101
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Tourigny DS. Dynamic metabolic resource allocation based on the maximum entropy principle. J Math Biol 2020; 80:2395-2430. [PMID: 32424475 DOI: 10.1007/s00285-020-01499-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 03/08/2020] [Indexed: 01/06/2023]
Abstract
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for uncertainty. This paper introduces a dynamic metabolic modelling framework that is a synthesis of recent ideas on resource allocation and the powerful optimal control formulation of Ramkrishna and colleagues. In particular, their work is extended based on the hypothesis that cellular resources are allocated among elementary flux modes according to the principle of maximum entropy. These concepts both generalise and unify prior approaches to dynamic metabolic modelling by establishing a smooth interpolation between dynamic flux balance analysis and dynamic metabolic models without regulation. The resulting theory is successful in describing 'bet-hedging' strategies employed by cell populations dealing with uncertainty in a fluctuating environment, including heterogenous resource investment, accumulation of reserves in growth-limiting conditions, and the observed behaviour of yeast growing in batch and continuous cultures. The maximum entropy principle is also shown to yield an optimal control law consistent with partitioning resources between elementary flux mode families, which has important practical implications for model reduction, selection, and simulation.
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Affiliation(s)
- David S Tourigny
- Columbia University Irving Medical Center, 630 West 168th Street, New York, NY, 10032, USA.
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102
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Transporters of glucose and other carbohydrates in bacteria. Pflugers Arch 2020; 472:1129-1153. [PMID: 32372286 DOI: 10.1007/s00424-020-02379-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
Glucose arguably is the most important energy carrier, carbon source for metabolites and building block for biopolymers in all kingdoms of life. The proper function of animal organs and tissues depends on the continuous supply of glucose from the bloodstream. Most animals can resorb only a small number of monosaccharides, mostly glucose, galactose and fructose, while all other sugars oligosaccharides and dietary fibers are degraded and metabolized by the microbiota of the lower intestine. Bacteria, in contrast, are omnivorous. They can import and metabolize structurally different sugars and, as a consortium of different species, utilize almost any sugar, sugar derivative and oligosaccharide occurring in nature. Bacteria have membrane transport systems for the uptake of sugars against steep concentration gradients energized by ATP, the proton motive force and the high energy glycolytic intermediate phosphoenolpyruvate (PEP). Different uptake mechanisms and the broad range of overlapping substrate specificities allow bacteria to quickly adapt to and colonize changing environments. Here, we review the structures and mechanisms of bacterial representatives of (i) ATP-dependent cassette (ABC) transporters, (ii) major facilitator (MFS) superfamily proton symporters, (iii) sodium solute symporters (SSS) and (iv) enzyme II integral membrane subunits of the bacterial PEP-dependent phosphotransferase system (PTS). We give a short overview on the distribution of transporter genes and their phylogenetic relationship in different bacterial species. Some sugar transporters are hijacked for import of bacteriophage DNA and antibacterial toxins (bacteriocins) and they facilitate the penetration of polar antibiotics. Finally, we describe how the expression and activity of certain sugar transporters are controlled in response to the availability of sugars and how the presence and uptake of sugars may affect pathogenicity and host-microbiota interactions.
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103
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Christofoleti-Furlan RM, Portugal CB, Varize CS, Muynarsk ESM, Alcarde AR, Basso LC. Unraveling Brazilian bioethanol yeasts as novel starters for high-gravity brewing. Food Res Int 2020; 135:109282. [PMID: 32527477 DOI: 10.1016/j.foodres.2020.109282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/14/2020] [Accepted: 04/29/2020] [Indexed: 01/21/2023]
Abstract
High-gravity (HG) brewing has broader application to succeed on beer differentiation and production optimization. However, such process imposes a handicap to yeasts, which must be able to deal with stressful conditions in fermentation. In this work, we assessed different physiological traits of 24 Saccharomyces cerevisiae strains isolated from Brazilian bioethanol distilleries for the selection of novel starters for HG brewing. Five yeast strains were selected with ability to overcome different stressors under HG beer fermentation, showing high fermentability rates, resilience to ethanol stress, low production of foam and hydrogen sulfide, as well as similar flocculation rates to brewer's yeasts. After five fermentation recycles, most strains sustained a viability rate higher than 90% and were able to efficiently accumulate trehalose and glycogen, besides presenting no detectable petite mutants at the final stage. In the sensory analysis, the beers obtained from the five selected strains showed greater aromatic complexity, with predominance of 'spicy', 'dried' and 'fresh fruits' descriptors. In conclusion, this study sheds light on the potential of yeast strains from Brazilian bioethanol process to produce distinctive specialty beers, aside from proposing an effective selection methodology based on relevant physiological attributes for HG brewing process.
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Affiliation(s)
- R M Christofoleti-Furlan
- Dept. Ciências Biológicas, Laboratório de Bioquímica e Tecnologia de Leveduras, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
| | - C B Portugal
- Dept. Agroindústria, Alimentos e Nutrição, Laboratório de Biotecnologia de Alimentos e Bebidas, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
| | - C S Varize
- Dept. Ciências Biológicas, Laboratório de Bioquímica e Tecnologia de Leveduras, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
| | - E S M Muynarsk
- Dept. Ciências Biológicas, Laboratório de Bioquímica e Tecnologia de Leveduras, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
| | - A R Alcarde
- Dept. Agroindústria, Alimentos e Nutrição, Laboratório de Tecnologia e Qualidade de Bebidas, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
| | - L C Basso
- Dept. Ciências Biológicas, Laboratório de Bioquímica e Tecnologia de Leveduras, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Avenida Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
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104
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Sommer S. Monitoring the Functionality and Stress Response of Yeast Cells Using Flow Cytometry. Microorganisms 2020; 8:microorganisms8040619. [PMID: 32344655 PMCID: PMC7232141 DOI: 10.3390/microorganisms8040619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 11/16/2022] Open
Abstract
Throughout fermentation, yeast faces continuously changing medium conditions and reacts by adapting its metabolism. The adaptation is a critical process and is dependent on the accurate functioning of the cell. A stable membrane potential, which is, among other roles, responsible for protecting the yeast from low pH, is an important attribute for evaluating functionality. Other factors are storage products such as glycogen, trehalose, and neutral lipids, as well as mitochondrial activity and the integrity of the DNA. These parameters can be complemented by the analysis of viability, cell cycle, intracellular pH, and reactive oxygen species in the cell. The correlation of all these factors provides valuable information for evaluating the performance of a yeast population during fermentation. In order to demonstrate the analytical capabilities of flow cytometry, a Saccharomyces cerevisiae yeast strain was observed in a modified growth medium for 384 h (16 days). The results confirm observations made with other methods and reports from the literature. However, with flow cytometry, it is possible to gain deeper insight into stress response and adaptation behavior of yeast at a cellular level. The causality from the formation of oxygen-radicals to cell death, for example, can be shown, as well as the dependency of the intracellular pH on the stability of the membrane. The proposed bio-monitoring system has the potential to provide applicable information as a process control tool for wineries.
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Affiliation(s)
- Stephan Sommer
- Viticulture and Enology Research Center, California State University, 2360 E. Barstow Ave, Fresno, CA 93740, USA
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105
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Bacterial Glycogen Provides Short-Term Benefits in Changing Environments. Appl Environ Microbiol 2020; 86:AEM.00049-20. [PMID: 32111592 DOI: 10.1128/aem.00049-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/26/2020] [Indexed: 11/20/2022] Open
Abstract
Changing nutritional conditions challenge microbes and shape their evolutionary optimization. Here, we used real-time metabolomics to investigate the role of glycogen in the dynamic physiological adaptation of Escherichia coli to fluctuating nutrients following carbon starvation. After the depletion of environmental glucose, we found significant metabolic activity remaining, which was linked to rapid utilization of intracellular glycogen. Glycogen was depleted by 80% within minutes of glucose starvation and was similarly replenished within minutes of glucose availability. These fast time scales of glycogen utilization correspond to the short-term benefits that glycogen provided to cells undergoing various physiological transitions. Cells capable of utilizing glycogen exhibited shorter lag times than glycogen mutants when starved between periods of exposure to different carbon sources. The ability to utilize glycogen was also important for the transition between planktonic and biofilm lifestyles and enabled increased glucose uptake during pulses of limited glucose availability. While wild-type and mutant strains exhibited comparable growth rates in steady environments, mutants deficient in glycogen utilization grew more poorly in environments that fluctuated on minute scales between carbon availability and starvation. Taken together, these results highlight an underappreciated role of glycogen in rapidly providing carbon and energy in changing environments, thereby increasing survival and competition capabilities under fluctuating and nutrient-poor conditions.IMPORTANCE Nothing is constant in life, and microbes in particular have to adapt to frequent and rapid environmental changes. Here, we used real-time metabolomics and single-cell imaging to demonstrate that the internal storage polymer glycogen plays a crucial role in such dynamic adaptations. Glycogen is depleted within minutes of glucose starvation and similarly is replenished within minutes of glucose availability. Cells capable of utilizing glycogen exhibited shorter lag times than glycogen mutants when starved between periods of exposure to different carbon sources. While wild-type and mutant strains exhibited comparable growth rates in steady environments, mutants deficient in glycogen utilization grew more poorly in environments that fluctuated on minute scales between carbon availability and starvation. These results highlight an underappreciated role of glycogen in rapidly providing carbon and energy in changing environments, thereby increasing survival and competition capabilities under fluctuating and nutrient-poor conditions.
