1
|
Wu X, Tong Y, Li T, Guo J, Liu W, Mo J. Metabolomic Response of Thalassiosira weissflogii to Erythromycin Stress: Detoxification Systems, Steroidal Metabolites, and Energy Metabolism. PLANTS (BASEL, SWITZERLAND) 2024; 13:354. [PMID: 38337887 PMCID: PMC10856835 DOI: 10.3390/plants13030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/12/2024]
Abstract
Erythromycin, a macrolide antibiotic, is a prioritized pollutant that poses a high risk to environmental health. It has been detected in different environmental matrices and can cause undesired effects in aquatic organisms, particularly freshwater algae, which are primary producers. However, the impact of erythromycin on marine algae remains largely unexplored. Erythromycin has been reported to induce hormetic effects in the marine diatom Thalassiosira weissflogii (T. weissflogii). These effects are associated with the molecular pathways and biological processes of ribosome assembly, protein translation, photosynthesis, and oxidative stress. However, the alterations in the global gene expression have yet to be validated at the metabolic level. The present study used non-targeted metabolomic analysis to reveal the altered metabolic profiles of T. weissflogii under erythromycin stress. The results showed that the increased cell density was possibly attributed to the accumulation of steroidal compounds with potential hormonic action at the metabolic level. Additionally, slight increases in the mitochondrial membrane potential (MMP) and viable cells were observed in the treatment of 0.001 mg/L of erythromycin (an environmentally realistic level). Contrarily, the 0.75 and 2.5 mg/L erythromycin treatments (corresponding to EC20 and EC50, respectively) showed decreases in the MMP, cell density, and viable algal cells, which were associated with modified metabolic pathways involving ATP-binding cassette (ABC) transporters, the metabolism of hydrocarbons and lipids, thiamine metabolism, and the metabolism of porphyrin and chlorophyll. These findings suggest that metabolomic analysis, as a complement to the measurement of apical endpoints, could provide novel insights into the molecular mechanisms of hormesis induced by antibiotic agents in algae.
Collapse
Affiliation(s)
- Xintong Wu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China (W.L.)
| | - Yongqi Tong
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China (W.L.)
| | - Tong Li
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China (W.L.)
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, Northwest University, Xi’an 710127, China;
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China (W.L.)
| | - Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China (W.L.)
| |
Collapse
|
2
|
Li Z, Gao C, Ye C, Guo L, Liu J, Chen X, Song W, Wu J, Liu L. Systems engineering of Escherichia coli for high-level shikimate production. Metab Eng 2023; 75:1-11. [PMID: 36328295 DOI: 10.1016/j.ymben.2022.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
To further increase the production efficiency of microbial shikimate, a valuable compound widely used in the pharmaceutical and chemical industries, ten key target genes contributing to shikimate production were identified by exploiting the enzyme constraint model ec_iML1515, and subsequently used for promoting metabolic flux towards shikimate biosynthesis in the tryptophan-overproducing strain Escherichia coli TRP0. The engineered E. coli SA05 produced 78.4 g/L shikimate via fed-batch fermentation. Deletion of quinate dehydrogenase and introduction of the hydroaromatic equilibration-alleviating shikimate dehydrogenase mutant AroET61W/L241I reduced the contents of byproducts quinate (7.5 g/L) and 3-dehydroshikimic acid (21.4 g/L) by 89.1% and 52.1%, respectively. Furthermore, a high concentration shikimate responsive promoter PrpoS was recruited to dynamically regulate the expression of the tolerance target ProV to enhance shikimate productivity by 23.2% (to 2 g/L/h). Finally, the shikimate titer was increased to 126.4 g/L, with a yield of 0.50 g/g glucose and productivity of 2.63 g/L/h, using a 30-L fermenter and the engineered strain E. coli SA09. This is, to the best of our knowledge, the highest reported shikimate titer and productivity in E. coli.
Collapse
Affiliation(s)
- Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| |
Collapse
|
3
|
Gregory GJ, Boyd EF. Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae. Comput Struct Biotechnol J 2021; 19:1014-1027. [PMID: 33613867 PMCID: PMC7876524 DOI: 10.1016/j.csbj.2021.01.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteria have evolved mechanisms that allow them to adapt to changes in osmolarity and some species have adapted to live optimally in high salinity environments such as in the marine ecosystem. Most bacteria that live in high salinity do so by the biosynthesis and/or uptake of compatible solutes, small organic molecules that maintain the turgor pressure of the cell. Osmotic stress response mechanisms and their regulation among marine heterotrophic bacteria are poorly understood. In this review, we discuss what is known about compatible solute metabolism and transport and new insights gained from studying marine bacteria belonging to the family Vibrionaceae.
