoparticles (Ag NPs).The observed differences in SERS spectra are attributed to the manner in which these Ag NPs interact with bacteria. Capped Ag NPs are able to partition through the surface polysaccharides of the bacterial cell to bind to the inner and outer cell membranes, as well as the periplasmic space between them. The resultant spectra show contributions due to the components of the cell envelope and cellular secretions. Uncapped Ag NPs are unable to partition through the polysaccharide outer structures of the cells. Spectral features observed for these uncapped Ag NPs are secretions primarily due to the metabolites of purine degradation.
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Affiliation(s)
- P A Mosier-Boss
- GEC, 5101B Backlick Rd., Annandale, VA 22003, United States of America.
| | - K C Sorensen
- Naval Information Warfare Center Pacific, San Diego, CA 92152, United States of America
| | - R D George
- Naval Information Warfare Center Pacific, San Diego, CA 92152, United States of America
| | - P C Sims
- Naval Information Warfare Center Pacific, San Diego, CA 92152, United States of America
| | - A Obraztsova
- San Diego State University Research Foundation, San Diego, CA 92182, United States of America
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76
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Abdullah MR, Batuecas MT, Jennert F, Voß F, Westhoff P, Kohler TP, Molina R, Hirschmann S, Lalk M, Hermoso JA, Hammerschmidt S. Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA. J Mol Biol 2020; 433:166723. [PMID: 33242497 DOI: 10.1016/j.jmb.2020.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
Abstract
Nucleotides are important for RNA and DNA synthesis and, despite a de novo synthesis by bacteria, uptake systems are crucial. Streptococcus pneumoniae, a facultative human pathogen, produces a surface-exposed nucleoside-binding protein, PnrA, as part of an ABC transporter system. Here we demonstrate the binding affinity of PnrA to nucleosides adenosine, guanosine, cytidine, thymidine and uridine by microscale thermophoresis and indicate the consumption of adenosine and guanosine by 1H NMR spectroscopy. In a series of five crystal structures we revealed the PnrA structure and provide insights into how PnrA can bind purine and pyrimidine ribonucleosides but with preference for purine ribonucleosides. Crystal structures of PnrA:nucleoside complexes unveil a clear pattern of interactions in which both the N- and C- domains of PnrA contribute. The ribose moiety is strongly recognized through a conserved network of H-bond interactions, while plasticity in loop 27-36 is essential to bind purine- or pyrimidine-based nucleosides. Further, we deciphered the role of PnrA in pneumococcal fitness in infection experiments. Phagocytosis experiments did not show a clear difference in phagocytosis between PnrA-deficient and wild-type pneumococci. In the acute pneumonia infection model the deficiency of PnrA attenuated moderately virulence of the mutant, which is indicated by a delay in the development of severe lung infections. Importantly, we confirmed the loss of fitness in co-infections, where the wild-type out-competed the pnrA-mutant. In conclusion, we present the PnrA structure in complex with individual nucleosides and show that the consumption of adenosine and guanosine under infection conditions is required for virulence.
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Affiliation(s)
- Mohammed R Abdullah
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany; Present Address: Institut für Klinische Chemie und Laboratoriumsmedizin, Universitätsmedizin Greifswald, Germany
| | - María T Batuecas
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Franziska Jennert
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany; Present Address: Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Franziska Voß
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany
| | - Philipp Westhoff
- Cellular Metabolism/Metabolomics, Institute of Biochemistry, University of Greifswald, D-17487 Greifswald, Germany; Present Address: Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Thomas P Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain; Present Address: Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen, 2200, Denmark
| | - Stephanie Hirschmann
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany
| | - Michael Lalk
- Cellular Metabolism/Metabolomics, Institute of Biochemistry, University of Greifswald, D-17487 Greifswald, Germany
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain.
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany.