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106
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Liu Q, Zhu Z, Wang M, Wang Y, Zhang P, Wang H, Liang M, Li Y, Deng B, Tang D, Gilbert RG, Wang L. Characterization of glycogen molecular structure in the worm Caenorhabditis elegans. Carbohydr Polym 2020; 237:116181. [PMID: 32241425 DOI: 10.1016/j.carbpol.2020.116181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 12/21/2022]
Abstract
Glycogen, a glucose homopolymer with many glucose chains, is the primary blood-sugar reservoir in many organisms. It comprises β particles (∼20 nm) which can bind together to form large α particles with a rosette morphology. When dimethyl sulfoxide (DMSO) is added to glycogen from diabetic livers, α particles break apart to β particles ('fragility'), possibly due to H-bond disruption; this is not seen in healthy livers. Glycogen α and β particles, and α-particle fragility, are observed in mammals and bacteria, and are examined here in the worm Caenorhabditis elegans, with glycogen from two C. elegans strains, cultured in normal and high-glucose conditions. There were mainly β particles, with some large α particles. Most particles were fragile in DMSO. Growing in a high-glucose medium results in more long chains and more fragility, consistent with previous observations in diabetic animal models. Why high glucose levels facilitate fragility is worthy of further investigation.
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Affiliation(s)
- Qinghua Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China; Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China; Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Yuechen Wang
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Peng Zhang
- School of Electronic Information and Engineering, Yangtze Normal University, Chongqing, 408003, China
| | - Hao Wang
- School of The First Clinical Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Mengyu Liang
- School of The First Clinical Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Ying Li
- Department of Clinical Microbiology, School of Medical Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Bin Deng
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China; Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China
| | - Robert G Gilbert
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Liang Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China; Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, China.
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107
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Wang L, Wang M, Wise MJ, Liu Q, Yang T, Zhu Z, Li C, Tan X, Tang D, Wang W. Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria. World J Microbiol Biotechnol 2020; 36:14. [PMID: 31897771 DOI: 10.1007/s11274-019-2795-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022]
Abstract
Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, 6009, Australia
- Computer Science and Software Engineering, Faculty of Engineering and Mathematical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Ting Yang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Chengcheng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinle Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Wei Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
- The First Affiliated Hospital, Medical College of Shantou University, Shantou, 515041, Guangdong, China
- School of Public Health, Taishan Medical University, Tai'an, 271000, Shandong, China
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108
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Transcriptional response of otsA, P5CR, glgX, nodC, and molecular chaperone genes under the PEG-induced drought stress in Mesorhizobium ciceri Ca181. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2019.101459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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109
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Visnapuu T, Meldre A, Põšnograjeva K, Viigand K, Ernits K, Alamäe T. Characterization of a Maltase from an Early-Diverged Non-Conventional Yeast Blastobotrys adeninivorans. Int J Mol Sci 2019; 21:E297. [PMID: 31906253 PMCID: PMC6981392 DOI: 10.3390/ijms21010297] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 11/17/2022] Open
Abstract
Genome of an early-diverged yeast Blastobotrys (Arxula) adeninivorans (Ba) encodes 88 glycoside hydrolases (GHs) including two α-glucosidases of GH13 family. One of those, the rna_ARAD1D20130g-encoded protein (BaAG2; 581 aa) was overexpressed in Escherichia coli, purified and characterized. We showed that maltose, other maltose-like substrates (maltulose, turanose, maltotriose, melezitose, malto-oligosaccharides of DP 4‒7) and sucrose were hydrolyzed by BaAG2, whereas isomaltose and isomaltose-like substrates (palatinose, α-methylglucoside) were not, confirming that BaAG2 is a maltase. BaAG2 was competitively inhibited by a diabetes drug acarbose (Ki = 0.8 µM) and Tris (Ki = 70.5 µM). BaAG2 was competitively inhibited also by isomaltose-like sugars and a hydrolysis product-glucose. At high maltose concentrations, BaAG2 exhibited transglycosylating ability producing potentially prebiotic di- and trisaccharides. Atypically for yeast maltases, a low but clearly recordable exo-hydrolytic activity on amylose, amylopectin and glycogen was detected. Saccharomyces cerevisiae maltase MAL62, studied for comparison, had only minimal ability to hydrolyze these polymers, and its transglycosylating activity was about three times lower compared to BaAG2. Sequence identity of BaAG2 with other maltases was only moderate being the highest (51%) with the maltase MalT of Aspergillus oryzae.
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Affiliation(s)
| | | | | | | | | | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia; (T.V.); (A.M.); (K.P.); (K.V.); (K.E.)
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110
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Appadurai D, Gay L, Moharir A, Lang MJ, Duncan MC, Schmidt O, Teis D, Vu TN, Silva M, Jorgensen EM, Babst M. Plasma membrane tension regulates eisosome structure and function. Mol Biol Cell 2019; 31:287-303. [PMID: 31851579 PMCID: PMC7183764 DOI: 10.1091/mbc.e19-04-0218] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eisosomes are membrane furrows at the cell surface of yeast that have been shown to function in two seemingly distinct pathways, membrane stress response and regulation of nutrient transporters. We found that many stress conditions affect both of these pathways by changing plasma membrane tension and thus the morphology and composition of eisosomes. For example, alkaline stress causes swelling of the cell and an endocytic response, which together increase membrane tension, thereby flattening the eisosomes. The flattened eisosomes affect membrane stress pathways and release nutrient transporters, which aids in their down-regulation. In contrast, glucose starvation or hyperosmotic shock causes cell shrinking, which results in membrane slack and the deepening of eisosomes. Deepened eisosomes are able to trap nutrient transporters and protect them from rapid endocytosis. Therefore, eisosomes seem to coordinate the regulation of both membrane tension and nutrient transporter stability.
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Affiliation(s)
- Daniel Appadurai
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112
| | - Lincoln Gay
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112
| | - Akshay Moharir
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112
| | - Michael J Lang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Oliver Schmidt
- Division of Cell Biology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - David Teis
- Division of Cell Biology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Thien N Vu
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112
| | - Malan Silva
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112
| | - Erik M Jorgensen
- School of Biological Sciences, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112
| | - Markus Babst
- Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112
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111
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Liu HH, Lin YC, Chung CS, Liu K, Chang YH, Yang CH, Chen Y, Ni YH, Chang PF. Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes. Sci Rep 2019; 9:16836. [PMID: 31727954 PMCID: PMC6856387 DOI: 10.1038/s41598-019-53173-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Bowel microbiota is a "metaorgan" of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the "other glycan degradation" pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = -0.97, p < 0.002) between the scores and the abundance of "glycogen degradation" in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10-4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10-5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.
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Affiliation(s)
- Hong-Hsing Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan. .,Pediatrics, En Chu Kong Hospital, Sanxia District, New Taipei City, 237, Taiwan.
| | - Yu-Chen Lin
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan.,Electronic Engineering, Oriental Institute of Technology, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Chen-Shuan Chung
- Internal Medicine, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Kevin Liu
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Ya-Hui Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan
| | - Chung-Hsiang Yang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, 350, Taiwan
| | - Yun Chen
- Pediatric Surgery, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan
| | - Yen-Hsuan Ni
- Pediatrics, National Taiwan University Hospital, Zhongzheng District, Taipei, 100, Taiwan
| | - Pi-Feng Chang
- Pediatrics, Far Eastern Memorial Hospital, Pan-Chiao District, New Taipei City, 220, Taiwan. .,Electronic Engineering, Oriental Institute of Technology, Pan-Chiao District, New Taipei City, 220, Taiwan.
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112
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van Dijk M, Erdei B, Galbe M, Nygård Y, Olsson L. Strain-dependent variance in short-term adaptation effects of two xylose-fermenting strains of Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2019; 292:121922. [PMID: 31398543 DOI: 10.1016/j.biortech.2019.121922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 06/10/2023]
Abstract
The limited tolerance of Saccharomyces cerevisiae to the inhibitors present in lignocellulosic hydrolysates is a major challenge in second-generation bioethanol production. Short-term adaptation of the yeast to lignocellulosic hydrolysates during cell propagation has been shown to improve its tolerance, and thus its performance in lignocellulose fermentation. The aim of this study was to investigate the short-term adaptation effects in yeast strains with different genetic backgrounds. Fed-batch propagation cultures were supplemented with 40% wheat straw hydrolysate during the feed phase to adapt two different pentose-fermenting strains, CR01 and KE6-12. The harvested cells were used to inoculate fermentation media containing 80% or 90% wheat straw hydrolysate. The specific ethanol productivity during fermentation was up to 3.6 times higher for CR01 and 1.6 times higher for KE6-12 following adaptation. The influence of physiological parameters such as viability, storage carbohydrate content, and metabolite yields following short-term adaptation demonstrated that short-term adaptation was strain dependent.
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Affiliation(s)
- Marlous van Dijk
- Chalmers University of Technology, Dept. Biology and Bioengineering, Division of Industrial Biotechnology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Borbála Erdei
- Lund University, Dept. Chemical Engineering, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mats Galbe
- Lund University, Dept. Chemical Engineering, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Yvonne Nygård
- Chalmers University of Technology, Dept. Biology and Bioengineering, Division of Industrial Biotechnology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Lisbeth Olsson
- Chalmers University of Technology, Dept. Biology and Bioengineering, Division of Industrial Biotechnology, Kemivägen 10, SE-412 96 Göteborg, Sweden.
