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Dierksheide KJ, Li GW. A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001455. [PMID: 38602388 PMCID: PMC11084560 DOI: 10.1099/mic.0.001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Since the 1980s, chromosome-integration vectors have been used as a core method of engineering Bacillus subtilis. One of the most frequently used vector backbones contains chromosomally derived regions that direct homologous recombination into the amyE locus. Here, we report a gap in the homology region inherited from the original amyE integration vector, leading to erroneous recombination in a subset of transformants and a loss-of-function mutation in the downstream gene. Internal to the homology arm that spans the 3' portion of amyE and the downstream gene ldh, an unintentional 227 bp deletion generates two crossover events. The major event yields the intended genotype, but the minor event, occurring in ~10 % of colonies, results in a truncation of ldh, which encodes lactate dehydrogenase. Although both types of colonies test positive for amyE disruption by starch plating, the potential defect in fermentative metabolism may be left undetected and confound the results of subsequent experiments.
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Affiliation(s)
- K. Julia Dierksheide
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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2
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Bai J, Xie Y, Li M, Huang X, Guo Y, Sun J, Tang Y, Liu X, Wei C, Li J, Yang Y. Ultrasound-assisted extraction of emodin from Rheum officinale Baill and its antibacterial mechanism against Streptococcus suis based on CcpA. ULTRASONICS SONOCHEMISTRY 2024; 102:106733. [PMID: 38150957 PMCID: PMC10765492 DOI: 10.1016/j.ultsonch.2023.106733] [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: 03/01/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Emodin was extracted from Rheum officinale Baill by ultrasound-assisted extraction (UAE), and ethanol was chosen as the suitable solvent through SEM and molecular dynamic simulation. Under the optimum conditions (power 541 W, time 23 min, liquid to material ratio 13:1 mL/g, ethanol concentration 83 %) predicted by RSM, the yield of emodin was 2.18 ± 0.11 mg/g. Moreover, ultrasound power and time displayed the significant effects on the extraction process. Extracting dynamics analysis indicated that the extraction process of emodin by UAE conformed to Fick's second diffusion law. The results of antibacterial experiments suggested that emodin can damage cell membrane and inhibit the expression of cps2A, sao, mrp, epf, neu and the hemolytic activity of S. suis. Biolayer interferometry and FT-IR multi-peak fitting assays demonstrated that emodin induced a secondary conformational shift in CcpA. Molecular docking and molecular dynamics confirmed that emodin bound to CcpA through hydrogen bonding (ALA248, GLU249, GLY129 and ASN196) and π-π T-shaped interaction (TYR225 and TYR130), and the mutation of amino acid residues affected the affinity of CcpA to emodin. Therefore, emodin inhibited the sugar utilization of S. suis through binding to CcpA, and CcpA may be a potential target to inhibit the growth of S. suis.
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Affiliation(s)
- Jingwen Bai
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Xie
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Miao Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xianjun Huang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yujia Guo
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jingwen Sun
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yang Tang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xuantong Liu
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Chi Wei
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jianqiang Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Yang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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Xiao F, Zhang Y, Zhang L, Ding Z, Shi G, Li Y. Construction of the genetic switches in response to mannitol based on artificial MtlR box. BIORESOUR BIOPROCESS 2023; 10:9. [PMID: 38647829 PMCID: PMC10992428 DOI: 10.1186/s40643-023-00634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Synthetic biology has rapidly advanced from the setup of native genetic devices to the design of artificial elements able to provide organisms with highly controllable functions. In particular, genetic switches are crucial for deploying new layers of regulation into the engineered organisms. While the assembly and mutagenesis of native elements have been extensively studied, limited progress has been made in rational design of genetic switches due to a lack of understanding of the molecular mechanism by which a specific transcription factor interacts with its target gene. Here, a reliable workflow is presented for designing two categories of genetic elements, one is the switch element-MtlR box and the other is the transcriptional regulatory element- catabolite control protein A (CcpA) box. The MtlR box was designed for ON/OFF-state selection and is controlled by mannitol. The rational design of MtlR box-based molecular structures can flexibly tuned the selection of both ON and OFF states with different output switchability in response to varied kind effectors. Different types of CcpA boxes made the switches with more markedly inducer sensitivities. Ultimately, the OFF-state value was reduced by 90.69%, and the maximum change range in the presence of two boxes was 15.31-fold. This study presents a specific design of the switch, in a plug-and-play manner, which has great potential for controlling the flow of the metabolic pathway in synthetic biology.
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Affiliation(s)
- Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu, People's Republic of China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
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Roux AE, Robert S, Bastat M, Rosinski-Chupin I, Rong V, Holbert S, Mereghetti L, Camiade E. The Role of Regulator Catabolite Control Protein A (CcpA) in Streptococcus agalactiae Physiology and Stress Response. Microbiol Spectr 2022; 10:e0208022. [PMID: 36264242 PMCID: PMC9784791 DOI: 10.1128/spectrum.02080-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Streptococcus agalactiae is a leading cause of infections in neonates. This opportunistic pathogen colonizes the vagina, where it has to cope with acidic pH and hydrogen peroxide produced by lactobacilli. Thus, in the host, this bacterium possesses numerous adaptation mechanisms in which the pleiotropic regulators play a major role. The transcriptional regulator CcpA (catabolite control protein A) has previously been shown to be the major regulator involved in carbon catabolite repression in Gram-positive bacteria but is also involved in other functions. By transcriptomic analysis, we characterized the CcpA-dependent gene regulation in S. agalactiae. Approximately 13.5% of the genome of S. agalactiae depends on CcpA for regulation and comprises genes involved in sugar uptake and fermentation, confirming the role of CcpA in carbon metabolism. We confirmed by electrophoretic mobility shift assays (EMSAs) that the DNA binding site called cis-acting catabolite responsive element (cre) determined for other streptococci was effective in S. agalactiae. We also showed that CcpA is of capital importance for survival under acidic and oxidative stresses and is implicated in macrophage survival by regulating several genes putatively or already described as involved in stress response. Among them, we focused our study on SAK_1689, which codes a putative UspA protein. We demonstrated that SAK_1689, highly downregulated by CcpA, is overexpressed under oxidative stress conditions, this overexpression being harmful for the bacterium in a ΔccpA mutant. IMPORTANCE Streptococcus agalactiae is a major cause of disease burden leading to morbidity and mortality in neonates worldwide. Deciphering its adaptation mechanisms is essential to understand how this bacterium manages to colonize its host. Here, we determined the regulon of the pleiotropic regulator CcpA in S. agalactiae. Our findings reveal that CcpA is not only involved in carbon catabolite repression, but is also important for acidic and oxidative stress resistance and survival in macrophages.
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Affiliation(s)
| | | | | | - Isabelle Rosinski-Chupin
- Unité Écologie et Évolution de la Résistance aux Antibiotiques, CNRS UMR3525, Institut Pasteur, Paris, France
| | | | | | - Laurent Mereghetti
- ISP, Université de Tours, INRAE, Tours, France
- CHRU Tours, Service de Bactériologie-Virologie-Hygiène, Tours, France
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Liang J, van Kranenburg R, Bolhuis A, Leak DJ. Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542. Front Microbiol 2022; 13:985465. [PMID: 36338101 PMCID: PMC9631020 DOI: 10.3389/fmicb.2022.985465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium of interest for lignocellulosic biomass fermentation. However, carbon catabolite repression (CCR) hinders co-utilization of pentoses and hexoses in the biomass substrate. Hence, to optimize the fermentation process, it is critical to remove CCR in the fermentation strains with minimal fitness cost. In this study, we investigated whether CCR could be removed from P. thermoglucosidasius DSM 2542 by mutating the Ser46 regulatory sites on HPr and Crh to a non-reactive alanine residue. It was found that neither the ptsH1 (HPr-S46A) nor the crh1 (Crh-S46A) mutation individually eliminated CCR in P. thermoglucosidasius DSM 2542. However, it was not possible to generate a ptsH1 crh1 double mutant. While the Crh-S46A mutation had no obvious fitness effect in DSM 2542, the ptsH1 mutation had a negative impact on cell growth and sugar utilization under fermentative conditions. Under these conditions, the ptsH1 mutation was associated with the production of a brown pigment, believed to arise from methylglyoxal production, which is harmful to cells. Subsequently, a less directed adaptive evolution approach was employed, in which DSM 2542 was grown in a mixture of 2-deoxy-D-glucose(2-DG) and xylose. This successfully removed CCR from P. thermoglucosidasius DSM 2542. Two selection strategies were applied to optimize the phenotypes of evolved strains. Genome sequencing identified key mutations affecting the PTS components PtsI and PtsG, the ribose operon repressor RbsR and adenine phosphoribosyltransferase APRT. Genetic complementation and bioinformatics analysis revealed that the presence of wild type rbsR and apt inhibited xylose uptake or utilization, while ptsI and ptsG might play a role in the regulation of CCR in P. thermoglucosidasius DSM 2542.