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77
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Timofeev VI, Fateev IV, Kostromina MA, Abramchik YA, Konstantinova ID, Volkov VV, Lykoshin DD, Mikheeva OO, Muravieva TI, Esipov RS, Kuranova IP. The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27. J Biomol Struct Dyn 2020; 40:3626-3641. [PMID: 33225840 DOI: 10.1080/07391102.2020.1848628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction were realized. As a result, it was determined that the TthPNPI is specific to guanosine while the TthPNPII to adenosine. According to the results of the size exclusion chromatography and SAXS study both enzymes are hexameric molecules. Based on the sequence alignment with homologous purine nucleoside phosphorylases (PNPs), Asn was identified as a purine base recognizing residue in the active site of TthPNPI and Asp in TthPNPII. The three-dimensional structure of TthPNPII was solved at 2.5 Å resolution by molecular replacement method using crystals grown in microgravity. Position of phosphate in the active site cavity is located. The possible arrangement of adenosine and guanosine in TthPNPII active site cavity is considered using superposition with the structures of homologous trimeric and hexameric PNPs complexed with corresponding substrates. The peculiarities of oligomeric structure of TthPNPII in comparison with homologous PNPs are described. It is shown that two trimeric molecules of TthPNPII in the asymmetric part of the unit cell are connected by three two-fold axis into a hexamer with 32-point symmetry. This type of hexameric structure of PNP is found for the first time. The interface area between the subunits in trimeric molecule and between the trimers in TthPNPII hexamer is described.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya V Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Kostromina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuliya A Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Volkov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry D Lykoshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga O Mikheeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana I Muravieva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman S Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
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78
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Meng L, Li S, Liu G, Fan X, Qiao Y, Zhang A, Lin Y, Zhao X, Huang K, Feng Z. The nutrient requirements of Lactobacillus acidophilus LA-5 and their application to fermented milk. J Dairy Sci 2020; 104:138-150. [PMID: 33131816 DOI: 10.3168/jds.2020-18953] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/18/2020] [Indexed: 11/19/2022]
Abstract
Lactobacillus acidophilus LA-5 is a suitable probiotic for food application, but because of its slow growth in milk, an increase in its efficiency is desired. To shorten the time required for fermentation, the nutrient requirements of L. acidophilus LA-5 were analyzed, including the patterns of consumption of amino acids, purines, pyrimidines, vitamins, and metal ions. The nutrients required by L. acidophilus LA-5 were Asn, Asp, Cys, Leu, Met, riboflavin, guanine, uracil, and Mn2+, and when they were added to milk, the fermentation time of fermented milk prepared by L. acidophilus LA-5 alone was shortened by 9 h, with high viable cell counts that were maintained during storage of nutrient-supplemented fermented milk compared with the control. For fermented milk prepared by fermentation with Streptococcus thermophilus, Lactobacillus delbrueckii ssp. bulgaricus, and L. acidophilus LA-5, viable cell counts of L. acidophilus LA-5 increased 1.3-fold and were maintained during storage of nutrient-supplemented fermented milk compared with the control. Adding nutrients had no negative effect on the quality of the fermented milk. The results indicated that suitable nutrients enhanced the growth of L. acidophilus LA-5 and increased its viable cell counts in fermented milk prepared by L. acidophilus LA-5 alone and mixed starter culture, respectively.
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Affiliation(s)
- Li Meng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Shuang Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Gefei Liu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Xuejing Fan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Yali Qiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Ao Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Yanan Lin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Xingming Zhao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Kai Huang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, 600 Changjiang Road, Harbin, 150030, Heilongjiang, China.
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79
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Huo T, Zhao Y, Tang X, Zhao H, Ni S, Gao Q, Liu S. Metabolic acclimation of anammox consortia to decreased temperature. ENVIRONMENT INTERNATIONAL 2020; 143:105915. [PMID: 32652345 DOI: 10.1016/j.envint.2020.105915] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Widespread application of anammox process has been primarily limited to the high sensitivity of anammox consortia to fluctuations of temperature. However, the metabolic acclimation of anammox consortia to decreased temperature remains unclear, which is the core of developing potential strategies for improving their low-temperature resistance. Here, we operated anammox reactors at 25 °C and 35 °C to explore the acclimation mechanism of anammox consortia in terms of metabolic responses and cross-feedings. Accordingly, we found that the adaptation of anammox consortia to ambient temperature (25 °C) was significantly linked to energy conservation strategy, resulting in decreased extracellular polymeric substance secretion, accumulation of ATP and amino acids. The expression patterns of cold shock proteins and core enzymes caused the apparent metabolic advantage of Candidatus Brocadia fulgida for acclimation to ambient temperature compared to other anammox species. Importantly, strengthened cross-feedings of amino acids, nitrite and glycine betaine benefited adaptation of anammox consortia to ambient temperature. Our work not only uncovers the temperature-adaptive mechanisms of anammox consortia, but also emphasizes the important role of metabolic cross-feeding in the temperature adaptation of microbial community.
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Affiliation(s)
- Tangran Huo
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yunpeng Zhao
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xi Tang
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Huazhang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
| | - Sitong Liu
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
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80
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Yamada N, Saito C, Kano H, Fukuuchi T, Yamaoka N, Kaneko K, Asami Y. Lactobacillus gasseri PA-3 directly incorporates purine mononucleotides and utilizes them for growth. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 41:221-230. [PMID: 32954967 DOI: 10.1080/15257770.2020.1815768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Lactococcus lactis has been reported unable to directly incorporate mononucleotides but instead requires their external dephosphorylation by nucleotidases to the corresponding nucleosides prior to their incorporation. Although Lactobacillus gasseri PA-3 (PA-3), a strain of lactic acid bacteria, has been found to incorporate purine mononucleotides such as adenosine 5'-monophosphate (AMP), it remains unclear whether these bacteria directly incorporate these mononucleotides or incorporate them after dephosphorylation to the corresponding nucleosides. This study evaluated whether PA-3 incorporated radioactively-labeled mononucleotides in the presence or absence of the 5'-nucleotidase inhibitor α,β-methylene ADP (APCP). PA-3 took up 14C-AMP in the presence of APCP, as well as incorporating 32P-AMP. Furthermore, radioactivity was detected in the RNA/DNA of bacterial cells cultured in the presence of 32P-AMP. Taken together, these findings indicated that PA-3 incorporated purine mononucleotides directly rather than after their dephosphorylation to purine nucleosides and that PA-3 utilizes these purine mononucleotides in the synthesis of RNA and DNA. Although additional studies are required to identify purine mononucleotide transporters in PA-3, this study is the first to show that some lactic acid bacteria directly incorporate purine mononucleotides and use them for growth.