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Mock M, Schmid A, Bühler K. Photoautotrophic production of succinate via the oxidative branch of the tricarboxylic acid cycle influences glycogen accumulation in Synechocystis sp. PCC 6803. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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114
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Zeitz MA, Tanveer Z, Openshaw AT, Schmidt M. Genetic Regulators and Physiological Significance of Glycogen Storage in Candida albicans. J Fungi (Basel) 2019; 5:jof5040102. [PMID: 31671578 PMCID: PMC6958490 DOI: 10.3390/jof5040102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 01/31/2023] Open
Abstract
The dimorphic human fungal pathogen C. albicans has broad metabolic flexibility that allows it to adapt to the nutrient conditions in different host habitats. C. albicans builds large carbohydrate stores (glycogen) at the end of exponential growth and begins consumption of stored carbohydrates when nutrients become limiting. The expression of genes required for the successful transition between host environments, including the factors controlling glycogen content, is controlled by protein kinase A signaling through the transcription factor Efg1. In addition to the inability to transition to hyphal growth, C. albicans efg1 mutants have low glycogen content and reduced long-term survival, suggesting that carbohydrate storage is required for viability during prolonged culture. To test this assumption, we constructed a glycogen-deficient C. albicans mutant and assessed its viability during extended culture. Pathways and additional genetic factors controlling C. albicans glycogen synthesis were identified through the screening of mutant libraries for strains with low glycogen content. Finally, a part of the Efg1-regulon was screened for mutants with a shortened long-term survival phenotype. We found that glycogen deficiency does not affect long-term survival, growth, metabolic flexibility or morphology of C. albicans. We conclude that glycogen is not an important contributor to C. albicans fitness.
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Affiliation(s)
- Marcus A Zeitz
- Department of Biochemistry and Nutrition, College of Osteopathic Medicine, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
| | - Zainab Tanveer
- Department of Biochemistry and Nutrition, College of Osteopathic Medicine, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
| | - Anatole T Openshaw
- Department of Biochemistry and Nutrition, College of Osteopathic Medicine, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
| | - Martin Schmidt
- Department of Biochemistry and Nutrition, College of Osteopathic Medicine, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
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115
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Some molecular structural features of glycogen in the kidneys of diabetic rats. Carbohydr Polym 2019; 229:115526. [PMID: 31826402 DOI: 10.1016/j.carbpol.2019.115526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/09/2019] [Accepted: 10/22/2019] [Indexed: 12/27/2022]
Abstract
Glycogen, a highly-branched glucose polymer, functions as a sugar reservoir in many organs and tissues. Liver glycogen comprises small β particles which can bind to form into large agglomerates (α particles) which readily degrade to β particles in diabetic livers. Muscle glycogen has only β particles, optimal for quick energy release. Healthy kidney contains negligible glycogen, but there is an abnormally high accumulation in diabetic kidneys. We here compare the molecular structure of glycogen in diabetic kidneys with that in liver and muscle, using a diabetic rat model. This involved exploring extraction techniques to minimize glycogen degradation. Using size exclusion chromatography and transmission electron microscopy, it was found that there were only β particles in diabetic kidneys. These are postulated to form during periods of abnormally high blood sugar, the driving force being the need to reduce blood sugar under such circumstances.
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116
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Zarkani AA, Schierstaedt J, Becker M, Krumwiede J, Grimm M, Grosch R, Jechalke S, Schikora A. Salmonella adapts to plants and their environment during colonization of tomatoes. FEMS Microbiol Ecol 2019; 95:5582605. [DOI: 10.1093/femsec/fiz152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/01/2019] [Indexed: 02/04/2023] Open
Abstract
ABSTRACT
Humans and animals are considered typical hosts for Salmonella, however, also plants can be colonized. Tomatoes were linked to salmonellosis outbreaks already on several occasions. The aim of this study was, therefore, to establish a comprehensive view on the interaction between Salmonella enterica and tomatoes, and to test the hypothesis that colonization of plants is an interactive process. We assessed the persistence of Salmonella in agricultural soil, the colonization pattern in and on tomatoes, as well as the reciprocal responses of tomatoes to different Salmonella strains and Salmonella to root exudates and tomato-related media. This study revealed that Salmonella can persist in the soil and inside the tomato plant. Additionally, we show that Salmonella strains have particular colonization pattern, although the persistence inside the plant differs between the tested strains. Furthermore, the transcriptome response of tomato showed an up-regulation of several defense-related genes. Salmonella transcriptome analysis in response to the plant-based media showed differentially regulated genes related to amino acid and fatty acid synthesis and stress response, while the response to root exudates revealed regulation of the glyoxylate cycle. Our results indicate that both organisms actively engage in the interaction and that Salmonella adapts to the plant environment.
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Affiliation(s)
- Azhar A Zarkani
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
- University of Baghdad, Department of Biotechnology, Al-Jadriya, Baghdad 10071, Iraq
| | - Jasper Schierstaedt
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, Großbeeren 14979, Germany
| | - Marlies Becker
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Johannes Krumwiede
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Maja Grimm
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, Großbeeren 14979, Germany
| | - Sven Jechalke
- Justus Liebig University Giessen, Institute for Phytopathology, Heinrich-Buff-Ring 26–32 (iFZ), Giessen 35392, Germany
| | - Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, Braunschweig 38104, Germany
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117
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Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
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118
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Abstract
While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.
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119
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Ullah S, Ai C, Huang S, Zhang J, Jia L, Ma J, Zhou W, He P. The responses of extracellular enzyme activities and microbial community composition under nitrogen addition in an upland soil. PLoS One 2019; 14:e0223026. [PMID: 31568535 PMCID: PMC6768454 DOI: 10.1371/journal.pone.0223026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/11/2019] [Indexed: 11/18/2022] Open
Abstract
Tremendous amounts of nitrogen (N) fertilizer have been added to arable lands, often resulting in substantial effects on terrestrial ecosystems, including soil acidification, altered enzyme activities and changes in microbial community composition. Soil microbes are the major drivers of soil carbon (C) and N cycling; therefore, understanding the response of microbial communities to elevated N inputs is of significant importance. This study was carried out to investigate the influences of different N fertilization rates (0, 182, and 225 kg ha-1 representing control, low, and high N supply for each crop season for summer maize and winter wheat) on soil biochemical attributes, extracellular enzyme activities, and the microbial community composition in a winter wheat-summer maize rotation cropping system in north-central China. The results showed that N addition significantly decreased the soil pH in both the wheat and maize seasons. Microbial biomass N (MBN) decreased following N fertilization in the wheat season, while the opposite trend in MBN was observed in the maize season. Response ratio analysis showed that the activities of enzymes involved in C, N, and phosphorus cycling were significantly enhanced under N enrichment in both the wheat and maize seasons, and higher enzyme activities were noted in the high N addition treatment than in the low N addition treatment. A linear increase in fungal abundance with the N addition gradient was observed in the wheat season, whereas the fungal abundance increased and then decreased in the maize season. The bacterial abundance showed an increased and then decreased trend in response to the N addition gradient in both the wheat and maize crop seasons. Moreover, the partial least squares path model (PLS-PM) analysis showed that soil pH and soil organic carbon (SOC) were the most important soil variables, causing shifts in the soil bacteria. Furthermore, compared with the N-cycling enzymes, the C-cycling enzymes were significantly affected by the soil pH and SOC. Taken together, these results suggest that the effect of N addition on enzyme activities was consistent in both crop seasons, while the effects on MBN and microbial community composition to N addition were highly variable in the two crop seasons. Moreover, N fertilization-induced changes in the soil chemical properties such as soil acidity and SOC played a substantial role in shaping the microbial community.
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Affiliation(s)
- Sami Ullah
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Chao Ai
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Shaohui Huang
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Jiajia Zhang
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Liangliang Jia
- Hebei Academy of Agriculture and Forestry Sciences, Hebei, PR China
| | - Jinchuan Ma
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Wei Zhou
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
| | - Ping He
- Ministry of Agriculture Key Laboratory of Plant Nutrition and Fertilizer, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing, PR China
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120
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Han SR, Kim DW, Kim B, Chi YM, Kang S, Park H, Jung SH, Lee JH, Oh TJ. Complete genome sequencing of Shigella sp. PAMC 28760: Identification of CAZyme genes and analysis of their potential role in glycogen metabolism for cold survival adaptation. Microb Pathog 2019; 137:103759. [PMID: 31560973 DOI: 10.1016/j.micpath.2019.103759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022]
Abstract
Shigella sp. PAMC 28760 (isolated from Himantormia sp. lichen in Antarctica) is a gram-negative, non-sporulating bacterium that has cellulolytic and amylolytic characteristics as well as glycogen metabolic pathways. In this study, we isolated S. sp. PAMC 28760 from Antarctic lichen, and present the complete genome sequence with annotations describing its unique features. The genome sequence has 58.85% GC content, 4,278 coding DNA sequences, 85 tRNAs, and 22 rRNA operons. 16S rRNA gene sequence analyses revealed strain PAMC 28760 as a potentially new species of genus Shigella, showing various differences from pathogenic bacteria reported previously. dbCAN2 analyses revealed 91 genes related to carbohydrate-metabolizing enzymes. S. sp. PAMC 28760 likely degrades polysaccharide starch to obtain glucose for energy conservation. This study provides a foundation for understanding Shigella survival adaptation mechanisms under extremely cold Antarctic conditions.
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Affiliation(s)
- So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Do Wan Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea
| | - Young Min Chi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seunghyun Kang
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Sang-Hee Jung
- Department of Dental Hygiene, Gangneung Yeongdong University, Gangneung, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, South Korea; Department of Polar Sciences, University of Science and Technology, Incheon, South Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, South Korea; Genome-based BioIT Convergence Institute, Asan, South Korea; Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, South Korea.