Collapse
Affiliation(s)
| | - E. Fidelma Boyd
- Corresponding author at: Department of Biological Sciences, 341 Wolf Hall, University of Delaware, Newark, DE 19716, United States.
| |
Collapse
|
4
|
Chaudhary R, Mishra S, Kota S, Misra H. Molecular interactions and their predictive roles in cell pole determination in bacteria. Crit Rev Microbiol 2021; 47:141-161. [PMID: 33423591 DOI: 10.1080/1040841x.2020.1857686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.
Collapse
Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
5
|
Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8–independent protection of respiration on Escherichia coli. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49909-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
6
|
Tempelhagen L, Ayer A, Culham DE, Stocker R, Wood JM. Cultivation at high osmotic pressure confers ubiquinone 8-independent protection of respiration on Escherichia coli. J Biol Chem 2019; 295:981-993. [PMID: 31826918 DOI: 10.1074/jbc.ra119.011549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ubiquinone 8 (coenzyme Q8 or Q8) mediates electron transfer within the aerobic respiratory chain, mitigates oxidative stress, and contributes to gene expression in Escherichia coli In addition, Q8 was proposed to confer bacterial osmotolerance by accumulating during growth at high osmotic pressure and altering membrane stability. The osmolyte trehalose and membrane lipid cardiolipin accumulate in E. coli cells cultivated at high osmotic pressure. Here, Q8 deficiency impaired E. coli growth at low osmotic pressure and rendered growth osmotically sensitive. The Q8 deficiency impeded cellular O2 uptake and also inhibited the activities of two proton symporters, the osmosensing transporter ProP and the lactose transporter LacY. Q8 supplementation decreased membrane fluidity in liposomes, but did not affect ProP activity in proteoliposomes, which is respiration-independent. Liposomes and proteoliposomes prepared with E. coli lipids were used for these experiments. Similar oxygen uptake rates were observed for bacteria cultivated at low and high osmotic pressures. In contrast, respiration was dramatically inhibited when bacteria grown at the same low osmotic pressure were shifted to high osmotic pressure. Thus, respiration was restored during prolonged growth of E. coli at high osmotic pressure. Of note, bacteria cultivated at low and high osmotic pressures had similar Q8 concentrations. The protection of respiration was neither diminished by cardiolipin deficiency nor conferred by trehalose overproduction during growth at low osmotic pressure, but rather might be achieved by Q8-independent respiratory chain remodeling. We conclude that osmotolerance is conferred through Q8-independent protection of respiration, not by altering physical properties of the membrane.
Collapse
Affiliation(s)
- Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Anita Ayer
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Roland Stocker
- Vascular Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, University of New South Wales Medicine, Kensington, New South Wales 2050, Australia
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
7
|
Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. Int J Mol Sci 2019; 20:ijms20082015. [PMID: 31022896 PMCID: PMC6514802 DOI: 10.3390/ijms20082015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.
Collapse
|
8
|
Christgen SL, Becker DF. Role of Proline in Pathogen and Host Interactions. Antioxid Redox Signal 2019; 30:683-709. [PMID: 29241353 PMCID: PMC6338583 DOI: 10.1089/ars.2017.7335] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/26/2017] [Accepted: 11/14/2017] [Indexed: 01/20/2023]
Abstract
SIGNIFICANCE Proline metabolism has complex roles in a variety of biological processes, including cell signaling, stress protection, and energy production. Proline also contributes to the pathogenesis of various disease-causing organisms. Understanding the mechanisms of how pathogens utilize proline is important for developing new strategies against infectious diseases. Recent Advances: The ability of pathogens to acquire amino acids is critical during infection. Besides protein biosynthesis, some amino acids, such as proline, serve as a carbon, nitrogen, or energy source in bacterial and protozoa pathogens. The role of proline during infection depends on the physiology of the host/pathogen interactions. Some pathogens rely on proline as a critical respiratory substrate, whereas others exploit proline for stress protection. CRITICAL ISSUES Disruption of proline metabolism and uptake has been shown to significantly attenuate virulence of certain pathogens, whereas in other pathogens the importance of proline during infection is not known. Inhibiting proline metabolism and transport may be a useful therapeutic strategy against some pathogens. Developing specific inhibitors to avoid off-target effects in the host, however, will be challenging. Also, potential treatments that target proline metabolism should consider the impact on intracellular levels of Δ1-pyrroline-5-carboxylate, a metabolite intermediate that can have opposing effects on pathogenesis. FUTURE DIRECTIONS Further characterization of how proline metabolism is regulated during infection would provide new insights into the role of proline in pathogenesis. Biochemical and structural characterization of proline metabolic enzymes from different pathogens could lead to new tools for exploring proline metabolism during infection and possibly new therapeutic compounds.