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Affiliation(s)
- N Yamada
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan.,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - C Saito
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan.,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - H Kano
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan.,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - T Fukuuchi
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - N Yamaoka
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - K Kaneko
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - Y Asami
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan
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81
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Canon F, Nidelet T, Guédon E, Thierry A, Gagnaire V. Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures. Front Microbiol 2020; 11:2088. [PMID: 33013761 PMCID: PMC7500094 DOI: 10.3389/fmicb.2020.02088] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms grow in concert, both in natural communities and in artificial or synthetic co-cultures. Positive interactions between associated microbes are paramount to achieve improved substrate conversion and process performance in biotransformation and fermented food production. The mechanisms underlying such positive interactions have been the focus of numerous studies in recent decades and are now starting to be well characterized. Lactic acid bacteria (LAB) contribute to the final organoleptic, nutritional, and health properties of fermented food products. However, interactions in LAB co-cultures have been little studied, apart from the well-characterized LAB co-culture used for yogurt manufacture. LAB are, however, multifunctional microorganisms that display considerable potential to create positive interactions between them. This review describes why LAB co-cultures are of such interest, particularly in foods, and how their extensive nutritional requirements can be used to favor positive interactions. In that respect, our review highlights the benefits of co-cultures in different areas of application, details the mechanisms underlying positive interactions and aims to show how mechanisms based on nutritional interactions can be exploited to create efficient LAB co-cultures.
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Affiliation(s)
| | - Thibault Nidelet
- SPO, INRAE, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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82
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Duggal Y, Fontaine BM, Dailey DM, Ning G, Weinert EE. RNase I Modulates Escherichia coli Motility, Metabolism, and Resistance. ACS Chem Biol 2020; 15:1996-2004. [PMID: 32551492 DOI: 10.1021/acschembio.0c00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacteria are constantly adapting to their environment by sensing extracellular factors that trigger production of intracellular signaling molecules, known as second messengers. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified in Escherichia coli and have emerged as possible novel signaling molecules. 2',3'-cNMPs are produced through endonucleolytic cleavage of short RNAs by the T2 endoribonuclease, RNase I; however, the physiological roles of RNase I remain unclear. Our transcriptomic analysis suggests that RNase I is involved in modulating numerous cellular processes, including nucleotide metabolism, motility, acid sensitivity, metal homeostasis, and outer membrane morphology. Through a combination of deletion strain and inhibitor studies, we demonstrate that RNase I plays a previously unknown role in E. coli stress resistance by affecting pathways that are part of the defense mechanisms employed by bacteria when introduced to external threats, including antibiotics. Thus, this work provides insight into the emerging roles of RNase I in bacterial signaling and physiology and highlights the potential of RNase I as a target for antibacterial adjuvants.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Benjamin M. Fontaine
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Deanna M. Dailey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Gang Ning
- Microscopy Facility, Huck Institute of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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83
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Li WM, Liao XW, Guo JS, Zhang YX, Chen YP, Fang F, Yan P. New insights into filamentous sludge bulking: The potential role of extracellular polymeric substances in sludge bulking in the activated sludge process. CHEMOSPHERE 2020; 248:126012. [PMID: 31995736 DOI: 10.1016/j.chemosphere.2020.126012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/29/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The control of filamentous sludge bulking has been regarded as an important issue in the activated sludge process due to there is still a lack of understanding of the bulking mechanisms. In this study, changes in the extracellular polymeric substances (EPS) and metabolic profile of bulking sludge based on the proteomics level was investigated to reveal the potential role of EPS in deteriorating sludge floc stability and structure during filamentous bulking. The results showed that the EPS content gradually decreased from 210.23 mg/g volatile suspended solids (VSS) to 131.34 mg/g VSS during sludge bulking. The protein (PN) content of the EPS significantly decreased from 173.33 mg/g VSS to 95.42 mg/g VSS during sludge bulking. However, a gradual increase in polysaccharides (PS) was observed. Bacterial aggregation was hindered by the changes in the EPS and its components. The excessive proliferation of filamentous bacteria had a significant effect on the molecular functions of the extracellular PN and metabolic pathways of the EPS. The proteins associated with the hydrophobic amino acid synthesis decreased, whereas the proteins associated with the hydrophilic amino acid synthesis increased during sludge bulking. Electric repulsion was the key factor affecting the aggregation and flocculation ability of the bacteria during sludge bulking. The changes in the EPS and its components induced by the excessive proliferation of filamentous bacteria resulted in a loose floc structure and poor settling performance during sludge bulking. These findings provide new insights into sludge bulking during the activated sludge process.