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121
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Aslan S, Noor E, Benito Vaquerizo S, Lindner SN, Bar-Even A. Design and engineering of E. coli metabolic sensor strains with a wide sensitivity range for glycerate. Metab Eng 2019; 57:96-109. [PMID: 31491545 DOI: 10.1016/j.ymben.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/05/2019] [Accepted: 09/02/2019] [Indexed: 11/16/2022]
Abstract
Microbial biosensors are used to detect the presence of compounds provided externally or produced internally. The latter case is commonly constrained by the need to screen a large library of enzyme or pathway variants to identify those that can efficiently generate the desired compound. To address this limitation, we suggest the use of metabolic sensor strains which can grow only if the relevant compound is present and thus replace screening with direct selection. We used a computational platform to design metabolic sensor strains with varying dependencies on a specific compound. Our method systematically explores combinations of gene deletions and identifies how the growth requirement for a compound changes with the media composition. We demonstrate this approach by constructing a set of E. coli glycerate sensor strains. In each of these strains a different set of enzymes is disrupted such that central metabolism is effectively dissected into multiple segments, each requiring a dedicated carbon source. We find an almost perfect match between the predicted and experimental dependence on glycerate and show that the strains can be used to accurately detect glycerate concentrations across two orders of magnitude. Apart from demonstrating the potential application of metabolic sensor strains, our work reveals key phenomena in central metabolism, including spontaneous degradation of central metabolites and the importance of metabolic sinks for balancing small metabolic networks.
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Affiliation(s)
- Selçuk Aslan
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Sara Benito Vaquerizo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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122
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Responses of Soil and Microbial C:N:P Stoichiometry to Vegetation Succession in a Karst Region of Southwest China. FORESTS 2019. [DOI: 10.3390/f10090755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Spontaneous vegetation succession after agricultural abandonment is a general phenomenon in many areas of the world. As important indicators of nutrient status and biogeochemical cycling in ecosystems, the stoichiometry of key elements such as carbon (C), nitrogen (N) and phosphorous (P) in soil and microbial biomass, and their responses to vegetation recolonization and succession after agricultural abandonment remain poorly understood. Here, based on a space-for-time substitution approach, surface soil samples (0–15 cm) were collected from four vegetation types, e.g., tussock grassland, shrubland, secondary forest, and primary forest, which represent four successional stages across this region. All samples were examined C, N and P concentrations and their ratios in soil and microbial biomass. The results showed that soil organic C and total N content increased synchronously but total soil P did not remarkably change along a progressive vegetation succession. Consequently, soil C:P and N:P ratios increased while C:N ratio stayed almost unchanged during vegetation succession. Soil microbial biomass C (SMBC) and microbial biomass N (SMBN) concentrations elevated while SMBP did not significantly change during vegetation succession. Unlike the soil C:N:P stoichiometry, however, microbial C:N and C:P ratios were significantly or marginally significantly greater in grassland than in the other three successional stages, while microbial N:P did not significantly vary across the four successional stages. Overall, the present study demonstrated that soil and microbial stoichiometry responded differently to secondary vegetation succession in a karst region of subtropical China.
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123
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Carere CR, McDonald B, Peach HA, Greening C, Gapes DJ, Collet C, Stott MB. Hydrogen Oxidation Influences Glycogen Accumulation in a Verrucomicrobial Methanotroph. Front Microbiol 2019; 10:1873. [PMID: 31474959 PMCID: PMC6706786 DOI: 10.3389/fmicb.2019.01873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
Metabolic flexibility in aerobic methane oxidizing bacteria (methanotrophs) enhances cell growth and survival in instances where resources are variable or limiting. Examples include the production of intracellular compounds (such as glycogen or polyhydroxyalkanoates) in response to unbalanced growth conditions and the use of some energy substrates, besides methane, when available. Indeed, recent studies show that verrucomicrobial methanotrophs can grow mixotrophically through oxidation of hydrogen and methane gases via respiratory membrane-bound group 1d [NiFe] hydrogenases and methane monooxygenases, respectively. Hydrogen metabolism is particularly important for adaptation to methane and oxygen limitation, suggesting this metabolic flexibility may confer growth and survival advantages. In this work, we provide evidence that, in adopting a mixotrophic growth strategy, the thermoacidophilic methanotroph, Methylacidiphilum sp. RTK17.1 changes its growth rate, biomass yields and the production of intracellular glycogen reservoirs. Under nitrogen-fixing conditions, removal of hydrogen from the feed-gas resulted in a 14% reduction in observed growth rates and a 144% increase in cellular glycogen content. Concomitant with increases in glycogen content, the total protein content of biomass decreased following the removal of hydrogen. Transcriptome analysis of Methylacidiphilum sp. RTK17.1 revealed a 3.5-fold upregulation of the Group 1d [NiFe] hydrogenase in response to oxygen limitation and a 4-fold upregulation of nitrogenase encoding genes (nifHDKENX) in response to nitrogen limitation. Genes associated with glycogen synthesis and degradation were expressed constitutively and did not display evidence of transcriptional regulation. Collectively these data further challenge the belief that hydrogen metabolism in methanotrophic bacteria is primarily associated with energy conservation during nitrogen fixation and suggests its utilization provides a competitive growth advantage within hypoxic habitats.
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Affiliation(s)
- Carlo R. Carere
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
| | - Ben McDonald
- Scion, Te Papa Tipu Innovation Park, Rotorua, New Zealand
| | - Hanna A. Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, GNS Science, Taupō, New Zealand
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | | | - Matthew B. Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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124
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Structural basis of glycogen metabolism in bacteria. Biochem J 2019; 476:2059-2092. [PMID: 31366571 DOI: 10.1042/bcj20170558] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023]
Abstract
The evolution of metabolic pathways is a major force behind natural selection. In the spotlight of such process lies the structural evolution of the enzymatic machinery responsible for the central energy metabolism. Specifically, glycogen metabolism has emerged to allow organisms to save available environmental surplus of carbon and energy, using dedicated glucose polymers as a storage compartment that can be mobilized at future demand. The origins of such adaptive advantage rely on the acquisition of an enzymatic system for the biosynthesis and degradation of glycogen, along with mechanisms to balance the assembly and disassembly rate of this polysaccharide, in order to store and recover glucose according to cell energy needs. The first step in the classical bacterial glycogen biosynthetic pathway is carried out by the adenosine 5'-diphosphate (ADP)-glucose pyrophosphorylase. This allosteric enzyme synthesizes ADP-glucose and acts as a point of regulation. The second step is carried out by the glycogen synthase, an enzyme that generates linear α-(1→4)-linked glucose chains, whereas the third step catalyzed by the branching enzyme produces α-(1→6)-linked glucan branches in the polymer. Two enzymes facilitate glycogen degradation: glycogen phosphorylase, which functions as an α-(1→4)-depolymerizing enzyme, and the debranching enzyme that catalyzes the removal of α-(1→6)-linked ramifications. In this work, we rationalize the structural basis of glycogen metabolism in bacteria to the light of the current knowledge. We describe and discuss the remarkable progress made in the understanding of the molecular mechanisms of substrate recognition and product release, allosteric regulation and catalysis of all those enzymes.
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125
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Cai C, Shi Y, Guo J, Tyson GW, Hu S, Yuan Z. Acetate Production from Anaerobic Oxidation of Methane via Intracellular Storage Compounds. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:7371-7379. [PMID: 31244078 DOI: 10.1021/acs.est.9b00077] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There is great interest in microbial conversion of methane, an abundant resource, into valuable liquid chemicals. While aerobic bioconversion of methane to liquid chemicals has been reported, studies of anaerobic methane bioconversion to liquid chemicals are rare. Here we show that a microbial culture dominated by Candidatus 'Methanoperedens nitroreducens', an anaerobic methanotrophic archaeon, anaerobically oxidizes methane to produce acetate, indirectly via reaction intermediate(s), when nitrate or nitrite is supplied as an electron acceptor under a rate-limiting condition. Isotopic labeling tests showed that acetate was produced from certain intracellular storage compounds that originated from methane. Fluorescence in situ hybridization and Nile red staining demonstrated that polyhydroxyalkanoate in M. nitroreducens was likely one of the intracellular storage compounds for acetate production, along with glycogen. Acetate is a common substrate for the production of more valuable chemicals. The microbial conversion discovered in this study potentially enables a new approach to the use of methane as a feedstock for the chemical market.