Collapse
Affiliation(s)
- Shelbi L. Christgen
- Department of Biochemistry, Redox Biology Center, University of Nebraska−Lincoln, Lincoln, Nebraska
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska−Lincoln, Lincoln, Nebraska
| |
Collapse
|
9
|
Culham DE, Marom D, Boutin R, Garner J, Ozturk TN, Sahtout N, Tempelhagen L, Lamoureux G, Wood JM. Dual Role of the C-Terminal Domain in Osmosensing by Bacterial Osmolyte Transporter ProP. Biophys J 2018; 115:2152-2166. [PMID: 30448037 PMCID: PMC6289098 DOI: 10.1016/j.bpj.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 11/23/2022] Open
Abstract
ProP is a member of the major facilitator superfamily, a proton-osmolyte symporter, and an osmosensing transporter. ProP proteins share extended cytoplasmic carboxyl terminal domains (CTDs) implicated in osmosensing. The CTDs of the best characterized, group A ProP orthologs, terminate in sequences that form intermolecular, antiparallel α-helical coiled coils (e.g., ProPEc, from Escherichia coli). Group B orthologs lack that feature (e.g., ProPXc, from Xanthomonas campestris). ProPXc was expressed and characterized in E. coli to further elucidate the role of the coiled coil in osmosensing. The activity of ProPXc was a sigmoid function of the osmolality in cells and proteoliposomes. ProPEc and ProPXc attained similar activities at the same expression level in E. coli. ProPEc transports proline and glycine betaine with comparable high affinities at low osmolality. In contrast, proline weakly inhibited high-affinity glycine-betaine uptake via ProPXc. The KM for proline uptake via ProPEc increases dramatically with the osmolality. The KM for glycine-betaine uptake via ProPXc did not. Thus, ProPXc is an osmosensing transporter, and the C-terminal coiled coil is not essential for osmosensing. The role of CTD-membrane interaction in osmosensing was examined further. As for ProPEc, the ProPXc CTD co-sedimented with liposomes comprising E. coli phospholipid. Molecular dynamics simulations illustrated association of the monomeric ProPEc CTD with the membrane surface. Comparison with the available NMR structure for the homodimeric coiled coil formed by the ProPEc-CTD suggested that membrane association and homodimeric coiled-coil formation by that peptide are mutually exclusive. The membrane fluidity in liposomes comprising E. coli phospholipid decreased with increasing osmolality in the range relevant for ProP activation. These data support the proposal that ProP activates as cellular dehydration increases cytoplasmic cation concentration, releasing the CTD from the membrane surface. For group A orthologs, this also favors α-helical coiled-coil formation that stabilizes the transporter in an active form.