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Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
- *Correspondence: Jinghui Liang
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Corbion, Gorinchem, Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
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7
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Fu H, Zhang H, Guo X, Yang L, Wang J. Elimination of carbon catabolite repression in Clostridium tyrobutyricum for enhanced butyric acid production from lignocellulosic hydrolysates. BIORESOURCE TECHNOLOGY 2022; 357:127320. [PMID: 35589044 DOI: 10.1016/j.biortech.2022.127320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Clostridium tyrobutyricum, a gram-positive anaerobic bacterium, is recognized as the promising butyric acid producer. But, the existence of carbon catabolite repression (CCR) is the major drawback for C. tyrobutyricum to efficiently use the lignocellulosic biomass. In this study, the xylose pathway genes were first identified and verified. Then, the potential regulatory mechanisms of CCR in C. tyrobutyricum were proposed and the predicted engineering targets were experimental validated. Inactivation of hprK blocked the CcpA-mediated CCR and resulted in simultaneous conversion of glucose and xylose, although xylose consumption was severe lagging behind. Deletion of xylR further shortened the lag phase of xylose utilization. When hprK and xylR were inactivated together, the CCR in C. tyrobutyricum was completely eliminated. Consequently, ATCC 25755/ΔhprKΔxylR showed significant increase in butyrate productivity (1.8 times faster than the control) and excellent butyric acid fermentation performance using both mixed sugars (11.0-11.9 g/L) and undetoxified lignocellulosic hydrolysates (12.4-13.4 g/L).
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Affiliation(s)
- Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huihui Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaolong Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lu Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China.
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Interplay of CodY and CcpA in Regulating Central Metabolism and Biofilm Formation in Staphylococcus aureus. J Bacteriol 2022; 204:e0061721. [PMID: 35735992 PMCID: PMC9295537 DOI: 10.1128/jb.00617-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Staphylococcus aureus is a medically important pathogen with high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, namely, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development, we constructed and characterized the codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control the cellular metabolic status by altering carbon flux through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of extracellular DNA (eDNA) into the biofilm matrix, whereas disrupting codY resulted in a robust structured biofilm tethered together with eDNA and polysaccharide intercellular adhesin (PIA). Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and reduces eDNA release in the double mutant. Compared with the inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, the codY ccpA mutant produced large amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Combined, the results of this study suggest that the coordinated action of CodY and CcpA modulate central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in. IMPORTANCE Staphylococcus aureus is a leading cause of biofilm-associated infections, including infective endocarditis, worldwide. A greater understanding of metabolic forces driving biofilm formation in S. aureus is essential for the identification of novel therapeutic targets and for the development of new strategies to combat this medically important pathogen. This study characterizes the interplay and regulation of central metabolism and biofilm development by two global transcriptional regulators, CodY and CcpA. We found that the lack of CcpA and/or CodY have different impacts on intracellular metabolic status leading to a formation of morphologically altered biofilms. Overall, the results of this study provide new insights into our understanding of metabolism-mediated regulation of biofilm development in S. aureus.
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Regulation of CcpA on the growth and organic acid production characteristics of ruminal Streptococcus bovis at different pH. BMC Microbiol 2021; 21:344. [PMID: 34911440 PMCID: PMC8672513 DOI: 10.1186/s12866-021-02404-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Catabolite control protein A (CcpA) regulates the transcription of lactate dehydrogenase and pyruvate formate-lyase in Streptococcus bovis, but knowledge of its role in response to different pH is still limited. In this study, a ccpA-knockout strain of S. bovis S1 was constructed and then used to examine the effects of ccpA gene deletion on the growth and fermentation characteristics of S. bovis S1 at pH 5.5 or 6.5. RESULTS There was a significant interaction between strain and pH for the maximum specific growth rate (μmax) and growth lag period (λ), which caused a lowest μmax and a longest λ in ccpA-knockout strain at pH 5.5. Deletion of ccpA decreased the concentration and molar percentage of lactic acid, while increased those of formic acid. Strains at pH 5.5 had decreased concentrations of lactic acid and formic acid compared to pH 6.5. The significant interaction between strain and pH caused the highest production of total organic acids and acetic acid in ccpA-knockout strain at pH 6.5. The activities of α-amylase and lactate dehydrogenase decreased in ccpA-knockout strain compared to the wild-type strain, and increased at pH 5.5 compared to pH 6.5. There was a significant interaction between strain and pH for the activity of acetate kinase, which was the highest in the ccpA-knockout strain at pH 6.5. The expression of pyruvate formate-lyase and acetate kinase was higher in the ccpA-knockout strain compared to wild-type strain. The lower pH improved the relative expression of pyruvate formate-lyase, while had no effect on the relative expression of acetate kinase. The strain × pH interaction was significant for the relative expression of lactate dehydrogenase and α-amylase, both of which were highest in the wild-type strain at pH 5.5 and lowest in the ccpA-knockout strain at pH 6.5. CONCLUSIONS Overall, low pH inhibited the growth of S. bovis S1, but did not affect the fermentation pattern. CcpA regulated S. bovis S1 growth and organic acid fermentation pattern. Moreover, there seemed to be an interaction effect between pH and ccpA deletion on regulating the growth and organic acids production of S. bovis S1.
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Tsujikawa Y, Ishikawa S, Sakane I, Yoshida KI, Osawa R. Identification of genes encoding a novel ABC transporter in Lactobacillus delbrueckii for inulin polymers uptake. Sci Rep 2021; 11:16007. [PMID: 34362962 PMCID: PMC8346543 DOI: 10.1038/s41598-021-95356-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Lactobacillus delbrueckii JCM 1002T grows on highly polymerized inulin-type fructans as its sole carbon source. When it was grown on inulin, a > 10 kb long gene cluster inuABCDEF (Ldb1381-1386) encoding a plausible ABC transporter was suggested to be induced, since a transcriptome analysis revealed that the fourth gene inuD (Ldb1384) was up-regulated most prominently. Although Bacillus subtilis 168 is originally unable to utilize inulin, it became to grow on inulin upon heterologous expression of inuABCDEF. When freshly cultured cells of the recombinant B. subtilis were then densely suspended in buffer containing inulin polymers and incubated, inulin gradually disappeared from the buffer and accumulated in the cells without being degraded, whereas levan-type fructans did not disappear. The results imply that inuABCDEF might encode a novel ABC transporter in L. delbrueckii to "monopolize" inulin polymers selectively, thereby, providing a possible advantage in competition with other concomitant inulin-utilizing bacteria.
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Affiliation(s)
- Yuji Tsujikawa
- Central Research Institute, ITO EN, Ltd., 21 Mekami, Makinohara, Shizuoka 421-0516 Japan ,grid.31432.370000 0001 1092 3077Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Shu Ishikawa
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501 Japan
| | - Iwao Sakane
- Central Research Institute, ITO EN, Ltd., 21 Mekami, Makinohara, Shizuoka 421-0516 Japan
| | - Ken-ichi Yoshida
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501 Japan
| | - Ro Osawa
- grid.31432.370000 0001 1092 3077Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
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11
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Kachan AV, Evtushenkov AN. Acidification of the Culture Medium by Products of Glucose Metabolism Inhibits the Synthesis of Heterologous Extracellular α-amylase by Bacillus subtilis 168. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821040062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
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Bacterial-induced pH shifts link individual cell physiology to macroscale collective behavior. Proc Natl Acad Sci U S A 2021; 118:2014346118. [PMID: 33795512 DOI: 10.1073/pnas.2014346118] [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: 11/18/2022] Open
Abstract
Bacteria have evolved a diverse array of signaling pathways that enable them to quickly respond to environmental changes. Understanding how these pathways reflect environmental conditions and produce an orchestrated response is an ongoing challenge. Herein, we present a role for collective modifications of environmental pH carried out by microbial colonies living on a surface. We show that by collectively adjusting the local pH value, Paenibacillus spp., specifically, regulate their swarming motility. Moreover, we show that such pH-dependent regulation can converge with the carbon repression pathway to down-regulate flagellin expression and inhibit swarming in the presence of glucose. Interestingly, our results demonstrate that the observed glucose-dependent swarming repression is not mediated by the glucose molecule per se, as commonly thought to occur in carbon repression pathways, but rather is governed by a decrease in pH due to glucose metabolism. In fact, modification of the environmental pH by neighboring bacterial species could override this glucose-dependent repression and induce swarming of Paenibacillus spp. away from a glucose-rich area. Our results suggest that bacteria can use local pH modulations to reflect nutrient availability and link individual bacterial physiology to macroscale collective behavior.