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Affiliation(s)
- Chen Cai
- Advanced Water Management Centre , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
| | - Ying Shi
- Advanced Water Management Centre , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
- School of Resource and Safety Engineering , Central South University , Changsha 410083 , China
| | - Jianhua Guo
- Advanced Water Management Centre , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
| | - Shihu Hu
- Advanced Water Management Centre , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , St Lucia, Brisbane , Queensland 4072 , Australia
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Moruno Algara M, Kuczyńska‐Wiśnik D, Dębski J, Stojowska‐Swędrzyńska K, Sominka H, Bukrejewska M, Laskowska E. Trehalose protects
Escherichia coli
against carbon stress manifested by protein acetylation and aggregation. Mol Microbiol 2019; 112:866-880. [DOI: 10.1111/mmi.14322] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2019] [Indexed: 12/22/2022]
Affiliation(s)
- María Moruno Algara
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Dorota Kuczyńska‐Wiśnik
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Janusz Dębski
- Mass Spectrometry Laboratory IBB PAS ul. Pawińskiego 5A02‐106Warsaw Poland
| | - Karolina Stojowska‐Swędrzyńska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Hanna Sominka
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Małgorzata Bukrejewska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Ewa Laskowska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
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127
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Wang L, Liu Q, Tan X, Wang Z, Wang M, Wise MJ, Li C, Ma C, Li E, Deng B, Du Y, Tang D, Gilbert RG. Molecular Structure of Glycogen in Escherichia coli. Biomacromolecules 2019; 20:2821-2829. [PMID: 31244022 DOI: 10.1021/acs.biomac.9b00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Glycogen, a randomly branched glucose polymer, provides energy storage in organisms. It forms small β particles which in animals bind to form composite α particles, which give better glucose release. Simulations imply β particle size is controlled only by activities and sizes of glycogen biosynthetic enzymes and sizes of polymer chains. Thus, storing more glucose requires forming more β particles, which are expected to sometimes form α particles. No α particles have been reported in bacteria, but the extraction techniques might have caused degradation. Using milder glycogen extraction techniques on Escherichia coli, transmission electron microscopy and size-exclusion chromatography showed α particles, consistent with this hypothesis for α-particle formation. Molecular density and size distributions show similarities with animal glycogen, despite very different metabolic processes. These general polymer constraints are such that any organism which needs to store and then release glucose will have similar α and β particle structures: a type of convergent evolution.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China.,Jiangsu Provincial Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Qinghua Liu
- Department of Bioinformatics, School of Medical Informatics , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China.,Department of Pharmaceutical Analysis, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Xinle Tan
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Ziyi Wang
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Mengmeng Wang
- Jiangsu Provincial Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China.,Department of Pharmaceutical Analysis, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Michael J Wise
- The Marshall Center for Infectious Diseases Research and Training, and Department of Computer Science and Software Engineering , University of Western Australia , Perth , Western Australia 6009 , Australia
| | - Chengcheng Li
- School of Bioengineering , Jiangnan University , Wuxi 214122 , Jiangsu Province , China
| | - Chao Ma
- Department of Bioinformatics, School of Medical Informatics , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Enpeng Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture , Yangzhou University , Yangzhou 225009 , Jiangsu Province , China
| | - Bin Deng
- Department of Pharmacy, Union Hospital, Tongji Medical College , Huazhong University of Science and Technology , Wuhan , Hubei 430030 , China
| | - Yan Du
- Jiangsu Provincial Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China.,Department of Pharmaceutical Analysis, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Daoquan Tang
- Jiangsu Provincial Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China.,Department of Pharmaceutical Analysis, School of Pharmacy , Xuzhou Medical University , Xuzhou 221000 , Jiangsu Province , China
| | - Robert G Gilbert
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland , Brisbane , Queensland 4072 , Australia.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture , Yangzhou University , Yangzhou 225009 , Jiangsu Province , China
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128
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Circadian clock regulation of the glycogen synthase ( gsn) gene by WCC is critical for rhythmic glycogen metabolism in Neurospora crassa. Proc Natl Acad Sci U S A 2019; 116:10435-10440. [PMID: 31048503 PMCID: PMC6534987 DOI: 10.1073/pnas.1815360116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Circadian rhythms enable organisms to anticipate daily environmental cycles and control the timing of numerous biological processes, including metabolism, to optimize the health and survival of organisms. Glycogen metabolism is a conserved glucose homeostatic process; however, the molecular mechanisms linking the circadian clock and glycogen metabolism remain largely unknown. In this report, we demonstrate that circadian clock-dependent transcriptional regulation of glycogen synthase, gsn, regulates circadian oscillations of GSN protein and glycogen accumulation in the model filamentous fungus, Neurospora crassa. Circadian clocks generate rhythms in cellular functions, including metabolism, to align biological processes with the 24-hour environment. Disruption of this alignment by shift work alters glucose homeostasis. Glucose homeostasis depends on signaling and allosteric control; however, the molecular mechanisms linking the clock to glucose homeostasis remain largely unknown. We investigated the molecular links between the clock and glycogen metabolism, a conserved glucose homeostatic process, in Neurospora crassa. We find that glycogen synthase (gsn) mRNA, glycogen phosphorylase (gpn) mRNA, and glycogen levels, accumulate with a daily rhythm controlled by the circadian clock. Because the synthase and phosphorylase are critical to homeostasis, their roles in generating glycogen rhythms were investigated. We demonstrate that while gsn was necessary for glycogen production, constitutive gsn expression resulted in high and arrhythmic glycogen levels, and deletion of gpn abolished gsn mRNA rhythms and rhythmic glycogen accumulation. Furthermore, we show that gsn promoter activity is rhythmic and is directly controlled by core clock component white collar complex (WCC). We also discovered that WCC-regulated transcription factors, VOS-1 and CSP-1, modulate the phase and amplitude of rhythmic gsn mRNA, and these changes are similarly reflected in glycogen oscillations. Together, these data indicate the importance of clock-regulated gsn transcription over signaling or allosteric control of glycogen rhythms, a mechanism that is potentially conserved in mammals and critical to metabolic homeostasis.
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129
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Blazier AS, Papin JA. Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PLoS Comput Biol 2019; 15:e1006507. [PMID: 30973869 PMCID: PMC6478342 DOI: 10.1371/journal.pcbi.1006507] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 04/23/2019] [Accepted: 03/06/2019] [Indexed: 11/30/2022] Open
Abstract
The identification of genes essential for bacterial growth and survival represents a promising strategy for the discovery of antimicrobial targets. Essential genes can be identified on a genome-scale using transposon mutagenesis approaches; however, variability between screens and challenges with interpretation of essentiality data hinder the identification of both condition-independent and condition-dependent essential genes. To illustrate the scope of these challenges, we perform a large-scale comparison of multiple published Pseudomonas aeruginosa gene essentiality datasets, revealing substantial differences between the screens. We then contextualize essentiality using genome-scale metabolic network reconstructions and demonstrate the utility of this approach in providing functional explanations for essentiality and reconciling differences between screens. Genome-scale metabolic network reconstructions also enable a high-throughput, quantitative analysis to assess the impact of media conditions on the identification of condition-independent essential genes. Our computational model-driven analysis provides mechanistic insight into essentiality and contributes novel insights for design of future gene essentiality screens and the identification of core metabolic processes.
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Affiliation(s)
- Anna S. Blazier
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason A. Papin
- Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Medicine, Infectious Diseases & International Health, University of Virginia, Charlottesville, Virginia, United States of America
- Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
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130
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Lai JYH, Zhang H, Chiang MHY, Lun CHI, Zhang R, Lau SCK. The putative functions of lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment. FEMS Microbiol Ecol 2019; 94:4780272. [PMID: 29293955 DOI: 10.1093/femsec/fix187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/25/2017] [Indexed: 01/07/2023] Open
Abstract
Escherichia coli colonizes various body parts of animal hosts as a commensal and a pathogen. It can also persist in the external environment in the absence of fecal pollution. It remains unclear how this species has evolved to adapt to such contrasting habitats. Lysogeny plays pivotal roles in the diversification of the phenotypic and ecologic characters of E. coli as a symbiont. We hypothesized that lysogeny could also confer fitness to survival in the external environment. To test this hypothesis, we used the induced phages of an E. coli strain originating from marine sediment to infect a fecal E. coli strain to obtain an isogenic lysogen of the latter. The three strains were tested for survivorship in microcosms of seawater, marine sediment and sediment interstitial water as well as swimming motility, glycogen accumulation, biofilm formation, substrate utilization and stress resistance. The results indicate that lysogenic infection led to tractable changes in many of the ecophysiological attributes tested. Particularly, the lysogen had better survivorship in the microcosms and had a substrate utilization profile resembling the sediment strain more than the wild type fecal strain. Our findings provide new insights into the understanding of how E. coli survives in the natural environment.
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Affiliation(s)
- Jennifer Yuet Ha Lai
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hao Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Miranda Hei Yin Chiang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Clare Hau In Lun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Rui Zhang
- Institute of Marine Microbes and Ecospheres, and State Key Laboratory of Marine Environmental Science, Xiamen University, People's Republic of China
| | - Stanley Chun Kwan Lau
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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131
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Wang L, Liu Q, Hu J, Asenso J, Wise MJ, Wu X, Ma C, Chen X, Yang J, Tang D. Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria. Front Microbiol 2019; 9:3354. [PMID: 30692986 PMCID: PMC6339891 DOI: 10.3389/fmicb.2018.03354] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 12/31/2018] [Indexed: 01/02/2023] Open
Abstract
In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this study, we initially analyzed N-terminal domains of 169 manually reviewed bacterial GBEs based on hidden Markov models. A previously unreported group of GBEs (Type 3) with around 100 amino acids ahead of the N1 domains was identified. Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla, with the shorter, Type 2 GBEs predominantly found in Gram-positive species, while the longer Type 1 GBEs are found in Gram-negative species. Several in vitro studies have linked N1 domain with transfer of short oligosaccharide chains during glycogen formation, which could lead to small and compact glycogen structures. Compact glycogen degrades more slowly and, as a result, may serve as a durable energy reserve, contributing to the enhanced environmental persistence for bacteria. We were therefore interested in classifying GBEs based on their N-terminal domain via large-scale sequence analysis. In addition, we set to understand the evolutionary patterns of different GBEs through phylogenetic analysis at species and sequence levels. Three-dimensional modeling of GBE N-termini was also performed for structural comparisons. A further study of 9,387 GBE sequences identified 147 GBEs that might belong to a possibly novel group of Type 3 GBE, most of which fall into the phylum of Actinobacteria. We also attempted to correlate glycogen average chain length (ACL) with GBE types. However, no significant conclusions were drawn due to limited data availability. In sum, our study systematically investigated bacterial GBEs in terms of domain organizations from evolutionary point of view, which provides guidance for further experimental study of GBE N-terminal functions in glycogen structure and bacterial physiology.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Junfeng Hu
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - James Asenso
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Michael J Wise
- Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia.,The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Xiang Wu
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Chao Ma
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Xiuqing Chen
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Jianye Yang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Center for Experimental Animals, Xuzhou Medical University, Xuzhou, China
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132
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Tomova AA, Kujumdzieva AV, Petrova VY. Carbon source influences Saccharomyces cerevisiaeyeast cell survival strategies: quiescence or sporulation. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1674188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Anna Atanasova Tomova
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anna Vengelova Kujumdzieva
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Ventsislava Yankova Petrova
- Department “General and Industrial Microbiology”, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
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133
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Brewer MK, Gentry MS. Brain Glycogen Structure and Its Associated Proteins: Past, Present and Future. ADVANCES IN NEUROBIOLOGY 2019; 23:17-81. [PMID: 31667805 PMCID: PMC7239500 DOI: 10.1007/978-3-030-27480-1_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter reviews the history of glycogen-related research and discusses in detail the structure, regulation, chemical properties and subcellular distribution of glycogen and its associated proteins, with particular focus on these aspects in brain tissue.