Collapse
Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - David Marom
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Rebecca Boutin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jennifer Garner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada; Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada
| | - Tugba Nur Ozturk
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada
| | - Naheda Sahtout
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Tempelhagen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Guillaume Lamoureux
- Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec, Canada; Department of Physics, Concordia University, Montréal, Québec, Canada; Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| |
Collapse
|
10
|
Roles of osmolytes in protein folding and aggregation in cells and their biotechnological applications. Int J Biol Macromol 2018; 109:483-491. [DOI: 10.1016/j.ijbiomac.2017.12.100] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/19/2017] [Indexed: 12/19/2022]
|
11
|
Romantsov T, Gonzalez K, Sahtout N, Culham DE, Coumoundouros C, Garner J, Kerr CH, Chang L, Turner RJ, Wood JM. Cardiolipin synthase A colocalizes with cardiolipin and osmosensing transporter ProP at the poles of Escherichia coli cells. Mol Microbiol 2018; 107:623-638. [PMID: 29280215 DOI: 10.1111/mmi.13904] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/09/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022]
Abstract
Osmosensing by transporter ProP is modulated by its cardiolipin (CL)-dependent concentration at the poles of Escherichia coli cells. Other contributors to this phenomenon were sought with the BACterial Two-Hybrid System (BACTH). The BACTH-tagged variants T18-ProP and T25-ProP retained ProP function and localization. Their interaction confirmed the ProP homo-dimerization previously established by protein crosslinking. YdhP, YjbJ and ClsA were prominent among the putative ProP interactors identified by the BACTH system. The functions of YdhP and YjbJ are unknown, although YjbJ is an abundant, osmotically induced, soluble protein. ClsA (CL Synthase A) had been shown to determine ProP localization by mediating CL synthesis. Unlike a deletion of clsA, deletion of ydhP or yjbJ had no effect on ProP localization or function. All three proteins were concentrated at the cell poles, but only ClsA localization was CL-dependent. ClsA was shown to be N-terminally processed and membrane-anchored, with dual, cytoplasmic, catalytic domains. Active site amino acid replacements (H224A plus H404A) inactivated ClsA and compromised ProP localization. YdhP and YjbJ may be ClsA effectors, and interactions of YdhP, YjbJ and ClsA with ProP may reflect their colocalization at the cell poles. Targeted CL synthesis may contribute to the polar localization of CL, ClsA and ProP.
Collapse
Affiliation(s)
- Tatyana Romantsov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Karen Gonzalez
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Naheda Sahtout
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Chelsea Coumoundouros
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jennifer Garner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Craig H Kerr
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Limei Chang
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
12
|
Kan K, Chen J, Kawamura S, Koseki S. Characteristics of d-Tryptophan as an Antibacterial Agent: Effect of Sodium Chloride Concentration and Temperature on Escherichia coli Growth Inhibition. J Food Prot 2018; 81:25-30. [PMID: 29257726 DOI: 10.4315/0362-028x.jfp-17-229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We previously reported that d-tryptophan exhibits adverse effects on bacterial physiology under osmotic stress. However, the mechanism by which d-tryptophan acts as an inhibitor and/or incompatible solute for bacterial growth has not yet been investigated in detail. In this study, we aimed to determine how osmotic pressure and temperature affect the antimicrobial effect of d-tryptophan. Even at the same level of osmotic pressure, d-tryptophan in conjunction with sodium chloride (NaCl) had a stronger inhibitory effect on the growth of Escherichia coli than that obtained by incubation with potassium chloride (KCl) and sucrose. Because d-tryptophan with NaCl showed the strongest inhibitory effect, we determined the optimum concentration combination of d-tryptophan and NaCl. The growth inhibition boundary conditions as a function of d-tryptophan and NaCl concentrations were determined by a logistic regression model. We found that the minimum level of NaCl for E. coli growth inhibition was 2.5% (w/v) together with 40 mM d-tryptophan. Moreover, the higher the NaCl concentration, the lower the concentration of d-tryptophan that was needed to inhibit bacterial growth. The logistic regression model that we developed enabled us to predict the concentrations required to inhibit bacterial growth. Furthermore, we examined the effect of incubation temperatures ranging from 15 to 46°C on the antimicrobial effect of d-tryptophan. The higher the reaction temperature, the more rapid the decrease of viable E. coli that was observed. This trend is likely attributable to activation of physiological metabolism under the optimum growth temperature. Together, our findings should make a significant contribution to the development of a novel bacterial growth control strategy using d-tryptophan.
Collapse
Affiliation(s)
- Kaito Kan
- Graduate School of Agricultural Science, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Jian Chen
- Graduate School of Agricultural Science, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Shuso Kawamura
- Graduate School of Agricultural Science, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| | - Shigenobu Koseki
- Graduate School of Agricultural Science, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan
| |
Collapse
|
13
|
Rabbani G. WITHDRAWN: Role of osmolytes in protein folding and aggregation in cells and its applications in biotechnology. Int J Biol Macromol 2017:S0141-8130(17)32827-1. [PMID: 29137994 DOI: 10.1016/j.ijbiomac.2017.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Gulam Rabbani
- Department of Medical Biotechnology, YeungNam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
| |
Collapse
|
14
|
Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ. A geographically-diverse collection of 418 human gut microbiome pathway genome databases. Sci Data 2017; 4:170035. [PMID: 28398290 PMCID: PMC5387927 DOI: 10.1038/sdata.2017.35] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/10/2017] [Indexed: 01/16/2023] Open
Abstract
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.
