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Ma Q, Yi J, Tang Y, Geng Z, Zhang C, Sun W, Liu Z, Xiong W, Wu H, Xie X. Co-utilization of carbon sources in microorganisms for the bioproduction of chemicals. Biotechnol Adv 2024; 73:108380. [PMID: 38759845 DOI: 10.1016/j.biotechadv.2024.108380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Carbon source is crucial for the cell growth and metabolism in microorganisms, and its utilization significantly affects the synthesis efficiency of target products in microbial cell factories. Compared with a single carbon source, co-utilizing carbon sources provide an alternative approach to optimize the utilization of different carbon sources for efficient biosynthesis of many chemicals with higher titer/yield/productivity. However, the efficiency of bioproduction is significantly limited by the sequential utilization of a preferred carbon source and secondary carbon sources, attributed to carbon catabolite repression (CCR). This review aimed to introduce the mechanisms of CCR and further focus on the summary of the strategies for co-utilization of carbon sources, including alleviation of CCR, engineering of the transport and metabolism of secondary carbon sources, compulsive co-utilization in single culture, co-utilization of carbon sources via co-culture, and evolutionary approaches. The findings of representative studies with a significant improvement in the bioproduction of chemicals via the co-utilization of carbon sources were discussed in this review. It suggested that by combining rational metabolic engineering and irrational evolutionary approaches, co-utilizing carbon sources can significantly contribute to the bioproduction of chemicals.
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Affiliation(s)
- Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinhang Yi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yulin Tang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zihao Geng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chunyue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenchao Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhengkai Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenwen Xiong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China.
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Gubelt A, Blaschke L, Hahn T, Rupp S, Hirth T, Zibek S. Comparison of Different Lactobacilli Regarding Substrate Utilization and Their Tolerance Towards Lignocellulose Degradation Products. Curr Microbiol 2020; 77:3136-3146. [PMID: 32728792 PMCID: PMC7452873 DOI: 10.1007/s00284-020-02131-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/14/2020] [Indexed: 11/29/2022]
Abstract
Fermentative lactic acid production is currently impeded by low pH tolerance of the production organisms, the successive substrate consumption of the strains and/or the requirement to apply purified substrate streams. We identified Lactobacillus brevis IGB 1.29 in compost, which is capable of producing lactic acid at low pH values from lignocellulose hydrolysates, simultaneously consuming glucose and xylose. In this study, we compared Lactobacillus brevis IGB 1.29 with the reference strains Lactobacillus brevis ATCC 367, Lactobacillus plantarum NCIMB 8826 and Lactococcus lactis JCM 7638 with regard to the consumption of C5- and C6-sugars. Simultaneous conversion of C5- and C6-monosaccharides was confirmed for L. brevis IGB 1.29 with consumption rates of 1.6 g/(L h) for glucose and 1.0 g/(L h) for xylose. Consumption rates were lower for L. brevis ATCC 367 with 0.6 g/(L h) for glucose and 0.2 g/(L h) for xylose. Further trials were carried out to determine the sensitivity towards common toxic degradation products in lignocellulose hydrolysates: acetate, hydroxymethylfurfural, furfural, formate, levulinic acid and phenolic compounds from hemicellulose fraction. L. lactis was the least tolerant strain towards the inhibitors, whereas L. brevis IGB 1.29 showed the highest tolerance. L. brevis IGB 1.29 exhibited only 10% growth reduction at concentrations of 26.0 g/L acetate, 1.2 g/L furfural, 5.0 g/L formate, 6.6 g/L hydroxymethylfurfural, 9.2 g/L levulinic acid or 2.2 g/L phenolic compounds. This study describes a new strain L. brevis IGB 1.29, that enables efficient lactic acid production with a lignocellulose-derived C5- and C6-sugar fraction.