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Wang J, Jiang Y, Yu P, Lee YK, Liu X, Zhao J, Zhang H, Chen W. Effect of carbon catabolite repression on lactose and galactose catabolism in Lacticaseibacillus paracasei. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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15
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DebRoy S, Aliaga-Tobar V, Galvez G, Arora S, Liang X, Horstmann N, Maracaja-Coutinho V, Latorre M, Hook M, Flores AR, Shelburne SA. Genome-wide analysis of in vivo CcpA binding with and without its key co-factor HPr in the major human pathogen group A Streptococcus. Mol Microbiol 2020; 115:1207-1228. [PMID: 33325565 PMCID: PMC8359418 DOI: 10.1111/mmi.14667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/01/2023]
Abstract
Catabolite control protein A (CcpA) is a master regulator of carbon source utilization and contributes to the virulence of numerous medically important Gram‐positive bacteria. Most functional assessments of CcpA, including interaction with its key co‐factor HPr, have been performed in nonpathogenic bacteria. In this study we aimed to identify the in vivo DNA binding profile of CcpA and assess the extent to which HPr is required for CcpA‐mediated regulation and DNA binding in the major human pathogen group A Streptococcus (GAS). Using a combination RNAseq/ChIP‐seq approach, we found that CcpA affects transcript levels of 514 of 1667 GAS genes (31%) whereas direct DNA binding was identified for 105 GAS genes. Three of the directly regulated genes encode the key GAS virulence factors Streptolysin S, PrtS (IL‐8 degrading proteinase), and SpeB (cysteine protease). Mutating CcpA Val301 to Ala (strain 2221‐CcpA‐V301A) abolished interaction between CcpA and HPr and impacted the transcript levels of 205 genes (40%) in the total CcpA regulon. By ChIP‐seq analysis, CcpAV301A bound to DNA from 74% of genes bound by wild‐type CcpA, but generally with lower affinity. These data delineate the direct CcpA regulon and clarify the HPr‐dependent and independent activities of CcpA in a key pathogenic bacterium.
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Affiliation(s)
- Sruti DebRoy
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Victor Aliaga-Tobar
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gabriel Galvez
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Nicola Horstmann
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vinicius Maracaja-Coutinho
- Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Independencia, Chile.,Centro de Modelamiento Molecular, Biofísica y Bioinformática (CM2B2), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Laboratorio de Bioingeniería, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases Infection Control and Employee Health, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Antimicrobial Resistance and Microbial Genomics, University of Texas Health Science Center McGovern Medical School, Houston, TX, USA.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston TX, USA
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Zhang J, Meng L, Zhang Y, Sang L, Liu Q, Zhao L, Liu F, Wang G. GapB Is Involved in Biofilm Formation Dependent on LrgAB but Not the SinI/R System in Bacillus cereus 0-9. Front Microbiol 2020; 11:591926. [PMID: 33365021 PMCID: PMC7750190 DOI: 10.3389/fmicb.2020.591926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Bacillus cereus 0-9, a Gram-positive endospore-forming bacterium isolated from healthy wheat roots, has biological control capacity against several soil-borne plant diseases of wheat such as sharp eyespot and take-all. The bacterium can produce various biofilms that differ in their architecture and formation mechanisms, possibly for adapting to different environments. The gapB gene, encoding a glyceraldehyde-3-phosphate dehydrogenase (GAPDH), plays a key role in B. cereus 0-9 biofilm formation. We studied the function of GapB and the mechanism of its involvement in regulating B. cereus 0-9 biofilm formation. GapB has GAPDH activities for both NAD+- and NADP+-dependent dehydrogenases and is a key enzyme in gluconeogenesis. Biofilm yield of the ΔgapB strain decreased by 78.5% compared with that of wild-type B. cereus 0-9 in lysogeny broth supplemented with some mineral salts (LBS), and the ΔgapB::gapB mutants were recovered with gapB gene supplementation. Interestingly, supplementing the LBS medium with 0.1-0.5% glycerol restored the biofilm formation capacity of the ΔgapB mutants. Therefore, GapB regulates biofilm formation relative to its function in gluconeogenesis. To illustrate how GapB is involved in regulating biofilm formation through gluconeogenesis, we carried out further research. The results indicate that the GapB regulated the B. cereus 0-9 biofilm formation independently of the exopolysaccharides and regulatory proteins in the typical SinI/R system, likely owing to the release of extracellular DNA in the matrix. Transcriptome analysis showed that the gapB deletion caused changes in the expression levels of only 18 genes, among which, lrgAB was the most significantly increased by 6.17-fold. We confirmed this hypothesis by counting the dead and living cells in the biofilms and found the number of living cells in the biofilm formed by the ΔgapB strain was nearly 7.5 times than that of wild-type B. cereus 0-9. Therefore, we concluded that the GapB is involved in the extracellular DNA release and biofilm formation by regulating the expression or activities of LrgAB. These results provide a new insight into the regulatory mechanism of bacterial biofilm formation and a new foundation for further studying the stress resistance of B. cereus.
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Affiliation(s)
- Juanmei Zhang
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng, China.,School of Pharmaceutical, Henan University, Kaifeng, China
| | - Li Meng
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yubing Zhang
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lidan Sang
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qing Liu
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Linlin Zhao
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Fengying Liu
- Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
| | - Gang Wang
- Engineering Research Center for Applied Microbiology of Henan Province, Kaifeng, China.,Institute of Microbial Engineering, Laboratory of Bioresource and Applied Microbiology, School of Life Sciences, Henan University, Kaifeng, China
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17
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Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature. Toxins (Basel) 2020; 12:toxins12100645. [PMID: 33036317 PMCID: PMC7601483 DOI: 10.3390/toxins12100645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
Cellular proteomes and exoproteomes are dynamic, allowing pathogens to respond to environmental conditions to sustain growth and virulence. Bacillus cereus is an important food-borne pathogen causing intoxication via emetic toxin and/or multiple protein exotoxins. Here, we compared the dynamics of the cellular proteome and exoproteome of emetic B. cereus cells grown at low (16 °C) and high (30 °C) temperature. Tandem mass spectrometry (MS/MS)-based shotgun proteomics analysis identified 2063 cellular proteins and 900 extracellular proteins. Hierarchical clustering following principal component analysis indicated that in B. cereus the abundance of a subset of these proteins—including cold-stress responders, and exotoxins non-hemolytic enterotoxin (NHE) and hemolysin I (cereolysin O (CLO))—decreased at low temperature, and that this subset governs the dynamics of the cellular proteome. NHE, and to a lesser extent CLO, also contributed significantly to exoproteome dynamics; with decreased abundances in the low-temperature exoproteome, especially in late growth stages. Our data therefore indicate that B. cereus may reduce its production of secreted protein toxins to maintain appropriate proteome dynamics, perhaps using catabolite repression to conserve energy for growth in cold-stress conditions, at the expense of virulence.
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18
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Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
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19
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Wen Z, Lu M, Ledesma-Amaro R, Li Q, Jin M, Yang S. TargeTron Technology Applicable in Solventogenic Clostridia: Revisiting 12 Years' Advances. Biotechnol J 2019; 15:e1900284. [PMID: 31475782 DOI: 10.1002/biot.201900284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/20/2019] [Indexed: 12/11/2022]
Abstract
Clostridium has great potential in industrial application and medical research. But low DNA repair capacity and plasmids transformation efficiency severely delay development and application of genetic tools based on homologous recombination (HR). TargeTron is a gene editing technique dependent on the mobility of group II introns, rather than homologous recombination, which makes it very suitable for gene disruption of Clostridium. The application of TargeTron technology in solventogenic Clostridium is academically reported in 2007 and this tool has been introduced in various clostridia as it is easy to operate, time saving, and reliable. TargeTron has made great progress in solventogenic Clostridium in the aspects of acetone-butanol-ethanol (ABE) fermentation pathway modification, important functional genes identification, and xylose metabolic pathway analysis and reconstruction. In the review, 12 years' advances of TargeTron technology applicable in solventogenic Clostridium, including its principle, technical characteristics, application, and efforts to expand its capabilities, or to avoid potential drawbacks, are revisisted. Some other technologies as putative competitors or collaborators are also discussed. It is believed that TargeTron combined with CRISPR/Cas-assisted gene/base editing and gene-expression regulation system will make a better future for clostridial genetic modification.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | | | - Qi Li
- College of Life Sciences, Sichuan Normal University, Longquan, Chengdu, 610101, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, 210094, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhejiang, 313000, China
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20
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Denham EL, Piersma S, Rinket M, Reilman E, de Goffau MC, van Dijl JM. Differential expression of a prophage-encoded glycocin and its immunity protein suggests a mutualistic strategy of a phage and its host. Sci Rep 2019; 9:2845. [PMID: 30808982 PMCID: PMC6391423 DOI: 10.1038/s41598-019-39169-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/31/2018] [Indexed: 01/12/2023] Open
Abstract
Sublancin 168 is a highly potent and stable antimicrobial peptide secreted by the Gram-positive bacterium Bacillus subtilis. Production of sublancin gives B. subtilis a major competitive growth advantage over a range of other bacteria thriving in the same ecological niches, the soil and plant rhizosphere. B. subtilis protects itself against sublancin by producing the cognate immunity protein SunI. Previous studies have shown that both the sunA gene for sublancin and the sunI immunity gene are encoded by the prophage SPβ. The sunA gene is under control of several transcriptional regulators. Here we describe the mechanisms by which sunA is heterogeneously expressed within a population, while the sunI gene encoding the immunity protein is homogeneously expressed. The key determinants in heterogeneous sunA expression are the transcriptional regulators Spo0A, AbrB and Rok. Interestingly, these regulators have only a minor influence on sunI expression and they have no effect on the homogeneous expression of sunI within a population of growing cells. Altogether, our findings imply that the homogeneous expression of sunI allows even cells that are not producing sublancin to protect themselves at all times from the active sublancin produced at high levels by their isogenic neighbors. This suggests a mutualistic evolutionary strategy entertained by the SPβ prophage and its Bacillus host, ensuring both stable prophage maintenance and a maximal competitive advantage for the host at minimal costs.