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Affiliation(s)
- Wei-Ming Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Xi-Wen Liao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Yu-Xin Zhang
- State Key Laboratory of Mechanical Transmissions, College of Materials Science and Engineering, Chongqing University, Chongqing, 400044, PR China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
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84
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Kano H, Saito C, Yamada N, Fukuuchi T, Yamaoka N, Kaneko K, Asami Y. Species-dependent patterns of incorporation of purine mononucleotides and nucleosides by lactic acid bacteria. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1440-1448. [PMID: 32397874 DOI: 10.1080/15257770.2020.1733604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Although most lactic acid bacteria do not directly incorporate purine nucleotides, the strain Lactobacillus gasseri PA-3 was found to incorporate purine mononucleotides. To determine whether the direct uptake of purine mononucleotides is dependent on the species or strain of lactic acid bacteria, incorporation of purine mononucleotides was assessed in L. gasseri, Lactcoccus lactis sbsp. lactis, Streptococcus thermophilus and other species of lactic acid bacteria. Each bacterial strain was incubated with 32P-AMP or 14C-adenosine and the incorporation of each purine was evaluated by measuring their radioactivity. All investigated strains of L. gasseri incorporated 32P-AMP, whereas strains of S. thermophilus and most strains of L. lactis did not. Incorporation of 32P-AMP into strains of Pediococcus was dependent on the strain or species of that genus of bacteria. All investigated strains, except for one strain of L. gasseri, incorporated 14C-adenosine, with S. thermophilus, L. lactis and Pediococcus generally displaying greater incorporation of 14C-adenosine than L. gasseri. Although most lactic acid bacteria such as S. thermophiles and L. lactis do not incorporate purine mononucleotides, some species such as L. gasseri directly incorporate purine mononucleotides. These findings indicate that the preferential incorporation of purine mononucleotides or nucleosides by lactic acid bacteria is dependent on the species or strain.
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Affiliation(s)
- H Kano
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan
| | - C Saito
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan
| | - N Yamada
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan
| | - T Fukuuchi
- Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - N Yamaoka
- Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - K Kaneko
- Faculty of Pharma Sciences, Teikyo University, Tokyo, Japan
| | - Y Asami
- Food Microbiology Research Laboratories, R&D Division, Meiji Co., Ltd, Tokyo, Japan
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85
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Alreshidi MM. Selected Metabolites Profiling of Staphylococcus aureus Following Exposure to Low Temperature and Elevated Sodium Chloride. Front Microbiol 2020; 11:834. [PMID: 32457719 PMCID: PMC7225588 DOI: 10.3389/fmicb.2020.00834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/07/2020] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus is one of the main foodborne pathogens that can cause food poisoning. Due to this reason, one of the essential aspects of food safety focuses on bacterial adaptation and proliferation under preservative conditions. This study was aimed to determine the metabolic changes that can occur following the exposure of S. aureus to either low temperature conditions or elevated concentrations of sodium chloride (NaCl). The results revealed that most of the metabolites measured were reduced in cold-stressed cells, when compared to reference controls. The major reduction was observed in nucleotides and organic acids, whereas mannitol was significantly increased in response to low temperature. However, when S. aureus was exposed to elevated NaCl, a significant increase was observed in the metabolite levels, particularly purine and pyrimidine bases along with organic acids. The majority of carbohydrates remained constant in the cells grown under ideal conditions and those exposed to elevated NaCl concentrations. Partial least square discriminate analysis (PLS-DA) of the metabolomic data indicated that both, prolonged cold stress and osmotic stress conditions, generated cells with different metabolic profiles, in comparison to the reference controls. These results provide evidence that, when bacterial cells exposed to low temperatures or high concentrations of NaCl, experience in situ homeostatic alterations to adapt to new environmental conditions. These data supported the hypothesis that changes in metabolic homeostasis were critical to the adaptive processes required for survival under alterations in the environmental conditions.