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Affiliation(s)
- M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, Epilepsy and Brain Metabolism Center, Lafora Epilepsy Cure Initiative, and Center for Structural Biology, University of Kentucky College of Medicine, Lexington, KY, USA.
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134
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de Assis LJ, Manfiolli A, Mattos E, Fabri JHTM, Malavazi I, Jacobsen ID, Brock M, Cramer RA, Thammahong A, Hagiwara D, Ries LNA, Goldman GH. Protein Kinase A and High-Osmolarity Glycerol Response Pathways Cooperatively Control Cell Wall Carbohydrate Mobilization in Aspergillus fumigatus. mBio 2018; 9:e01952-18. [PMID: 30538182 PMCID: PMC6299480 DOI: 10.1128/mbio.01952-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus mitogen-activated protein kinases (MAPKs) are involved in maintaining the normal morphology of the cell wall and providing resistance against cell wall-damaging agents. Upon cell wall stress, cell wall-related sugars need to be synthesized from carbohydrate storage compounds. Here we show that this process is dependent on cAMP-dependent protein kinase A (PKA) activity and regulated by the high-osmolarity glycerol response (HOG) MAPKs SakA and MpkC. These protein kinases are necessary for normal accumulation/degradation of trehalose and glycogen, and the lack of these genes reduces glucose uptake and glycogen synthesis. Alterations in glycogen synthesis were observed for the sakA and mpkC deletion mutants, which also displayed alterations in carbohydrate exposure on the cell wall. Carbohydrate mobilization is controlled by SakA interaction with PkaC1 and PkaR, suggesting a putative mechanism where the PkaR regulatory subunit leaves the complex and releases the SakA-PkaC1 complex for activation of enzymes involved in carbohydrate mobilization. This work reveals the communication between the HOG and PKA pathways for carbohydrate mobilization for cell wall construction.IMPORTANCEAspergillus fumigatus is an opportunistic human pathogen causing allergic reactions or systemic infections such as invasive pulmonary aspergillosis, especially in immunocompromised patients. The fungal cell wall is the main component responsible for recognition by the immune system, due to the specific composition of polysaccharide carbohydrates exposed on the surface of the fungal cell wall called pathogen-associated molecular patterns (PAMPs). Key enzymes in the fungal cell wall biosynthesis are a good target for fungal drug development. This report elucidates the cooperation between the HOG and PKA pathways in the mobilization of carbohydrates for fungal cell wall biosynthesis. We suggest that the reduced mobilization of simple sugars causes defects in the structure of the fungal cell wall. In summary, we propose that SakA is important for PKA activity, therefore regulating the availability and mobilization of monosaccharides for fungal cell wall biosynthesis during cell wall damage and the osmotic stress response.
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Affiliation(s)
- Leandro José de Assis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Manfiolli
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Eliciane Mattos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - João H T Marilhano Fabri
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Matthias Brock
- Fungal Genetics and Biology Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert A Cramer
- Geisel School of Medicine at Dartmouth, Department of Microbiology and Immunology, Hanover, New Hampshire, USA
| | - Arsa Thammahong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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135
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Parzych KR, Klionsky DJ. Vacuolar hydrolysis and efflux: current knowledge and unanswered questions. Autophagy 2018; 15:212-227. [PMID: 30422029 DOI: 10.1080/15548627.2018.1545821] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hydrolysis within the vacuole in yeast and the lysosome in mammals is required for the degradation and recycling of a multitude of substrates, many of which are delivered to the vacuole/lysosome by autophagy. In humans, defects in lysosomal hydrolysis and efflux can have devastating consequences, and contribute to a class of diseases referred to as lysosomal storage disorders. Despite the importance of these processes, many of the proteins and regulatory mechanisms involved in hydrolysis and efflux are poorly understood. In this review, we describe our current knowledge of the vacuolar/lysosomal degradation and efflux of a vast array of substrates, focusing primarily on what is known in the yeast Saccharomyces cerevisiae. We also highlight many unanswered questions, the answers to which may lead to new advances in the treatment of lysosomal storage disorders. Abbreviations: Ams1: α-mannosidase; Ape1: aminopeptidase I; Ape3: aminopeptidase Y; Ape4: aspartyl aminopeptidase; Atg: autophagy related; Cps1: carboxypeptidase S; CTNS: cystinosin, lysosomal cystine transporter; CTSA: cathepsin A; CTSD: cathepsin D; Cvt: cytoplasm-to-vacuole targeting; Dap2: dipeptidyl aminopeptidase B; GS-bimane: glutathione-S-bimane; GSH: glutathione; LDs: lipid droplets; MVB: multivesicular body; PAS: phagophore assembly site; Pep4: proteinase A; PolyP: polyphosphate; Prb1: proteinase B; Prc1: carboxypeptidase Y; V-ATPase: vacuolar-type proton-translocating ATPase; VTC: vacuolar transporter chaperone.
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Affiliation(s)
- Katherine R Parzych
- a Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Daniel J Klionsky
- a Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
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136
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Sekar K, Rusconi R, Sauls JT, Fuhrer T, Noor E, Nguyen J, Fernandez VI, Buffing MF, Berney M, Jun S, Stocker R, Sauer U. Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria. Mol Syst Biol 2018; 14:e8623. [PMID: 30397005 PMCID: PMC6217170 DOI: 10.15252/msb.20188623] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/01/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
In natural environments, microbes are typically non-dividing and gauge when nutrients permit division. Current models are phenomenological and specific to nutrient-rich, exponentially growing cells, thus cannot predict the first division under limiting nutrient availability. To assess this regime, we supplied starving Escherichia coli with glucose pulses at increasing frequencies. Real-time metabolomics and microfluidic single-cell microscopy revealed unexpected, rapid protein, and nucleic acid synthesis already from minuscule glucose pulses in non-dividing cells. Additionally, the lag time to first division shortened as pulsing frequency increased. We pinpointed division timing and dependence on nutrient frequency to the changing abundance of the division protein FtsZ. A dynamic, mechanistic model quantitatively relates lag time to FtsZ synthesis from nutrient pulses and FtsZ protease-dependent degradation. Lag time changed in model-congruent manners, when we experimentally modulated the synthesis or degradation of FtsZ. Thus, limiting abundance of FtsZ can quantitatively predict timing of the first cell division.
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Affiliation(s)
- Karthik Sekar
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Roberto Rusconi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - John T Sauls
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Tobias Fuhrer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jen Nguyen
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vicente I Fernandez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Marieke F Buffing
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Suckjoon Jun
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
- Section of Molecular Biology, Division of Biological Science, University of California at San Diego, La Jolla, CA, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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137
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Almagro G, Viale AM, Montero M, Muñoz FJ, Baroja-Fernández E, Mori H, Pozueta-Romero J. A cAMP/CRP-controlled mechanism for the incorporation of extracellular ADP-glucose in Escherichia coli involving NupC and NupG nucleoside transporters. Sci Rep 2018; 8:15509. [PMID: 30341391 PMCID: PMC6195507 DOI: 10.1038/s41598-018-33647-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/03/2018] [Indexed: 12/29/2022] Open
Abstract
ADP-glucose is the precursor of glycogen biosynthesis in bacteria, and a compound abundant in the starchy plant organs ingested by many mammals. Here we show that the enteric species Escherichia coli is capable of scavenging exogenous ADP-glucose for use as a glycosyl donor in glycogen biosynthesis and feed the adenine nucleotide pool. To unravel the molecular mechanisms involved in this process, we screened the E. coli single-gene deletion mutants of the Keio collection for glycogen content in ADP-glucose-containing culture medium. In comparison to wild-type (WT) cells, individual ∆nupC and ∆nupG mutants lacking the cAMP/CRP responsive inner-membrane nucleoside transporters NupC and NupG displayed reduced glycogen contents and slow ADP-glucose incorporation. In concordance, ∆cya and ∆crp mutants accumulated low levels of glycogen and slowly incorporated ADP-glucose. Two-thirds of the glycogen-excess mutants identified during screening lacked functions that underlie envelope biogenesis and integrity, including the RpoE specific RseA anti-sigma factor. These mutants exhibited higher ADP-glucose uptake than WT cells. The incorporation of either ∆crp, ∆nupG or ∆nupC null alleles sharply reduced the ADP-glucose incorporation and glycogen content initially witnessed in ∆rseA cells. Overall, the data showed that E. coli incorporates extracellular ADP-glucose through a cAMP/CRP-regulated process involving the NupC and NupG nucleoside transporters that is facilitated under envelope stress conditions.