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Affiliation(s)
- Emma L Denham
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Sjouke Piersma
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marleen Rinket
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Ewoud Reilman
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Marcus C de Goffau
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Wellcome Sanger Institute, Cambridge, UK
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
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21
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Lu Y, Song S, Tian H, Yu H, Zhao J, Chen C. Functional analysis of the role of CcpA in Lactobacillus plantarum grown on fructooligosaccharides or glucose: a transcriptomic perspective. Microb Cell Fact 2018; 17:201. [PMID: 30593274 PMCID: PMC6309078 DOI: 10.1186/s12934-018-1050-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/24/2018] [Indexed: 12/19/2022] Open
Abstract
Background The catabolite control protein A (CcpA) is a master regulator of many important cellular processes in Gram-positive bacteria. In Lactobacillus plantarum, CcpA directly or indirectly controls the transcription of a large number of genes that are involved in carbohydrate metabolism, aerobic and anaerobic growth, stress response and metabolite production, but its role in response to different carbon sources remains unclear. Results Here a combined transcriptomic and physiological approach was used to survey the global alterations that occurred during the logarithmic growth phase of wild-type and ccpA mutant strains of L. plantarum ST-III using fructooligosaccharides (FOS) or glucose as the sole carbon source. The inactivation of ccpA significantly affected the growth and production of metabolites under both carbon sources. About 15% of the total genes were significantly altered between wild-type and ccpA strains grown on glucose and the value is deceased to 12% when these two strains were compared on FOS, while only 7% were obviously changed due to the loss of CcpA when comparing strains grown on glucose and FOS. Although most of the differentially expressed genes mediated by CcpA are glucose dependent, FOS can also induce carbon catabolite repression (CCR) through the CcpA pathway. Moreover, the inactivation of ccpA led to a transformation from homolactic fermentation to mixed fermentation under aerobic conditions. CcpA can control genes directly by binding in the regulatory region of the target genes (mixed fermentation), indirectly through local regulators (fatty acid biosynthesis), or have a double effect via direct and indirect regulation (FOS metabolism). Conclusion Overall, our results show that CcpA plays a central role in response to carbon source and availability of L. plantarum and provide new insights into the complex and extended regulatory network of lactic acid bacteria.![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-1050-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanqing Lu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Sichao Song
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China
| | - Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China.
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Yang Y, Nie X, Jiang Y, Yang C, Gu Y, Jiang W. Metabolic regulation in solventogenic clostridia: regulators, mechanisms and engineering. Biotechnol Adv 2018; 36:905-914. [DOI: 10.1016/j.biotechadv.2018.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/05/2018] [Accepted: 02/20/2018] [Indexed: 12/31/2022]
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Distinct Regulatory Role of Carbon Catabolite Protein A (CcpA) in Oral Streptococcal spxB Expression. J Bacteriol 2018; 200:JB.00619-17. [PMID: 29378884 DOI: 10.1128/jb.00619-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/12/2018] [Indexed: 12/14/2022] Open
Abstract
Pyruvate oxidase (SpxB)-dependent H2O2 production is under the control of carbon catabolite protein A (CcpA) in the oral species Streptococcus sanguinis and Streptococcus gordonii Interestingly, both species react differently to the presence of the preferred carbohydrate source glucose. S. gordonii CcpA-dependent regulation of spxB follows classical carbon catabolite repression. Conversely, spxB expression in S. sanguinis is not influenced by glucose but is repressed by CcpA. Here, we constructed strains expressing the heterologous versions of CcpA or the spxB promoter region to learn if the distinct regulation of spxB expression is transferable from S. gordonii to S. sanguinis and vice versa. While cross-species binding of CcpA to the spxB promoter is conserved in vitro, we were unable to swap the species-specific regulation. This suggests that a regulatory mechanism upstream of CcpA most likely is responsible for the observed difference in spxB expression. Moreover, the overall ecological significance of differential spxB regulation in the presence of various glucose concentrations was tested with additional oral streptococcus isolates and demonstrated that carbohydrate-dependent and carbohydrate-independent mechanisms exist to control expression of spxB in the oral biofilm. Overall, our data demonstrate the unexpected finding that metabolic pathways between two closely related oral streptococcal species can be regulated differently despite an exceptionally high DNA sequence identity.IMPORTANCE Polymicrobial diseases are the result of interactions among the residential microbes, which can lead to a dysbiotic community. Streptococcus sanguinis and Streptococcus gordonii are considered commensal species that are present in the healthy dental biofilm. Both species are able to produce significant amounts of H2O2 via the enzymatic action of the pyruvate oxidase SpxB. H2O2 is able to inhibit species associated with oral diseases. SpxB and its gene-regulatory elements present in both species are highly conserved. Nonetheless, a differential response to the presence of glucose was observed. Here, we investigate the mechanisms that lead to this differential response. Detailed knowledge of the regulatory mechanisms will aid in a better understanding of oral disease development and how to prevent dysbiosis.
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Coordinated Regulation of the EII Man and fruRKI Operons of Streptococcus mutans by Global and Fructose-Specific Pathways. Appl Environ Microbiol 2017; 83:AEM.01403-17. [PMID: 28821551 DOI: 10.1128/aem.01403-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/15/2017] [Indexed: 11/20/2022] Open
Abstract
The glucose/mannose-phosphotransferase system (PTS) permease EIIMan encoded by manLMN in the dental caries pathogen Streptococcus mutans has a dominant influence on sugar-specific, CcpA-independent catabolite repression (CR). Mutations in manL affect energy metabolism and virulence-associated traits, including biofilm formation, acid tolerance, and competence. Using promoter::reporter fusions, expression of the manLMN and the fruRKI operons, encoding a transcriptional regulator, a fructose-1-phosphate kinase and a fructose-PTS permease EIIFru, respectively, was monitored in response to carbohydrate source and in mutants lacking CcpA, FruR, and components of EIIMan Expression of genes for EIIMan and EIIFru was directly regulated by CcpA and CR, as evinced by in vivo and in vitro methods. Unexpectedly, not only was the fruRKI operon negatively regulated by FruR, but also so was manLMN Carbohydrate transport by EIIMan had a negative influence on expression of manLMN but not fruRKI In agreement with the proposed role of FruR in regulating these PTS operons, loss of fruR or fruK substantially altered growth on a number of carbohydrates, including fructose. RNA deep sequencing revealed profound changes in gene regulation caused by deletion of fruK or fruR Collectively, these findings demonstrate intimate interconnection of the regulation of two major PTS permeases in S. mutans and reveal novel and important contributions of fructose metabolism to global regulation of gene expression.IMPORTANCE The ability of Streptococcus mutans and other streptococcal pathogens to survive and cause human diseases is directly dependent upon their capacity to metabolize a variety of carbohydrates, including glucose and fructose. Our research reveals that metabolism of fructose has broad influences on the regulation of utilization of glucose and other sugars, and mutants with changes in certain genes involved in fructose metabolism display profoundly different abilities to grow and express virulence-related traits. Mutants lacking the FruR regulator or a particular phosphofructokinase, FruK, display changes in expression of a large number of genes encoding transcriptional regulators, enzymes required for energy metabolism, biofilm development, biosynthetic and degradative processes, and tolerance of a spectrum of environmental stressors. Since fructose is a major component of the modern human diet, the results have substantial significance in the context of oral health and the development of dental caries.
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Yang XY, Xu JY, Wei QX, Sun X, He QY. Comparative Proteomics of Streptococcus pneumoniae Response to Vancomycin Treatment. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:531-539. [PMID: 28934029 DOI: 10.1089/omi.2017.0098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Streptococcus pneumoniae is a gram-positive pathogen that causes otitis media, pneumonia, meningitis, and other serious diseases. Vancomycin is one of the most important drugs currently used for the treatment of gram-positive bacterial infections, representing, importantly, the last line of defense against bacteria that have developed resistance to other antibiotics. While primary efforts of most investigations focused on the antibacterial mechanism of vancomycin, few studies have been performed to assess the tolerance mechanism of bacteria to vancomycin. In this work, whole cellular proteins were extracted from S. pneumoniae D39 with or without vancomycin treatment. Subsequently, differentially expressed proteins (DEPs) were identified with two-dimensional gel electrophoresis coupled with matrix-assisted laser desorption/ionization mass spectrometry (MS)/MS. In total, 27 proteins were upregulated and four proteins were downregulated in vancomycin-treated S. pneumoniae. Gene ontology analysis indicated that these DEPs were mainly involved in the nucleic acid, protein, and carbohydrate biosynthetic processes. Verification experiments with real-time quantitative polymerase chain reaction showed that the gene expression profiles were consistent with proteomic data. These new observations may serve as a valuable resource for future investigations of vancomycin tolerance mechanisms of S. pneumoniae.