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Affiliation(s)
- Mousa M Alreshidi
- Department of Biology, College of Science, University of Ha'il, Hail, Saudi Arabia
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86
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Liu J, Yu M, Chatnaparat T, Lee JH, Tian Y, Hu B, Zhao Y. Comparative transcriptomic analysis of global gene expression mediated by (p) ppGpp reveals common regulatory networks in Pseudomonas syringae. BMC Genomics 2020; 21:296. [PMID: 32272893 PMCID: PMC7146990 DOI: 10.1186/s12864-020-6701-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/25/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Pseudomonas syringae is an important plant pathogen, which could adapt many different environmental conditions. Under the nutrient-limited and other stress conditions, P. syringae produces nucleotide signal molecules, i.e., guanosine tetra/pentaphosphate ((p)ppGpp), to globally regulate gene expression. Previous studies showed that (p) ppGpp played an important role in regulating virulence factors in P. syringae pv. tomato DC3000 (PstDC3000) and P. syringae pv. syringae B728a (PssB728a). Here we present a comparative transcriptomic analysis to uncover the overall effects of (p)ppGpp-mediated stringent response in P. syringae. RESULTS In this study, we investigated global gene expression profiles of PstDC3000 and PssB728a and their corresponding (p)ppGpp0 mutants in hrp-inducing minimal medium (HMM) using RNA-seq. A total of 1886 and 1562 differentially expressed genes (DEGs) were uncovered between the (p)ppGpp0 mutants and the wild-type in PstDC3000 and PssB728a, respectively. Comparative transcriptomics identified 1613 common DEGs, as well as 444 and 293 unique DEGs in PstDC3000 and PssB728a, respectively. Functional cluster analysis revealed that (p) ppGpp positively regulated a variety of virulence-associated genes, including type III secretion system (T3SS), type VI secretion system (T6SS), cell motility, cell division, and alginate biosynthesis, while negatively regulated multiple basic physiological processes, including DNA replication, RNA processes, nucleotide biosynthesis, fatty acid metabolism, ribosome protein biosynthesis, and amino acid metabolism in both PstDC3000 and PssB728a. Furthermore, (p) ppGpp had divergent effects on other processes in PstDC3000 and PssB728a, including phytotoxin, nitrogen regulation and general secretion pathway (GSP). CONCLUSION In this study, comparative transcriptomic analysis reveals common regulatory networks in both PstDC3000 and PssB728a mediated by (p) ppGpp in HMM. In both P. syringae systems, (p) ppGpp re-allocate cellular resources by suppressing multiple basic physiological activities and enhancing virulence gene expression, suggesting a balance between growth, survival and virulence. Our research is important in that due to similar global gene expression mediated by (p) ppGpp in both PstDC3000 and PssB728a, it is reasonable to propose that (p) ppGpp could be used as a target to develop novel control measures to fight against important plant bacterial diseases.
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Affiliation(s)
- Jun Liu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA
| | - Yanli Tian
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Baishi Hu
- College of Plant Protection, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, 210095, P. R. China.
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL, 61801, USA.
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87
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Yang HW, Yu M, Lee JH, Chatnaparat T, Zhao Y. The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora. BMC Genomics 2020; 21:261. [PMID: 32228459 PMCID: PMC7106674 DOI: 10.1186/s12864-020-6699-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/24/2020] [Indexed: 01/30/2023] Open
Abstract
Background The nucleotide second messengers, i.e., guanosine tetraphosphate and pentaphosphate [collectively referred to as (p) ppGpp], trigger the stringent response under nutrient starvation conditions and play an essential role in virulence in the fire blight pathogen Erwinia amylovora. Here, we present transcriptomic analyses to uncover the overall effect of (p) ppGpp-mediated stringent response in E. amylovora in the hrp-inducing minimal medium (HMM). Results In this study, we investigated the transcriptomic changes of the (p) ppGpp0 mutant under the type III secretion system (T3SS)-inducing condition using RNA-seq. A total of 1314 differentially expressed genes (DEGs) was uncovered, representing more than one third (36.8%) of all genes in the E. amylovora genome. Compared to the wild-type, the (p) ppGpp0 mutant showed down-regulation of genes involved in peptide ATP-binding cassette (ABC) transporters and virulence-related processes, including type III secretion system (T3SS), biofilm, and motility. Interestingly, in contrast to previous reports, the (p) ppGpp0 mutant showed up-regulation of amino acid biosynthesis genes, suggesting that it might be due to that these amino acid biosynthesis genes are indirectly regulated by (p) ppGpp in E. amylovora or represent specific culturing condition used. Furthermore, the (p) ppGpp0 mutant exhibited up-regulation of genes involved in translation, SOS response, DNA replication, chromosome segregation, as well as biosynthesis of nucleotide, fatty acid and lipid. Conclusion These findings suggested that in HMM environment, E. amylovora might use (p) ppGpp as a signal to activate virulence gene expression, and simultaneously mediate the balance between virulence and survival by negatively regulating DNA replication, translation, cell division, as well as biosynthesis of nucleotide, amino acid, fatty acid, and lipid. Therefore, (p) ppGpp could be a promising target for developing novel control measures to fight against this devastating disease of apples and pears.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Tiyakhon Chatnaparat
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr, Urbana, IL, 61801, USA.