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Affiliation(s)
- Goizeder Almagro
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Alejandro M Viale
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET), Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 521, 2000, Rosario, Argentina
| | - Manuel Montero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Francisco José Muñoz
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain
| | - Hirotada Mori
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Iruñako etorbidea 123, 31192, Mutiloa, Nafarroa, Spain.
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138
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Velmurugan R, Incharoensakdi A. Disruption of Polyhydroxybutyrate Synthesis Redirects Carbon Flow towards Glycogen Synthesis in Synechocystis sp. PCC 6803 Overexpressing glgC/glgA. PLANT & CELL PHYSIOLOGY 2018; 59:2020-2029. [PMID: 29931091 DOI: 10.1093/pcp/pcy121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/14/2018] [Indexed: 05/24/2023]
Abstract
The photoautotrophic Synechocystis sp. PCC 6803 (hereafter Synechocystis) is known for its α-polyglucan (glycogen) synthesis to serve as a carbon storage compound. In this study, the glgC- and glgA-overexpressing Synechocystis strain with the disruption of polyhydroxybutyrate (PHB) synthesis (▴GCAX-ΔBK) showed an increased glycogen production. This engineered strain had a high glycogen content of 38.3% (g g-1 dry cell weight) as compared with 27.4% in the phaA knockout strain (ΔBK) and 34.8% in the glgC/glgA-overexpressing strain (▴GCAX) after 20 d growth. Under nitrogen-deprived growth conditions for 3 d, the ▴GCAX-ΔBK strain showed a further increase in glycogen content from 27.0% to 36.0%. Furthermore, the engineered strains grown under ionic, osmotic or oxidative stress conditions had an increase of glycogen accumulation, whereas no increase was observed in the wild type. The maximum glycogen content was 54.0% in the ▴GCAX-ΔBK strain treated with 3 mM H2O2. The overall results indicated that in the absence of PHB synthesis, Synechocystis cells redirected the carbon flow towards the synthesis of glycogen as an alternative physiological responsive compound especially under stress conditions.
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Affiliation(s)
- Rajendran Velmurugan
- Department of Biochemistry, Cyanobacterial Biotechnology Laboratory, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Aran Incharoensakdi
- Department of Biochemistry, Cyanobacterial Biotechnology Laboratory, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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139
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Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, Meyer RL, Albertsen M, Nielsen PH, Dueholm MS. Novel prosthecate bacteria from the candidate phylum Acetothermia. THE ISME JOURNAL 2018; 12:2225-2237. [PMID: 29884828 PMCID: PMC6092417 DOI: 10.1038/s41396-018-0187-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 03/20/2018] [Indexed: 02/05/2023]
Abstract
Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy, and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.
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Affiliation(s)
- Liping Hao
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Hüsnü Aslan
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
| | - Morten Simonsen Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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140
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Schmidt M, Tran-Nguyen D, Chizek P. Influence of boric acid on energy metabolism and stress tolerance of Candida albicans. J Trace Elem Med Biol 2018; 49:140-145. [PMID: 29895364 DOI: 10.1016/j.jtemb.2018.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/08/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
Boron presents at physiological pH in the form of boric acid (BA), a molecule that has both positive and negative effects on biological processes. In medicine, BA is used as a topical treatment for vaginal yeast infections by Candida species because of its well-documented but poorly understood effect on inhibition of growth in general and of invasive, hyphal growth in particular. The present study examines the influence of BA on carbohydrate energy metabolism of this common human pathogen. Starting from previous findings about an inhibition of key NAD-dependent enzymes by BA in vitro, we confirmed that such an inhibition occurs in permeabilized C. albicans cells. Cultures growing even with moderate concentrations of BA experience mitochondrial failure, increase ethanol production from glucose and decrease the deposition of carbohydrate stores in the form of glycogen. Cells growing on the non-fermentable, FAD-generating carbon source lactate have a higher BA tolerance, which suggests that the toxicity of BA is rooted in an inhibition of NAD-dependent reactions and the increased production of ethanol. Boric acid exposure sensitizes C. albicans selectively to the toxic effects of ethanol. This additive effect suggests that the endogenously produced ethanol increases the load on ethanol resistance mechanisms. Lastly, combination studies showed no interactions of BA with common antifungal drugs, meaning that addition of BA to topical formulations can provide an additive antifungal effect regardless of the chosen active ingredient.
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Affiliation(s)
- Martin Schmidt
- Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
| | | | - Patrick Chizek
- Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312, USA.
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141
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Łopieńska-Biernat E, Żółtowska K, Zaobidna EA, Dmitryjuk M, Bąk B. Developmental changes in gene expression and enzyme activities of anabolic and catabolic enzymes for storage carbohydrates in the honeybee, Apis mellifera. INSECTES SOCIAUX 2018; 65:571-580. [PMID: 30416205 PMCID: PMC6208630 DOI: 10.1007/s00040-018-0648-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 06/29/2018] [Accepted: 07/07/2018] [Indexed: 06/09/2023]
Abstract
Glycogen and trehalose are important sources of energy in insects. The expression of genes encoding the key metabolic enzymes-glycogen synthase (GS), glycogen phosphorylase (GP), trehalose-6-phosphate synthase (TPS-1), soluble trehalase (Tre-1) and membrane-bound trehalase (Tre-2)-was analyzed in 12 developmental stages of Apis mellifera worker brood. The content of GS and GP proteins, TPS activity, total trehalase activity, and the activity of Tre-1 and Tre-2 were determined. Transcript quantity was not always correlated with the content of the encoded GS or GP protein. The correlation was higher for GS (r = 0.797) than GP (r = 0.651). The expression of the glycogen synthase gene (gs) and the glycogen phosphorylase gene (gp) was high in 4- and 7-day-old larvae and in pupae, excluding the last pupal stage. The expression of the tps-1 gene was highest in the mid-pupal stage and contributed to higher enzyme activity in that stage. The expression of the tre-1 gene was higher than the expression of the tre-2 gene throughout development. In newly hatched workers, the expression of genes encoding catabolic enzymes of both carbohydrates, gp and tre-1, was higher than the expression of genes encoding anabolic enzymes. The results of this study suggest that sugar metabolism genes have somewhat different control mechanisms during larval development and metamorphosis.
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Affiliation(s)
- E. Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - K. Żółtowska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - E. A. Zaobidna
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - M. Dmitryjuk
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - B. Bąk
- Department of Apiculture, Faculty of Animal Bioengineering, University Warmia and Mazury in Olsztyn, Słoneczna 48, 10-957 Olsztyn, Poland
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142
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Roenneke B, Rosenfeldt N, Derya SM, Novak JF, Marin K, Krämer R, Seibold GM. Production of the compatible solute α-D-glucosylglycerol by metabolically engineered Corynebacterium glutamicum. Microb Cell Fact 2018; 17:94. [PMID: 29908566 PMCID: PMC6004087 DOI: 10.1186/s12934-018-0939-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/05/2018] [Indexed: 01/01/2023] Open
Abstract
Background α-d-Glucosylglycerol (αGG) has beneficial functions as a moisturizing agent in cosmetics and potential as a health food material, and therapeutic agent. αGG serves as compatible solute in various halotolerant cyanobacteria such as Synechocystis sp. PCC 6803, which synthesizes αGG in a two-step reaction: The enzymatic condensation of ADP-glucose and glycerol 3-phosphate by GG-phosphate synthase (GGPS) is followed by the dephosphorylation of the intermediate by the GG-phosphate phosphatase (GGPP). The Gram-positive Corynebacterium glutamicum, an industrial workhorse for amino acid production, does not utilize αGG as a substrate and was therefore chosen for the development of a heterologous microbial production platform for αGG. Results Plasmid-bound expression of ggpS and ggpP from Synechocystis sp. PCC 6803 enabled αGG synthesis exclusively in osmotically stressed cells of C. glutamicum (pEKEx2-ggpSP), which is probably due to the unique intrinsic control mechanism of GGPS activity in response to intracellular ion concentrations. C. glutamicum was then engineered to optimize precursor supply for αGG production: The precursor for αGG synthesis ADP-glucose gets metabolized by both the glgA encoded glycogen synthase and the otsA encoded trehalose-6-phosphate synthase. Upon deletion of both genes the αGG concentration in culture supernatants was increased from 0.5 mM in C. glutamicum (pEKEx3-ggpSP) to 2.9 mM in C. glutamicum ΔotsA IMglgA (pEKEx3-ggpSP). Upon nitrogen limitation, which inhibits synthesis of amino acids as compatible solutes, C. glutamicum ΔotsA IMglgA (pEKEx3-ggpSP) produced more than 10 mM αGG (about 2 g L−1). Conclusions Corynebacterium glutamicum can be engineered as efficient platform for the production of the compatible solute αGG. Redirection of carbon flux towards αGG synthesis by elimination of the competing pathways for glycogen and trehalose synthesis as well as optimization of nitrogen supply is an efficient strategy to further optimize production of αGG. Electronic supplementary material The online version of this article (10.1186/s12934-018-0939-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin Roenneke
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany.,Gutachterbüro U. Borchardt, Hennef (Sieg), Germany
| | - Natalie Rosenfeldt
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Sami M Derya
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Jens F Novak
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Kay Marin
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany.,Evonik Degussa GmbH, Halle (Westphalia), Germany
| | - Reinhard Krämer
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Gerd M Seibold
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany. .,Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein Allee 11, 89081, Ulm, Germany.