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Affiliation(s)
- Xiao-Yan Yang
- 1 The First Affiliated Hospital of Jinan University , Guangzhou, China .,2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Jing-Yu Xu
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Qiu-Xia Wei
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Xuesong Sun
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
| | - Qing-Yu He
- 2 Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , Guangzhou, China
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Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production from glucose and xylose. Metab Eng 2017; 40:50-58. [DOI: 10.1016/j.ymben.2016.12.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/25/2016] [Accepted: 12/26/2016] [Indexed: 12/28/2022]
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A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria. mBio 2017; 8:mBio.02004-16. [PMID: 28119470 PMCID: PMC5263246 DOI: 10.1128/mbio.02004-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Catabolite control protein A (CcpA) is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR) and carbon catabolite activation (CCA), two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt) consensus site that is called a catabolite response element (cre) within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named crevar, has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA). It was found that the length of the intervening spacer of crevar can affect CcpA binding affinity, and moreover, the core palindromic sequence of crevar is the key structure for regulation. Such a variable architecture of crevar shows potential importance for CcpA’s diverse and fine regulation. A total of 103 potential crevar sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs), and 30 sites were confirmed to be bound by CcpA. These 30 crevar sites are associated with 27 genes involved in many important pathways. Also of significance, the crevar sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria. In Gram-positive bacteria, the global regulator CcpA controls a large number of important physiological and metabolic processes. Although a typical consensus CcpA-binding site, cre, has been identified, it remains poorly explored for the diversity of CcpA-mediated catabolite regulation. Here, we discovered a novel flexible CcpA-binding site architecture (crevar) that is highly variable in both length and base composition but follows certain principles, providing new insights into how CcpA can differentially recognize a variety of target genes to form a complicated regulatory network. A comprehensive search further revealed the wide distribution of crevar sites in Gram-positive bacteria, indicating it may have a universal function. This finding is the first to characterize such a highly flexible transcription factor-binding site architecture, which would be valuable for deeper understanding of CcpA-mediated global catabolite regulation in bacteria.
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Wei P, Lin M, Wang Z, Fu H, Yang H, Jiang W, Yang ST. Metabolic engineering of Propionibacterium freudenreichii subsp. shermanii for xylose fermentation. BIORESOURCE TECHNOLOGY 2016; 219:91-97. [PMID: 27479799 DOI: 10.1016/j.biortech.2016.07.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 05/12/2023]
Abstract
Propionibacterium freudenreichii cannot use xylose, the second most abundant sugar in lignocellulosic biomass. Although Propionibacterium acidipropionici can use xylose as a carbon source, it is difficult to genetically modify, impeding further improvement through metabolic engineering. This study identified three xylose catabolic pathway genes encoding for xylose isomerase (xylA), xylose transporter (xylT), and xylulokinase (xylB) in P. acidipropionici and overexpressed them in P. freudenreichii subsp. shermanii via an expression plasmid pKHEM01, enabling the mutant to utilize xylose efficiently even in the presence of glucose without glucose-induced carbon catabolite repression. The mutant showed similar fermentation kinetics with glucose, xylose, and the mixture of glucose and xylose, respectively, as carbon source, and with or without the addition of antibiotic for selection pressure. The engineered P. shermanii thus can provide a novel cell factory for industrial production of propionic acid and other value-added products from lignocellulosic biomass.
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Affiliation(s)
- Peilian Wei
- School of Biological and Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China; William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Meng Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA; Bioprocessing Innovative Company, 4734 Bridle Path Ct., Dublin, OH 43017, USA
| | - Zhongqiang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Hongxin Fu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Hopen Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Wenyan Jiang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA.
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Fleming E, Camilli A. ManLMN is a glucose transporter and central metabolic regulator in Streptococcus pneumoniae. Mol Microbiol 2016; 102:467-487. [PMID: 27472033 PMCID: PMC5116393 DOI: 10.1111/mmi.13473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2016] [Indexed: 01/24/2023]
Abstract
Streptococcus pneumoniae is a common colonizer of the human nasopharynx and a leading cause of bacterial pneumonia and otitis media, among other invasive diseases. During both colonization and invasive disease S. pneumoniae ferments host-derived carbohydrates as its primary means of generating energy. This pathogen is adept at transporting and metabolizing a wide variety of carbohydrates. We found the highly conserved PTS ManLMN contributes to growth on glucose and is also essential for growth on a variety of nonpreferred carbohydrates, suggesting it is a multisubstrate transporter. Exploration of this phenotype revealed ManLMN is required for inducing expression of downstream metabolic genes in response to carbohydrate stimuli. We further demonstrate that ManLMN's role as a constitutively expressed transporter is likely unique and integral to pneumococcus's strategy of carbon catabolite repression (CCR). Using a selection for suppressors, we explored how ManLMN is integrated into the CCR regulatory framework in S. pneumoniae. We identified two hypothetical small proteins and the virulence regulator SmrC as potential mediators of CCR in connection with ManLMN. Characterization of these two hypothetical proteins revealed they influence transcriptional regulation of carbohydrate transporters. We propose a model unifying these observations in which ManLMN is a versatile surveyor of available carbohydrates in S. pneumoniae.
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Affiliation(s)
- Eleanor Fleming
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Andrew Camilli
- Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Howard Hughes Medical Institute, and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA.
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Kim SK, Jung KH, Chai YG. Changes in Bacillus anthracis CodY regulation under host-specific environmental factor deprived conditions. BMC Genomics 2016; 17:645. [PMID: 27530340 PMCID: PMC4987991 DOI: 10.1186/s12864-016-3004-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/09/2016] [Indexed: 02/07/2023] Open
Abstract
Background Host-specific environmental factors induce changes in Bacillus anthracis gene transcription during infection. A global transcription regulator, CodY, plays a pivotal role in regulating central metabolism, biosynthesis, and virulence in B. anthracis. In this study, we utilized RNA-sequencing to assess changes in the transcriptional patterns of CodY-regulated B. anthracis genes in response to three conditions of environmental starvation: iron, CO2, or glucose deprivation. In addition, we performed chromatin immunoprecipitation on newly identified CodY-mediated genes. Results Environmental deprivation induced transcriptional changes in CodY-regulated genes in both wild-type and codY null strains, and both CodY-specific and environment-specific patterns were observed. In the iron-depleted condition, overexpression of iron homeostasis genes was observed independent of codY deletion; however, transcription of siderophore and amino acid biosynthesis genes was CodY dependent. Although CodY has a significant regulatory role in central metabolism and the carbon overflow pathway, metabolism-associated genes exhibited CodY-independent expression patterns under glucose starvation. Genes that were differentially expressed in response to CO2 availability showed CodY-dependent regulation, though their maximal expression did require a supply of CO2/bicarbonate. Conclusions We speculate that CodY regulates the expression of environmental-responsive genes in a hierarchical manner and is likely associated with other transcription regulators that are specific for a particular environmental change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3004-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Se Kye Kim
- Department of Molecular and Life Science, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Kyoung Hwa Jung
- Department of Molecular and Life Science, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Young Gyu Chai
- Department of Molecular and Life Science, Hanyang University ERICA, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do, 15588, Republic of Korea. .,Department of Bionanotechnology, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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Rossi F, Zotta T, Iacumin L, Reale A. Theoretical insight into the heat shock response (HSR) regulation in Lactobacillus casei and L. rhamnosus. J Theor Biol 2016; 402:21-37. [DOI: 10.1016/j.jtbi.2016.04.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023]
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Zhu M, Lu Y, Wang J, Li S, Wang X. Carbon Catabolite Repression and the Related Genes of ccpA, ptsH and hprK in Thermoanaerobacterium aotearoense. PLoS One 2015; 10:e0142121. [PMID: 26540271 PMCID: PMC4634974 DOI: 10.1371/journal.pone.0142121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/16/2015] [Indexed: 01/09/2023] Open
Abstract
The strictly anaerobic, Gram-positive bacterium, Thermoanaerobacterium aotearoense SCUT27, is capable of producing ethanol, hydrogen and lactic acid by directly fermenting glucan, xylan and various lignocellulosically derived sugars. By using non-metabolizable and metabolizable sugars as substrates, we found that cellobiose, galactose, arabinose and starch utilization was strongly inhibited by the existence of 2-deoxyglucose (2-DG). However, the xylose and mannose consumptions were not markedly affected by 2-DG at the concentration of one-tenth of the metabolizable sugar. Accordingly, T. aotearoense SCUT27 could consume xylose and mannose in the presence of glucose. The carbon catabolite repression (CCR) related genes, ccpA, ptsH and hprK were confirmed to exist in T. aotearoense SCUT27 through gene cloning and protein characterization. The highly purified Histidine-containing Protein (HPr) could be specifically phosphorylated at Serine 46 by HPr kinase/phosphatase (HPrK/P) with no need to add fructose-1,6-bisphosphate (FBP) or glucose-6-phosphate (Glc-6-P) in the reaction mixture. The specific protein-interaction of catabolite control protein A (CcpA) and phosphorylated HPr was proved via affinity chromatography in the absence of formaldehyde. The equilibrium binding constant (KD) of CcpA and HPrSerP was determined as 2.22 ± 0.36 nM by surface plasmon resonance (SPR) analysis, indicating the high affinity between these two proteins.