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88
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Leonard A, Möhlis K, Schlüter R, Taylor E, Lalk M, Methling K. Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. J Antibiot (Tokyo) 2020; 73:441-454. [PMID: 32210362 PMCID: PMC7292801 DOI: 10.1038/s41429-020-0296-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
The Gram-positive bacterium Streptococcus pneumoniae is one of the common causes of community acquired pneumonia, meningitis, and otitis media. Analyzing the metabolic adaptation toward environmental stress conditions improves our understanding of its pathophysiology and its dependency on host-derived nutrients. In this study, extra- and intracellular metabolic profiles were evaluated to investigate the impact of antimicrobial compounds targeting different pathways of the metabolome of S. pneumoniae TIGR4Δcps. For the metabolomics approach, we analyzed the complex variety of metabolites by using 1H NMR, HPLC-MS, and GC–MS as different analytical techniques. Through this combination, we detected nearly 120 metabolites. For each antimicrobial compound, individual metabolic effects were detected that often comprised global biosynthetic pathways. Cefotaxime altered amino acids metabolism and carbon metabolism. The purine and pyrimidine metabolic pathways were mostly affected by moxifloxacin treatment. The combination of cefotaxime and azithromycin intensified the stress response compared with the use of the single antibiotic. However, we observed that three cell wall metabolites were altered only by treatment with the combination of the two antibiotics. Only moxifloxacin stress-induced alternation in CDP-ribitol concentration. Teixobactin-Arg10 resulted in global changes of pneumococcal metabolism. To meet the growing requirements for new antibiotics, our metabolomics approach has shown to be a promising complement to other OMICs investigations allowing insights into the mode of action of novel antimicrobial compounds.
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Affiliation(s)
- Anne Leonard
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Kevin Möhlis
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, F.-L-Jahn-Str. 15, 17489, Greifswald, Germany
| | - Edward Taylor
- University of Lincoln, School of Life Sciences, Green Lane, LN67DL, Lincoln, England, United Kingdom
| | - Michael Lalk
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Karen Methling
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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89
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Zhang Y, Meng L, Ai M, Qiao Y, Liu G, Fan X, Lv X, Feng Z. Nutrient requirements of Lactobacillus casei Shirota and their application in fermented milk. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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90
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Torres AC, Elean M, Hebert EM, Saavedra L, Taranto MP. Metabolic shift in the production of corrinoid compounds by Lactobacillus coryniformis in the absence of purines. Biochimie 2020; 168:185-189. [DOI: 10.1016/j.biochi.2019.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022]
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91
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Li B, Liu Y, Wang L, Hong J, Chen Y, Ying H. RNA accumulation in Candida tropicalis based on cofactor engineering. FEMS Yeast Res 2019; 19:5426822. [PMID: 30942847 DOI: 10.1093/femsyr/foz028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/02/2019] [Indexed: 11/12/2022] Open
Abstract
Redox cofactors play an important role in biosynthetic and catabolic reactions and the transfer of energy for the cell. Therefore, studying the relationship between cofactor perturbation and metabolism is a useful approach to improve the yield of target products. To study RNA accumulation and metabolism when intracellular cofactor balance was impaired, the water-forming NADH oxidase (NoxE) from Lactococcus lactis and membrane-bound transhydrogenase (PntAB) from Escherichia coli were expressed in Candidatropicalis no. 121, respectively. Expression of noxE significantly decreased the intracellular NADH/NAD+ ratio, but the NADPH/NADP+ ratio did not differ significantly. PntAB increased the intracellular NADH pool, while the NADPH/NADP+ ratio decreased. The perturbation of the cofactors caused a large redistribution of metabolic fluxes. The biomass and RNA content decreased by 11.0% and 10.6% in pAUR-noxE strain, respectively, while the RNA content increased by 5.5% and the biomass showed no signification difference in pAUR-pntAB strain. Expression of noxE and pntAB led to decreases and increases in the ATP concentration and yield of RNA, respectively, which also indicated that ATP plays an important role in the RNA biosynthesis.