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143
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Arnal G, Cockburn DW, Brumer H, Koropatkin NM. Structural basis for the flexible recognition of α-glucan substrates by Bacteroides thetaiotaomicron SusG. Protein Sci 2018; 27:1093-1101. [PMID: 29603462 PMCID: PMC5980535 DOI: 10.1002/pro.3410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 11/09/2022]
Abstract
Bacteria that reside in the mammalian intestinal tract efficiently hydrolyze dietary carbohydrates, including starch, that escape digestion in the small intestine. Starch is an abundant dietary carbohydrate comprised of α1,4 and α1,6 linked glucose, yet mammalian intestinal glucoamylases cannot effectively hydrolyze starch that has frequent α1,6 branching as these structures hinder recognition and processing by α1,4-specific amylases. Here we present the structure of the cell surface amylase SusG from Bacteroides thetaiotaomicron complexed with a mixed linkage amylosaccharide generated from transglycosylation during crystallization. Although SusG is specific for α1,4 glucosidic bonds, binding of this new oligosaccharide at the active site demonstrates that SusG can accommodate α1,6 branch points at subsite -3 to -2, and also at subsite+1 adjacent to the site of hydrolysis, explaining how this enzyme may be able to process a wide range of limit dextrins in the intestinal environment. These data suggest that B. thetaiotaomicron and related organisms may have a selective advantage for amylosaccharide scavenging in the gut.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East MallVancouverBritish ColumbiaV6T 1Z4Canada
| | - Darrell W. Cockburn
- Department of Microbiology and ImmunologyUniversity of Michigan Medical School, 1150 W Medical Center DriveAnn ArborMichigan
- Present address:
Department of Food SciencePennsylvania State UniversityUniversity ParkPennsylvania
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East MallVancouverBritish ColumbiaV6T 1Z4Canada
- Department of ChemistryUniversity of British Columbia, 2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada
- Department of Biochemistry and Molecular BiologyUniversity of British Columbia, 2350 Health Sciences MallVancouverBritish ColumbiaV6T 1Z3Canada
| | - Nicole M. Koropatkin
- Department of Microbiology and ImmunologyUniversity of Michigan Medical School, 1150 W Medical Center DriveAnn ArborMichigan
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144
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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145
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Madueño L, Coppotelli B, Festa S, Alvarez H, Morelli I. Insights into the mechanisms of desiccation resistance of the Patagonian PAH-degrading strainSphingobiumsp. 22B. J Appl Microbiol 2018; 124:1532-1543. [DOI: 10.1111/jam.13742] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 01/05/2023]
Affiliation(s)
- L. Madueño
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - B.M. Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - S. Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - H.M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia); Consejo Nacional de Investigaciones Científicas y Técnicas; Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Comodoro Rivadavia Chubut Argentina
| | - I.S. Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA); Buenos Aires Argentina
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146
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Engholm DH, Kilian M, Goodsell DS, Andersen ES, Kjærgaard RS. A visual review of the human pathogen Streptococcus pneumoniae. FEMS Microbiol Rev 2018; 41:854-879. [PMID: 29029129 DOI: 10.1093/femsre/fux037] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Being the principal causative agent of bacterial pneumonia, otitis media, meningitis and septicemia, the bacterium Streptococcus pneumoniae is a major global health problem. To highlight the molecular basis of this problem, we have portrayed essential biological processes of the pneumococcal life cycle in eight watercolor paintings. The paintings are done to a consistent nanometer scale based on currently available data from structural biology and proteomics. In this review article, the paintings are used to provide a visual review of protein synthesis, carbohydrate metabolism, cell wall synthesis, cell division, teichoic acid synthesis, virulence, transformation and pilus synthesis based on the available scientific literature within the field of pneumococcal biology. Visualization of the molecular details of these processes reveals several scientific questions about how molecular components of the pneumococcal cell are organized to allow biological function to take place. By the presentation of this visual review, we intend to stimulate scientific discussion, aid in the generation of scientific hypotheses and increase public awareness. A narrated video describing the biological processes in the context of a whole-cell illustration accompany this article.
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Affiliation(s)
- Ditte Høyer Engholm
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Rutgers, the State University of New Jersey, NJ 08901, USA
| | - Ebbe Sloth Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark.,Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus, Denmark
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147
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Fernandes SO, Surya Prakash L, Balan Binish M, Padinchati Krishnan K, John Kurian P. Changes in morphology and metabolism enable Mn-oxidizing bacteria from mid-oceanic ridge environment to counter metal-induced stress. J Basic Microbiol 2018. [DOI: 10.1002/jobm.201700580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Palayil John Kurian
- National Centre for Antarctic and Ocean Research; Headland Sada; Vasco-da-Gama Goa India
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148
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Tachedjian G, O’Hanlon DE, Ravel J. The implausible "in vivo" role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota. MICROBIOME 2018; 6:29. [PMID: 29409534 PMCID: PMC5801833 DOI: 10.1186/s40168-018-0418-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 01/30/2018] [Indexed: 05/29/2023]
Abstract
In the cervicovaginal environment, the production of hydrogen peroxide (H2O2) by vaginal Lactobacillus spp. is often mentioned as a critical factor to the in vivo vaginal microbiota antimicrobial properties. We present several lines of evidence that support the implausibility of H2O2 as an "in vivo" contributor to the cervicovaginal milieu antimicrobial properties. An alternative explanation is proposed, supported by previous reports ascribing protective and antimicrobial properties to other factors produced by Lactobacillus spp. capable of generating H2O2. Under this proposal, lactic acid rather than H2O2 plays an important role in the antimicrobial properties of protective vaginal Lactobacillus spp. We hope this commentary will help future research focus on more plausible mechanisms by which vaginal Lactobacillus spp. exert their antimicrobial and beneficial properties, and which have in vivo and translational relevance.
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Affiliation(s)
- Gilda Tachedjian
- Disease Elimination Program, Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, Victoria 3004 Australia
- Department of Microbiology, Monash University, Clayton, VIC 3168 Australia
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3010 Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3000 Australia
| | - Deirdre E. O’Hanlon
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA
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Intrinsic and extrinsic carbohydrates in the vagina: A short review on vaginal glycogen. Int J Biol Macromol 2018; 112:203-206. [PMID: 29391223 DOI: 10.1016/j.ijbiomac.2018.01.166] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/03/2018] [Accepted: 01/24/2018] [Indexed: 12/11/2022]
Abstract
The reasons for (i) the presence and (ii) mechanisms of utilisation of glycogen by the lactic acid bacteria in the human vaginal tract are not well understood. It is probable that the vaginal epithelia produce both glycogen and α-amylase where the enzyme depolymerises the polysaccharide within the vagina itself. Only these depolymerised residues are then utilised for growth by the lactic acid bacteria. The lactic acid bacteria cannot metabolise the glycogen directly due to their incapacity to produce the α-amylase enzyme. These bacteria may, however, metabolise exogenous carbohydrates (such as prebiotics) selectively for growth effectively. These carbohydrate utilisation issues within the vagina are considered in this short review.
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Lu KJ, Pfister B, Jenny C, Eicke S, Zeeman SC. Distinct Functions of STARCH SYNTHASE 4 Domains in Starch Granule Formation. PLANT PHYSIOLOGY 2018; 176:566-581. [PMID: 29133376 PMCID: PMC5761780 DOI: 10.1104/pp.17.01008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/09/2017] [Indexed: 05/20/2023]
Abstract
The formation of normal starch granules in Arabidopsis (Arabidopsis thaliana) leaf chloroplasts requires STARCH SYNTHASE 4 (SS4). In plants lacking SS4, chloroplasts typically produce only one round granule rather than multiple lenticular granules. The mechanisms by which SS4 determines granule number and morphology are not understood. The N-terminal region of SS4 is unique among SS isoforms and contains several long coiled-coil motifs, typically implicated in protein-protein interactions. The C-terminal region contains the catalytic glucosyltransferase domains, which are widely conserved in plant SS and bacterial glycogen synthase (GS) isoforms. We investigated the specific roles of the N- and C-terminal regions of SS4 by expressing truncated versions of SS4 and a fusion between the N-terminal region of SS4 and GS in the Arabidopsis ss4 mutant. Expression of the N-terminal region of SS4 alone did not alter the ss4 mutant phenotype. Expression of the C-terminal region of SS4 alone increased granule initiation but did not rescue their aberrant round morphology. Expression of a self-priming GS from Agrobacterium tumefaciens also increased the number of round granules. Remarkably, fusion of the N-terminal region of SS4 to A. tumefaciens GS restored the development of wild-type-like lenticular starch granules. Interestingly, the N-terminal region of SS4 alone or when fused to GS conferred a patchy subchloroplastic localization similar to that of the full-length SS4 protein. Considered together, these data suggest that, while the glucosyltransferase activity of SS4 is important for granule initiation, the N-terminal part of SS4 serves to establish the correct granule morphology by properly localizing this activity.
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Affiliation(s)
- Kuan-Jen Lu
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | - Camilla Jenny
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Simona Eicke
- Department of Biology, ETH Zurich, 8092 Zurich, Switzerland
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