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Affiliation(s)
- Muzi Zhu
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Yanping Lu
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
- * E-mail:
| | - Xiaoning Wang
- State Key Laboratory of Kidney, the Institute of Life Sciences, Chinese PLA General Hospital, Beijing, China
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Vanden Broeck A, Van der Heiden E, Sauvage E, Dauvin M, Joris B, Duez C. A Lysine Cluster in Domain II of Bacillus subtilis PBP4a Plays a Role in the Membrane Attachment of This C1-PBP. PLoS One 2015; 10:e0140082. [PMID: 26460848 PMCID: PMC4604126 DOI: 10.1371/journal.pone.0140082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/21/2015] [Indexed: 11/28/2022] Open
Abstract
In PBP4a, a Bacillus subtilis class-C1 penicillin-binding protein (PBP), four clustered lysine (K) residues, K86, K114, K119, and K265, protrude from domain II. Replacement of these amino acids with glutamine (Q) residues by site-directed mutagenesis yielded Mut4KQ PBP4a. When produced in Escherichia coli without its predicted Sec-signal peptide, wild-type (WT) PBP4a was found mainly associated with the host cytoplasmic membrane, whereas Mut4KQ PBP4a remained largely unbound. After purification, the capacities of the two proteins to bind to B. subtilis membranes were compared. The results were similar to those obtained in E. coli: in vitro, a much higher percentage of WT PBP4a than of Mut4KQ PBP4a was found to interact with B. subtilis membranes. Immunodetection of PBP4a in B. subtilis membrane extracts revealed that a processed form of this PBP (as indicated by its size) associates with the B. subtilis cytoplasmic membrane. In the absence of any amphiphilic peptide in PBP4a, the crown of positive charges on the surface of domain II is likely responsible for the cellular localization of this PBP and its attachment to the cytoplasmic membrane.
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Affiliation(s)
- Arnaud Vanden Broeck
- Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium
| | - Edwige Van der Heiden
- Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium
| | - Eric Sauvage
- Centre for Protein Engineering, Institut de Physique B5a, University of Liège, Sart Tilman, Belgium
| | - Marjorie Dauvin
- Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium
| | - Bernard Joris
- Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium
| | - Colette Duez
- Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Sart Tilman, Belgium
- * E-mail:
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Yu L, Xu M, Tang IC, Yang ST. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production through co-utilization of glucose and xylose. Biotechnol Bioeng 2015; 112:2134-41. [PMID: 25894463 DOI: 10.1002/bit.25613] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/09/2023]
Abstract
The glucose-mediated carbon catabolite repression (CCR) in Clostridium tyrobutyricum impedes efficient utilization of xylose present in lignocellulosic biomass hydrolysates. In order to relieve the CCR and enhance xylose utilization, three genes (xylT, xylA, and xylB) encoding a xylose proton-symporter, a xylose isomerase and a xylulokinase, respectively, from Clostridium acetobutylicum ATCC 824 were co-overexpressed with aldehyde/alcohol dehydrogenase (adhE2) in C. tyrobutyricum (Δack). Compared to the strain Ct(Δack)-pM2 expressing only adhE2, the mutant Ct(Δack)-pTBA had a higher xylose uptake rate and was able to simultaneously consume glucose and xylose at comparable rates for butanol production. Ct(Δack)-pTBA produced more butanol (12.0 vs. 3.2 g/L) with a higher butanol yield (0.12 vs. 0.07 g/g) and productivity (0.17 vs. 0.07 g/L · h) from both glucose and xylose, while Ct(Δack)-pM2 consumed little xylose in the fermentation. The results confirmed that the CCR in C. tyrobutyricum could be overcome through overexpressing xylT, xylA, and xylB. The mutant was also able to co-utilize glucose and xylose present in soybean hull hydrolysate (SHH) for butanol production, achieving a high butanol titer of 15.7 g/L, butanol yield of 0.24 g/g, and productivity of 0.29 g/L · h. This study demonstrated the potential application of Ct(Δack)-pTBA for industrial biobutanol production from lignocellulosic biomass.
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Affiliation(s)
- Le Yu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, Ohio, 43210
| | - Mengmeng Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, Ohio, 43210
| | | | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, Ohio, 43210.
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Fleming E, Lazinski DW, Camilli A. Carbon catabolite repression by seryl phosphorylated HPr is essential to Streptococcus pneumoniae in carbohydrate-rich environments. Mol Microbiol 2015; 97:360-80. [PMID: 25898857 PMCID: PMC4836947 DOI: 10.1111/mmi.13033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
Carbon catabolite repression (CCR) is a regulatory phenomenon implemented by bacteria to hierarchically organize carbohydrate utilization in order to achieve maximal growth. CCR is likely of great importance to Streptococcus pneumoniae because the human host sites inhabited by this pathogen represent complex carbohydrate environments. In this species, inactivation of the prototypical Gram-positive CCR master regulator, ccpA, attenuates virulence in mice but does not relieve CCR of most metabolic enzymes, suggesting CcpA-independent CCR mechanisms predominate. Here we show the activities of three transcriptional regulators constitute the majority of transcriptional CCR of galactose metabolism operons. We determined seryl-phosphorylated histidine phosphocarrier protein (HPr-Ser∼P)-mediated regulation is a major CCR mechanism and an essential activity in the pneumococcus, as an HPr point mutation abolishing HPrK/P-dependent phosphorylation was not tolerated nor was deletion of hprk/p. The HPr-Ser∼P phosphomimetic mutant HPr S46D had reduced phosphotransferase system transport rates and limited induction of CCR-repressed genes. These results support a model of pneumococcal CCR in which HPr-Ser∼P directly affects the activity of CcpA while indirectly affecting the activity of pathway-specific transactional regulators. This report describes the first CcpA-independent CCR mechanism identified in the pneumococcus and the first example of lethality from loss of HPr-Ser∼P-mediated CCR in any species.
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Affiliation(s)
- Eleanor Fleming
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - David W Lazinski
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Andrew Camilli
- Howard Hughes Medical Institute and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
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Pasvolsky R, Zakin V, Ostrova I, Shemesh M. Butyric acid released during milk lipolysis triggers biofilm formation of Bacillus species. Int J Food Microbiol 2014; 181:19-27. [PMID: 24801271 DOI: 10.1016/j.ijfoodmicro.2014.04.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/03/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
Bacillus species form biofilms within milking pipelines and on surfaces of equipment in the dairy industry which represent a continuous hygiene problem and can lead to serious economic losses due to food spoilage and equipment impairment. Although much is known about the mechanism by which the model organism Bacillus subtilis forms biofilms in laboratory mediums in vitro, little is known of how these biofilms are formed in natural environments such as milk. Besides, little is known of the signaling pathways leading to biofilm formation in other Bacillus species, such as Bacillus cereus and Bacillus licheniformis, both of which are known to contaminate milk. In this study, we report that milk triggers the formation of biofilm-related structures, termed bundles. We show this to be a conserved phenomenon among all Bacillus members tested. Moreover, we demonstrate that the tasA gene, which encodes a major portion of the matrix which holds the biofilm together, is vital for this process. Furthermore, we show that the free fatty acid (FFA) - butyric acid (BA), which is released during lipolysis of milk fat and demonstrates antimicrobial activity, is the potent trigger for biofilm bundle formation. We finally show that BA-triggered biofilm bundle formation is mediated by the histidine kinase, KinD. Taken together, these observations indicate that BA, which is a major FFA within milk triggers biofilm formation in a conserved mechanism among members of the Bacillus genus.
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Affiliation(s)
- Ronit Pasvolsky
- Department of Food Quality and Safety, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Varda Zakin
- Department of Food Quality and Safety, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Ievgeniia Ostrova
- Department of Food Quality and Safety, Agricultural Research Organization (ARO), Bet-Dagan, Israel
| | - Moshe Shemesh
- Department of Food Quality and Safety, Agricultural Research Organization (ARO), Bet-Dagan, Israel.
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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Ferrando ML, van Baarlen P, Orrù G, Piga R, Bongers RS, Wels M, De Greeff A, Smith HE, Wells JM. Carbohydrate availability regulates virulence gene expression in Streptococcus suis. PLoS One 2014; 9:e89334. [PMID: 24642967 PMCID: PMC3958366 DOI: 10.1371/journal.pone.0089334] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/17/2014] [Indexed: 12/04/2022] Open
Abstract
Streptococcus suis is a major bacterial pathogen of young pigs causing worldwide economic problems for the pig industry. S. suis is also an emerging pathogen of humans. Colonization of porcine oropharynx by S. suis is considered to be a high risk factor for invasive disease. In the oropharyngeal cavity, where glucose is rapidly absorbed but dietary α-glucans persist, there is a profound effect of carbohydrate availability on the expression of virulence genes. Nineteen predicted or confirmed S. suis virulence genes that promote adhesion to and invasion of epithelial cells were expressed at higher levels when S. suis was supplied with the α-glucan starch/pullulan compared to glucose as the single carbon source. Additionally the production of suilysin, a toxin that damages epithelial cells, was increased more than ten-fold when glucose levels were low and S. suis was growing on pullulan. Based on biochemical, bioinformatics and in vitro and in vivo gene expression studies, we developed a biological model that postulates the effect of carbon catabolite repression on expression of virulence genes in the mucosa, organs and blood. This research increases our understanding of S. suis virulence mechanisms and has important implications for the design of future control strategies including the development of anti-infective strategies by modulating animal feed composition.