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Affiliation(s)
- Bingbing Li
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 367036, Henan, P.R. China.,Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China.,Henan Health Food Engineering and Technology Research Center, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China
| | - Ying Liu
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 367036, Henan, P.R. China.,Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China.,Henan Health Food Engineering and Technology Research Center, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China
| | - Lianzhe Wang
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 367036, Henan, P.R. China.,Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China.,Henan Health Food Engineering and Technology Research Center, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China
| | - Jun Hong
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 367036, Henan, P.R. China.,Henan Province Key Laboratory of Water Pollution Control and Rehabilitation Technology, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China.,Henan Health Food Engineering and Technology Research Center, Henan University of Urban Construction, Pingdingshan, 467036, Henan, P.R. China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, P.R. China.,National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, Nanjing, 211009, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 210009, P.R. China.,National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, Nanjing, 211009, China
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92
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Pelicaen R, Gonze D, Teusink B, De Vuyst L, Weckx S. Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. Front Microbiol 2019; 10:2801. [PMID: 31921009 PMCID: PMC6915089 DOI: 10.3389/fmicb.2019.02801] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
Acetobacter pasteurianus 386B is a candidate functional starter culture for the cocoa bean fermentation process. To allow in silico simulations of its related metabolism in response to different environmental conditions, a genome-scale metabolic model for A. pasteurianus 386B was reconstructed. This is the first genome-scale metabolic model reconstruction for a member of the genus Acetobacter. The metabolic network reconstruction process was based on extensive genome re-annotation and comparative genomics analyses. The information content related to the functional annotation of metabolic enzymes and transporters was placed in a metabolic context by exploring and curating a Pathway/Genome Database of A. pasteurianus 386B using the Pathway Tools software. Metabolic reactions and curated gene-protein-reaction associations were bundled into a genome-scale metabolic model of A. pasteurianus 386B, named iAp386B454, containing 454 genes, 322 reactions, and 296 metabolites embedded in two cellular compartments. The reconstructed model was validated by performing growth experiments in a defined medium, which revealed that lactic acid as the sole carbon source could sustain growth of this strain. Further, the reconstruction of the A. pasteurianus 386B genome-scale metabolic model revealed knowledge gaps concerning the metabolism of this strain, especially related to the biosynthesis of its cell envelope and the presence or absence of metabolite transporters.
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Affiliation(s)
- Rudy Pelicaen
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
| | - Didier Gonze
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
- Unité de Chronobiologie Théorique, Service de Chimie Physique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
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93
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Wu YW, Yang SH, Hwangbo M, Chu KH. Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system. PLoS One 2019; 14:e0222143. [PMID: 31513626 PMCID: PMC6742469 DOI: 10.1371/journal.pone.0222143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/22/2019] [Indexed: 01/25/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.
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Affiliation(s)
- Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Shih-Hung Yang
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
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94
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Genome, transcriptome and fermentation analyses of Lactobacillus plantarum LY-78 provide new insights into the mechanism of phenyllactate biosynthesis in lactic acid bacteria. Biochem Biophys Res Commun 2019; 519:351-357. [PMID: 31514995 DOI: 10.1016/j.bbrc.2019.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 09/04/2019] [Indexed: 11/21/2022]
Abstract
Phenyllactate (PLA) is found in a variety of fermented foods and is a promising antibacterial agent, drug and plastic synthetic precursor. Previous studies have shown that PLA is a product of Phe catabolism in lactic acid bacteria (LAB), and PLA biosynthesis is mainly related to lactate dehydrogenases (LDHs). Here, the genome, transcriptome and fermentation characteristics of PLA-producing Lactobacillus plantarum LY-78 were studied. The fermentation experiments demonstrated that L. plantarum LY-78 possesses the ability to synthesize PLA de novo. Secondly, the genome and transcriptome analyses revealed candidate pathways, operons and key genes for PLA biosynthesis in the strain. Finally, genome-wide transcriptome analysis revealed significant changes in the expression profile of strain LY-78 in the absence and presence of PPA. Overall, this work demonstrates for the first time that PLA can be a by-product of Phe anabolism in LAB, provides new insights and evidence for elucidating the mechanism of PLA biosynthesis in LAB, and may provide new candidate genes and research strategies for future PLA biosynthesis applications.
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95
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Abstract
Bacterial metabolism represents the biochemical space that bacteria can manipulate to produce energy, reducing equivalents and building blocks for replication. Gram-positive pathogens, such as Listeria monocytogenes, show remarkable flexibility, which allows for exploitation of diverse biological niches from the soil to the intracytosolic space. Although the human host represents a potentially rich source for nutrient acquisition, competition for nutrients with the host and hostile host defenses can constrain bacterial metabolism by various mechanisms, including nutrient sequestration. Here, we review metabolism in the model Gram-positive bacterium, L. monocytogenes, and highlight pathways that enable the replication, survival, and virulence of this bacterial pathogen.