Collapse
Affiliation(s)
- Aria S Hahn
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA
| | - Tomer Altman
- Biomedical Informatics, Stanford University School of Medicine, Stanford, California 94305, USA.,Whole Biome, Inc., 953 Indiana Street, San Francisco, California 94107, USA
| | - Kishori M Konwar
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA.,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Niels W Hanson
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Dongjae Kim
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Koonkie Inc., Menlo Park, California 94025, USA.,Ecosystem Services, Commercialization and Entrepreneurship (ECOSCOPE), University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
15
|
Ma Y, Wang Q, Gao X, Zhang Y. Biosynthesis and uptake of glycine betaine as cold-stress response to low temperature in fish pathogen Vibrio anguillarum. J Microbiol 2016; 55:44-55. [PMID: 28035596 DOI: 10.1007/s12275-017-6370-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 12/28/2022]
Abstract
Fish pathogen Vibrio anguillarum, a mesophile bacterium, is usually found in estuarine and marine coastal ecosystems worldwide that pose a constant stress to local organism by its fluctuation in salinity as well as notable temperature change. Though V. anguillarum is able to proliferate while maintain its pathogenicity under low temperature (5-18°C), so far, coldadaption molecular mechanism of the bacteria is unknown. In this study, V. anguillarum was found possessing a putative glycine betaine synthesis system, which is encoded by betABI and synthesizes glycine betaine from its precursor choline. Furthermore, significant up-regulation of the bet gene at the transcriptional level was noted in log phase in response to cold-stress. Moreover, the accumulation of betaine glycine was only found appearing at low growth temperatures, suggesting that response regulation of both synthesis system and transporter system are cold-dependent. Furthermore, in-frame deletion mutation in the two putative ABC transporters and three putative BCCT family transporters associated with glycine betaine uptake could not block cellular accumulation of betaine glycine in V. anguillarum under coldstress, suggesting the redundant feature in V. anguillarum betaine transporter system. These findings confirmed that glycine betaine serves as an effective cold stress protectant and highlighted an underappreciated facet of the acclimatization of V. anguillarum to cold environments.
Collapse
Affiliation(s)
- Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China
| | - Xiating Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China.
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China.
| |
Collapse
|
16
|
Romantsov T, Culham DE, Caplan T, Garner J, Hodges RS, Wood JM. ProP‐ProP and ProP‐phospholipid interactions determine the subcellular distribution of osmosensing transporter ProP inEscherichia coli. Mol Microbiol 2016; 103:469-482. [DOI: 10.1111/mmi.13569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Tatyana Romantsov
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelph ON CanadaN1G2W1
| | - Doreen E. Culham
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelph ON CanadaN1G2W1
| | - Tavia Caplan
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelph ON CanadaN1G2W1
| | - Jennifer Garner
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelph ON CanadaN1G2W1
| | - Robert S. Hodges
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Denver, School of MedicineP.O. Box 6511, Mail Stop 8101Aurora CO80045, USA
| | - Janet M. Wood
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelph ON CanadaN1G2W1
| |
Collapse
|
17
|
Culham DE, Shkel IA, Record MT, Wood JM. Contributions of Coulombic and Hofmeister Effects to the Osmotic Activation of Escherichia coli Transporter ProP. Biochemistry 2016; 55:1301-13. [PMID: 26871755 DOI: 10.1021/acs.biochem.5b01169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Osmosensing transporters mediate osmolyte accumulation to forestall cellular dehydration as the extracellular osmolality increases. ProP is a bacterial osmolyte-H(+) symporter, a major facilitator superfamily member, and a paradigm for osmosensing. ProP activity is a sigmoid function of the osmolality. It is determined by the osmolality, not the magnitude or direction of the osmotic shift, in cells and salt-loaded proteoliposomes. The activation threshold varies directly with the proportion of anionic phospholipid in cells and proteoliposomes. The osmosensory mechanism was probed by varying the salt composition and concentration outside and inside proteoliposomes. Data analysis was based on the hypothesis that the fraction of maximal transporter activity at a particular luminal salt concentration reflects the proportion of ProP molecules in an active conformation. ProP attained the same activity at the same osmolality when diverse, membrane-impermeant salts were added to the external medium. Contributions of Coulombic and/or Hofmeister salt effects to ProP activation were examined by varying the luminal salt cation (K(+) and Na(+)) and anion (chloride, phosphate, and sulfate) composition and then systematically increasing the luminal salt concentration by increasing the external osmolality. ProP activity increased with the sixth power of the univalent cation concentration, independent of the type of anion. This indicates that salt activation of ProP is a Coulombic, cation effect resulting from salt cation accumulation and not site-specific cation binding. Possible origins of this Coulombic effect include folding or assembly of anionic cytoplasmic ProP domains, an increase in local membrane surface charge density, and/or the juxtaposition of anionic protein and membrane surfaces during activation.