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Affiliation(s)
- M. Laura Ferrando
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Germano Orrù
- Oral Biotechnology Laboratory, University of Cagliari, Cagliari, Italy
| | - Rosaria Piga
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | | | | | - Astrid De Greeff
- Central Veterinary Institute, Animal Sciences Group, Wageningen University, Lelystad, The Netherlands
| | - Hilde E. Smith
- Central Veterinary Institute, Animal Sciences Group, Wageningen University, Lelystad, The Netherlands
| | - Jerry M. Wells
- Host-Microbe Interactomics, Animal Sciences, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Nathan S, Nair M. Engineering a repression-free catabolite-enhanced expression system for a thermophilic alpha-amylase from Bacillus licheniformis MSG. J Biotechnol 2013; 168:394-402. [DOI: 10.1016/j.jbiotec.2013.09.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 09/19/2013] [Accepted: 09/23/2013] [Indexed: 11/26/2022]
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Hartmann T, Zhang B, Baronian G, Schulthess B, Homerova D, Grubmüller S, Kutzner E, Gaupp R, Bertram R, Powers R, Eisenreich W, Kormanec J, Herrmann M, Molle V, Somerville GA, Bischoff M. Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator of tricarboxylic acid cycle activity in Staphylococcus aureus. J Biol Chem 2013; 288:36116-28. [PMID: 24194525 DOI: 10.1074/jbc.m113.516302] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tricarboxylic acid cycle (TCA cycle) is a central metabolic pathway that provides energy, reducing potential, and biosynthetic intermediates. In Staphylococcus aureus, TCA cycle activity is controlled by several regulators (e.g. CcpA, CodY, and RpiRc) in response to the availability of sugars, amino acids, and environmental stress. Developing a bioinformatic search for additional carbon catabolite-responsive regulators in S. aureus, we identified a LysR-type regulator, catabolite control protein E (CcpE), with homology to the Bacillus subtilis CcpC regulator. Inactivation of ccpE in S. aureus strain Newman revealed that CcpE is a positive transcriptional effector of the first two enzymes of the TCA cycle, aconitase (citB) and to a lesser extent citrate synthase (citZ). Consistent with the transcriptional data, aconitase activity dramatically decreased in the ccpE mutant relative to the wild-type strain. The effect of ccpE inactivation on citB transcription and the lesser effect on citZ transcription were also reflected in electrophoretic mobility shift assays where CcpE bound to the citB promoter but not the citZ promoter. Metabolomic studies showed that inactivation of ccpE resulted in increased intracellular concentrations of acetate, citrate, lactate, and alanine, consistent with a redirection of carbon away from the TCA cycle. Taken together, our data suggest that CcpE is a major direct positive regulator of the TCA cycle gene citB.
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Affiliation(s)
- Torsten Hartmann
- From the Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, 66421 Homburg/Saar, Germany
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Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA. Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One 2013; 8:e60465. [PMID: 23555977 PMCID: PMC3610829 DOI: 10.1371/journal.pone.0060465] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/25/2013] [Indexed: 12/20/2022] Open
Abstract
A bacterial transcriptome of the primary etiological agent of human dental caries, Streptococcus mutans, is described here using deep RNA sequencing. Differential expression profiles of the transcriptome in the context of carbohydrate source, and of the presence or absence of the catabolite control protein CcpA, revealed good agreement with previously-published DNA microarrays. In addition, RNA-seq considerably expanded the repertoire of DNA sequences that showed statistically-significant changes in expression as a function of the presence of CcpA and growth carbohydrate. Novel mRNAs and small RNAs were identified, some of which were differentially expressed in conditions tested in this study, suggesting that the function of the S. mutans CcpA protein and the influence of carbohydrate sources has a more substantial impact on gene regulation than previously appreciated. Likewise, the data reveal that the mechanisms underlying prioritization of carbohydrate utilization are more diverse than what is currently understood. Collectively, this study demonstrates the validity of RNA-seq as a potentially more-powerful alternative to DNA microarrays in studying gene regulation in S. mutans because of the capacity of this approach to yield a more precise landscape of transcriptomic changes in response to specific mutations and growth conditions.
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Affiliation(s)
- Lin Zeng
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Sang Chul Choi
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Charles G. Danko
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Michael J. Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Joyet P, Bouraoui H, Aké FMD, Derkaoui M, Zébré AC, Cao TN, Ventroux M, Nessler S, Noirot-Gros MF, Deutscher J, Milohanic E. Transcription regulators controlled by interaction with enzyme IIB components of the phosphoenolpyruvate: sugar phosphotransferase system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1415-24. [PMID: 23318733 DOI: 10.1016/j.bbapap.2013.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/27/2012] [Accepted: 01/04/2013] [Indexed: 11/16/2022]
Abstract
Numerous bacteria possess transcription activators and antiterminators composed of regulatory domains phosphorylated by components of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). These domains, called PTS regulation domains (PRDs), usually contain two conserved histidines as potential phosphorylation sites. While antiterminators possess two PRDs with four phosphorylation sites, transcription activators contain two PRDs plus two regulatory domains resembling PTS components (EIIA and EIIB). The activity of these transcription regulators is controlled by up to five phosphorylations catalyzed by PTS proteins. Phosphorylation by the general PTS components EI and HPr is usually essential for the activity of PRD-containing transcription regulators, whereas phosphorylation by the sugar-specific components EIIA or EIIB lowers their activity. For a specific regulator, for example the Bacillus subtilis mtl operon activator MtlR, the functional phosphorylation sites can be different in other bacteria and consequently the detailed mode of regulation varies. Some of these transcription regulators are also controlled by an interaction with a sugar-specific EIIB PTS component. The EIIBs are frequently fused to the membrane-spanning EIIC and EIIB-mediated membrane sequestration is sometimes crucial for the control of a transcription regulator. This is also true for the Escherichia coli repressor Mlc, which does not contain a PRD but nevertheless interacts with the EIIB domain of the glucose-specific PTS. In addition, some PRD-containing transcription activators interact with a distinct EIIB protein located in the cytoplasm. The phosphorylation state of the EIIB components, which changes in response to the presence or absence of the corresponding carbon source, affects their interaction with transcription regulators. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Philippe Joyet
- Institut National de la Recherche Agronomique, UMR1319 Microbiologie de l'alimentation au service de la santé humaine Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, F-78350 Jouy-en-Josas, France
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Ishii H, Tanaka T, Ogura M. The Bacillus subtilis response regulator gene degU is positively regulated by CcpA and by catabolite-repressed synthesis of ClpC. J Bacteriol 2013; 195:193-201. [PMID: 23123903 PMCID: PMC3553847 DOI: 10.1128/jb.01881-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/24/2012] [Indexed: 01/18/2023] Open
Abstract
In Bacillus subtilis, the response regulator DegU and its cognate kinase, DegS, constitute a two-component system that regulates many cellular processes, including exoprotease production and genetic competence. Phosphorylated DegU (DegU-P) activates its own promoter and is degraded by the ClpCP protease. We observed induction of degU by glucose in sporulation medium. This was abolished in two mutants: the ccpA (catabolite control protein A) and clpC disruptants. Transcription of the promoter of the operon containing clpC (PclpC) decreased in the presence of glucose, and the disruption of ccpA resulted in derepression of PclpC. However, this was not directly mediated by CcpA, because we failed to detect binding of CcpA to PclpC. Glucose decreased the expression of clpC, leading to low cellular concentrations of the ClpCP protease. Thus, degU is induced through activation of autoregulation by a decrease in ClpCP-dependent proteolysis of DegU-P. An electrophoretic mobility shift assay showed that CcpA bound directly to the degU upstream region, indicating that CcpA activates degU through binding. The bound region was narrowed down to 27 bases, which contained a cre (catabolite-responsive element) sequence with a low match to the cre consensus sequence. In a footprint analysis, CcpA specifically protected a region containing the cre sequence from DNase I digestion. The induction of degU by glucose showed complex regulation of the degU gene.