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96
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Li J, Yu L, Li J, Xie L, Zhang R, Wang H. Establishment of a high throughput-screening system for nucleoside deoxyribosyltransferase II mutant enzymes with altered substrate specificity. J Biosci Bioeng 2019; 128:22-27. [DOI: 10.1016/j.jbiosc.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/23/2022]
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97
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Quesille-Villalobos AM, Parra A, Maza F, Navarrete P, González M, Latorre M, Toro M, Reyes-Jara A. The Combined Effect of Cold and Copper Stresses on the Proliferation and Transcriptional Response of Listeria monocytogenes. Front Microbiol 2019; 10:612. [PMID: 30984140 PMCID: PMC6447683 DOI: 10.3389/fmicb.2019.00612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that can cause severe disease in susceptible humans. This microorganism has the ability to adapt to hostile environmental conditions such as the low temperatures used by the food industry for controlling microorganisms. Bacteria are able to adjust their transcriptional response to adapt to stressful conditions in order to maintain cell homeostasis. Understanding the transcriptional response of L. monocytogenes to stressing conditions could be relevant to develop new strategies to control the pathogen. A possible alternative for controlling microorganisms in the food industry could be to use copper as an antimicrobial agent. The present study characterized three L. monocytogenes strains (List2-2, Apa13-2, and Al152-2A) adapted to low temperature and challenged with different copper concentrations. Similar MIC-Cu values were observed among studied strains, but growth kinetic parameters revealed that strain List2-2 was the least affected by the presence of copper at 8°C. This strain was selected for a global transcriptional response study after a 1 h exposition to 0.5 mM of CuSO4 × 5H2O at 8 and 37°C. The results showed that L. monocytogenes apparently decreases its metabolism in response to copper, and this reduction is greater at 8°C than at 37°C. The most affected metabolic pathways were carbohydrates, lipids and nucleotides synthesis. Finally, 15 genes were selected to evaluate the conservation of the transcriptional response in the other two strains. Results indicated that only genes related to copper homeostasis showed a high degree of conservation between the strains studied, suggesting that a low number of genes is implicated in the response to copper stress in L. monocytogenes. These results contribute to the understanding of the molecular mechanisms used by bacteria to overcome a combination of stresses. This study concluded that the application of copper in low concentrations in cold environments may help to control foodborne pathogens as L. monocytogenes in the industry.
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Affiliation(s)
- Ana María Quesille-Villalobos
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Angel Parra
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Felipe Maza
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Paola Navarrete
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation (CGR), Santiago, Chile
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- FONDAP Center for Genome Regulation (CGR), Santiago, Chile
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile
- Instituto de Ciencias de la Ingeniería, Universidad de O’Higgins, Rancagua, Chile
| | - Magaly Toro
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
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98
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Siciliano RA, Pannella G, Lippolis R, Ricciardi A, Mazzeo MF, Zotta T. Impact of aerobic and respirative life-style on Lactobacillus casei N87 proteome. Int J Food Microbiol 2019; 298:51-62. [PMID: 30925356 DOI: 10.1016/j.ijfoodmicro.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/10/2019] [Accepted: 03/10/2019] [Indexed: 12/27/2022]
Abstract
Lactic acid bacteria (LAB) are used as starter, adjunct and/or probiotic cultures in fermented foods. Several species are recognized as oxygen-tolerant anaerobes, and aerobic and respiratory cultivations may provide them with physiological and technological benefits. In this light, mechanisms involved in the adaptation to aerobic and respiratory (supplementation with heme and menaquinone) growth conditions of the O2-tolerant strain Lactobacillus casei N87 were investigated by proteomics. In fact, in this bacterial strain, respiration induced an increase in biomass yield and robustness to oxidative, long-term starvation and freeze-drying stresses, while high concentrations of dissolved O2 (dO2 60%) negatively affected its growth and cell survival. Proteomic results well paralleled with physiological and metabolic features and clearly showed that aerobic life-style led to a higher abundance of several proteins involved in carbohydrate metabolism and stress response mechanisms and, concurrently, impaired the biosynthesis of proteins involved in nucleic acid formation and translation processes, thus providing evidence at molecular level of the significant damage to L.casei N87 fitness. On the contrary, the activation of respiratory pathways due to heme and menaquinone supplementation, led to a decreased amount of chaperones and other stress related proteins. These findings confirmed that respiration reduced oxidative stress condition, allowing to positively modulate the central carbohydrate and energy metabolism and improve growth and stress tolerance features. Results of this study could be potentially functional to develop competitive adjunct and probiotic cultures effectively focused on the improvement of quality of fermented foods and the promotion of human health.
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Affiliation(s)
- Rosa Anna Siciliano
- Institute of Food Sciences, National Research Council (CNR-ISA), Avellino, Italy
| | - Gianfranco Pannella
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Rosa Lippolis
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
| | - Annamaria Ricciardi
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | | | - Teresa Zotta
- Institute of Food Sciences, National Research Council (CNR-ISA), Avellino, Italy
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Xu D, Bechtner J, Behr J, Eisenbach L, Geißler AJ, Vogel RF. Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization. Int J Food Microbiol 2019; 290:141-149. [DOI: 10.1016/j.ijfoodmicro.2018.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/10/2018] [Accepted: 10/03/2018] [Indexed: 10/28/2022]
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100
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Doo EH, Schwab C, Chassard C, Lacroix C. Cumulative effect of yeast extract and fructooligosaccharide supplementation on composition and metabolic activity of elderly colonic microbiota in vitro. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.10.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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