Collapse
Affiliation(s)
- Doreen E Culham
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - Irina A Shkel
- Departments of Biochemistry and Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - M Thomas Record
- Departments of Biochemistry and Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, ON N1G 2W1, Canada
| |
Collapse
|
18
|
Lang S, Cressatti M, Mendoza KE, Coumoundouros CN, Plater SM, Culham DE, Kimber MS, Wood JM. YehZYXW of Escherichia coli Is a Low-Affinity, Non-Osmoregulatory Betaine-Specific ABC Transporter. Biochemistry 2015; 54:5735-47. [DOI: 10.1021/acs.biochem.5b00274] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shenhui Lang
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Marisa Cressatti
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Kris E. Mendoza
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Chelsea N. Coumoundouros
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Samantha M. Plater
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Doreen E. Culham
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Matthew S. Kimber
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| | - Janet M. Wood
- Department
of Molecular and
Cellular Biology, University of Guelph, 488 Gordon Street, Guelph, ON N1G
2W1, Canada
| |
Collapse
|
19
|
Affiliation(s)
- Janet M Wood
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
20
|
Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E. Abiotic stress protection by ecologically abundant dimethylsulfoniopropionate and its natural and synthetic derivatives: insights from Bacillus subtilis. Environ Microbiol 2014; 17:2362-78. [PMID: 25384455 DOI: 10.1111/1462-2920.12698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/28/2014] [Indexed: 12/01/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant osmolyte and anti-stress compound produced primarily in marine ecosystems. After its release into the environment, microorganisms can exploit DMSP as a source of sulfur and carbon, or accumulate it as an osmoprotectant. However, import systems for this ecophysiologically important compatible solute, and its stress-protective properties for microorganisms that do not produce it are insufficiently understood. Here we address these questions using a well-characterized set of Bacillus subtilis mutants to chemically profile the influence of DMSP import on stress resistance, the osmostress-adaptive proline pool and on osmotically controlled gene expression. We included in this study the naturally occurring selenium analogue of DMSP, dimethylseleniopropionate (DMSeP), as well as a set of synthetic DMSP derivatives. We found that DMSP is not a nutrient for B. subtilis, but it serves as an excellent stress protectant against challenges conferred by sustained high salinity or lasting extremes in both low and high growth temperatures. DMSeP and synthetic DMSP derivatives retain part of these stress protective attributes, but DMSP is clearly the more effective stress protectant. We identified the promiscuous and widely distributed ABC transporter OpuC as a high-affinity uptake system not only for DMSP, but also for its natural and synthetic derivatives.
Collapse
Affiliation(s)
- Sebastian Broy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Chiliang Chen
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Gabriele Nau-Wagner
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Mohamed Jebbar
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,Laboratory of Microbiology of Extreme Environments, UMR 6197 (CNRS - Ifremer - UBO), European Institute of Marine Studies, University of West Brittany (Brest), Technopole Brest-Iroise, F-29280, Plouzané, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitäts Str. 1, D-40225, Düsseldorf, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany.,Kekule-Institute for Organic Chemistry and Biochemistry, Friedrich Wilhelms-University Bonn, Gerhard-Domagk-Str. 1, D-53121, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| |
Collapse
|