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Affiliation(s)
- Hiroshi Ishii
- Institute of Oceanic Research and Development, Tokai University, Orido-Shimizu, Shizuoka, Japan
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Li J, Huang C, Zheng D, Wang Y, Yuan Z. CcpA-Mediated Enhancement of Sugar and Amino Acid Metabolism in Lysinibacillus sphaericus by NMR-Based Metabolomics. J Proteome Res 2012; 11:4654-61. [DOI: 10.1021/pr300469v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Li
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
People’s Republic of China
| | - Chongyang Huang
- Wuhan Center of
Magnetic Resonance,
State Key Laboratory of Magnetic Resonance and Atomic and Molecular
Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People’s
Republic of China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039,
People’s Republic of China
| | - Dasheng Zheng
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
| | - Yulan Wang
- Wuhan Center of
Magnetic Resonance,
State Key Laboratory of Magnetic Resonance and Atomic and Molecular
Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, People’s
Republic of China
| | - Zhiming Yuan
- Center for Applied and Environmental
Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic
of China
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Heravi KM, Wenzel M, Altenbuchner J. Regulation of mtl operon promoter of Bacillus subtilis: requirements of its use in expression vectors. Microb Cell Fact 2011; 10:83. [PMID: 22014119 PMCID: PMC3217849 DOI: 10.1186/1475-2859-10-83] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/20/2011] [Indexed: 11/10/2022] Open
Abstract
Background Several vector systems have been developed to express any gene desired to be studied in Bacillus subtilis. Among them, the transcriptionally regulated promoters involved in carbohydrate utilization are a research priority. Expression systems based on Bacillus promoters for xylose, maltose, and mannose utilization, as well as on the heterologous E. coli lactose promoter, have been successfully constructed. The promoter of the mtlAFD operon for utilization of mannitol is another promising candidate for its use in expression vectors. In this study, we investigated the regulation of the mtl genes in order to identify the elements needed to construct a strong mannitol inducible expression system in B. subtilis. Results Regulation of the promoters of mtlAFD operon (PmtlA) and mtlR (PmtlR) encoding the activator were investigated by fusion to lacZ. Identification of the PmtlA and PmtlR transcription start sites revealed the σA like promoter structures. Also, the operator of PmtlA was determined by shortening, nucleotide exchange, and alignment of PmtlA and PmtlR operator regions. Deletion of the mannitol-specific PTS genes (mtlAF) resulted in PmtlA constitutive expression demonstrating the inhibitory effect of EIICBMtl and EIIAMtl on MtlR in the absence of mannitol. Disruption of mtlD made the cells sensitive to mannitol and glucitol. Both PmtlA and PmtlR were influenced by carbon catabolite repression (CCR). However, a CcpA deficient mutant showed only a slight reduction in PmtlR catabolite repression. Similarly, using PgroE as a constitutive promoter, putative cre sites of PmtlA and PmtlR slightly reduced the promoter activity in the presence of glucose. In contrast, glucose repression of PmtlA and PmtlR was completely abolished in a ΔptsG mutant and significantly reduced in a MtlR (H342D) mutant. Conclusions The mtl operon promoter (PmtlA) is a strong promoter that reached a maximum of 13,000 Miller units with lacZ as a reporter on low copy plasmids. It is tightly regulated by just one copy of the mtlR gene on the chromosome and subject to CCR. CCR can be switched off by mutations in MtlR and the glucose transporter. These properties and the low costs of the inducers, i.e. mannitol and glucitol, make the promoter ideal for designing regulated expression systems.
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Yomantas YA, Abalakina EG, Golubeva LI, Gorbacheva LY, Mashko SV. Overproduction of Bacillus amyloliquefaciens extracellular glutamyl-endopeptidase as a result of ectopic multi-copy insertion of an efficiently-expressed mpr gene into the Bacillus subtilis chromosome. Microb Cell Fact 2011; 10:64. [PMID: 21819557 PMCID: PMC3166918 DOI: 10.1186/1475-2859-10-64] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 08/05/2011] [Indexed: 11/16/2022] Open
Abstract
Background Plasmid-less, engineered Bacillus strains have several advantages over plasmid-carrier variants. Specifically, their stability and potential ecological safety make them of use in industrial applications. As a rule, however, it is necessary to incorporate many copies of a key gene into a chromosome to achieve strain performance that is comparable to that of cells carrying multiple copies of a recombinant plasmid. Results A plasmid-less B. subtilis JE852-based strain secreting glutamyl-specific protease (GSP-the protein product of the mpr gene from B. amyloliquefaciens) was constructed that exhibits decreased levels of other extracellular proteases. Ten copies of an mprB.amy cassette in which the GSP gene was placed between the promoter of the B. amyloliquefaciens rplU-rpmA genes and the Rho-independent transcription terminator were ectopically inserted into designated (3 copies) and random (7 copies) points in the recipient chromosome. The resulting strain produced approximately 0.5 g/L of secreted GSP after bacterial cultivation in flasks with starch-containing media, and its performance was comparable to an analogous strain in which the mprB.amy cassette was carried on a multi-copy plasmid. Conclusion A novel strategy for ectopically integrating a cassette into multiple random locations in the B. subtilis chromosome was developed. This new method is based on the construction of DNA fragments in which the desired gene, marked by antibiotic resistance, is sandwiched between "front" and "back" portions of random chromosomal DNA restriction fragments. These fragments were subsequently inserted into the targeted sites of the chromosome using double-cross recombination. The construction of a marker-free strain was achieved by gene conversion between the integrated marked gene and a marker-less variant carried by plasmid DNA, which was later removed from the cells.
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Affiliation(s)
- Yurgis Av Yomantas
- Ajinomoto-Genetika Research Institute, 117545 Moscow, Russian Federation
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Self-inducible Bacillus subtilis expression system for reliable and inexpensive protein production by high-cell-density fermentation. Appl Environ Microbiol 2011; 77:6419-25. [PMID: 21803899 DOI: 10.1128/aem.05219-11] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel technically compliant expression system was developed for heterologous protein production in Bacillus subtilis with the aim of increasing product yields at the same time as decreasing production costs. Standard systems involve the positively regulated manP promoter of the mannose operon, which led to relatively high product yields of 5.3% (5.3 g enhanced green fluorescent protein [eGFP] per 100 g cell dry weight [CDW]) but required large quantities of mannose to induce the reactions, thus rendering the system's technical application rather expensive. To improve this situation, mutant B. subtilis strains were used: the ΔmanA (mannose metabolism) strain TQ281 and the ΔmanP (mannose uptake) strain TQ356. The total amount of inducer could be reduced with TQ281, which, however, displayed sensitivity to mannose. An inducer-independent self-induction system was developed with TQ356 to further improve the cost efficiency and product yield of the system, in which glucose prevents induction by carbon catabolite repression. To create optimal self-induction conditions, a glucose-limited process strategy, namely, a fed-batch process, was utilized as follows. The initiation of self-induction at the beginning of the glucose-restricted transition phase between the batch and fed-batch phase of fermentation and its maintenance throughout the glucose-limiting fed-batch phase led to a nearly 3-fold increase of product yield, to 14.6%. The novel B. subtilis self-induction system thus makes a considerable contribution to improving product yield and reducing the costs associated with its technical application.
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Ueda T, Kaito C, Omae Y, Sekimizu K. Sugar-responsive gene expression and the agr system are required for colony spreading in Staphylococcus aureus. Microb Pathog 2011; 51:178-85. [PMID: 21514374 DOI: 10.1016/j.micpath.2011.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 04/05/2011] [Accepted: 04/06/2011] [Indexed: 10/18/2022]
Abstract
Staphylococcus aureus spreads on soft agar surfaces, which is called "colony spreading". Here, we report that the colony spreading in S. aureus was promoted by the addition of glucose to soft agar plates. Disruption of ccpA and hprK, which are involved in catabolite repression, decreased the colony spreading ability promoted by glucose. Deletion of the agr locus, a virulence regulatory element whose expression is activated by glucose in a ccpA-dependent manner, abolished the colony spreading promoted by glucose. Disruption of clpP and arlRS, which contributes to agr expression, also decreased glucose-promoted colony spreading. These findings suggest that S. aureus colony spreading requires the expression of agr, which is positively regulated by environmental carbon sources, and that virulence gene expression and colony spreading induced by agr are simultaneously activated in the S. aureus infectious process.
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Affiliation(s)
- Tomofumi Ueda
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-Chome, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Glucose-dependent activation of Bacillus anthracis toxin gene expression and virulence requires the carbon catabolite protein CcpA. J Bacteriol 2010; 193:52-62. [PMID: 20971911 DOI: 10.1128/jb.01656-09] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sensing environmental conditions is an essential aspect of bacterial physiology and virulence. In Bacillus anthracis, the causative agent of anthrax, transcription of the two major virulence factors, toxin and capsule, is triggered by bicarbonate, a major compound in the mammalian body. Here it is shown that glucose is an additional signaling molecule recognized by B. anthracis for toxin synthesis. The presence of glucose increased the expression of the protective antigen toxin component-encoding gene (pagA) by stimulating induction of transcription of the AtxA virulence transcription factor. Induction of atxA transcription by glucose required the carbon catabolite protein CcpA via an indirect mechanism. CcpA did not bind specifically to any region of the extended atxA promoter. The virulence of a B. anthracis strain from which the ccpA gene was deleted was significantly attenuated in a mouse model of infection. The data demonstrated that glucose is an important host environment-derived signaling molecule and that CcpA is a molecular link between environmental sensing and B. anthracis pathogenesis.
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Identification and inactivation of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum. Metab Eng 2010; 12:446-54. [DOI: 10.1016/j.ymben.2010.05.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/05/2010] [Accepted: 05/10/2010] [Indexed: 11/21/2022]
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