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Affiliation(s)
- Angela Gubelt
- Institute of Interfacial Process Engineering and Plasma Technology, University Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany.,Institute for Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Lisa Blaschke
- Institute of Interfacial Process Engineering and Plasma Technology, University Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany.,Sartorius Stedim Cellca GmbH, Ulm, Germany
| | - Thomas Hahn
- Industrial Biotechnology, Fraunhofer Institute of Interfacial and Bioprocess Engineering, Stuttgart, Germany
| | - Steffen Rupp
- Institute of Interfacial Process Engineering and Plasma Technology, University Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany.,Industrial Biotechnology, Fraunhofer Institute of Interfacial and Bioprocess Engineering, Stuttgart, Germany
| | - Thomas Hirth
- Institute of Interfacial Process Engineering and Plasma Technology, University Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany.,Industrial Biotechnology, Fraunhofer Institute of Interfacial and Bioprocess Engineering, Stuttgart, Germany.,Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Susanne Zibek
- Institute of Interfacial Process Engineering and Plasma Technology, University Stuttgart, Nobelstraße 12, 70569, Stuttgart, Germany. .,Industrial Biotechnology, Fraunhofer Institute of Interfacial and Bioprocess Engineering, Stuttgart, Germany.
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Park H, McGill SL, Arnold AD, Carlson RP. Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor. Cell Mol Life Sci 2020; 77:395-413. [PMID: 31768608 PMCID: PMC7015805 DOI: 10.1007/s00018-019-03377-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
Microorganisms acquire energy and nutrients from dynamic environments, where substrates vary in both type and abundance. The regulatory system responsible for prioritizing preferred substrates is known as carbon catabolite repression (CCR). Two broad classes of CCR have been documented in the literature. The best described CCR strategy, referred to here as classic CCR (cCCR), has been experimentally and theoretically studied using model organisms such as Escherichia coli. cCCR phenotypes are often used to generalize universal strategies for fitness, sometimes incorrectly. For instance, extremely competitive microorganisms, such as Pseudomonads, which arguably have broader global distributions than E. coli, have achieved their success using metabolic strategies that are nearly opposite of cCCR. These organisms utilize a CCR strategy termed 'reverse CCR' (rCCR), because the order of preferred substrates is nearly reverse that of cCCR. rCCR phenotypes prefer organic acids over glucose, may or may not select preferred substrates to optimize growth rates, and do not allocate intracellular resources in a manner that produces an overflow metabolism. cCCR and rCCR have traditionally been interpreted from the perspective of monocultures, even though most microorganisms live in consortia. Here, we review the basic tenets of the two CCR strategies and consider these phenotypes from the perspective of resource acquisition in consortia, a scenario that surely influenced the evolution of cCCR and rCCR. For instance, cCCR and rCCR metabolism are near mirror images of each other; when considered from a consortium basis, the complementary properties of the two strategies can mitigate direct competition for energy and nutrients and instead establish cooperative division of labor.
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Affiliation(s)
- Heejoon Park
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - S Lee McGill
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - Adrienne D Arnold
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, USA.
- Department of Microbiology and Immunology, Montana State University, Bozeman, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, USA.
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Genetic and phenotypic analysis of carbohydrate metabolism and transport in Lactobacillus reuteri. Int J Food Microbiol 2018; 272:12-21. [DOI: 10.1016/j.ijfoodmicro.2018.02.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 02/14/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
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Koduru L, Kim Y, Bang J, Lakshmanan M, Han NS, Lee DY. Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria. Sci Rep 2017; 7:15721. [PMID: 29147021 PMCID: PMC5691038 DOI: 10.1038/s41598-017-16026-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/06/2017] [Indexed: 11/09/2022] Open
Abstract
Obligate heterofermentative lactic acid bacteria (LAB) are well-known for their beneficial health effects in humans. To delineate the incompletely characterized metabolism that currently limits their exploitation, at systems-level, we developed a genome-scale metabolic model of the representative obligate heterofermenting LAB, Leuconostoc mesenteroides (iLME620). Constraint-based flux analysis was then used to simulate several qualitative and quantitative phenotypes of L. mesenteroides, thereby evaluating the model validity. With established predictive capabilities, we subsequently employed iLME620 to elucidate unique metabolic characteristics of L. mesenteroides, such as the limited ability to utilize amino acids as energy source, and to substantiate the role of malolactic fermentation (MLF) in the reduction of pH-homeostatic burden on F0F1-ATPase. We also reported new hypothesis on the MLF mechanism that could be explained via a substrate channelling-like phenomenon mainly influenced by intracellular redox state rather than the intermediary reactions. Model simulations further revealed possible proton-symporter dependent activity of the energy efficient glucose-phosphotransferase system in obligate heterofermentative LAB. Moreover, integrated transcriptomic analysis allowed us to hypothesize transcriptional regulatory bias affecting the intracellular redox state. The insights gained here about the low ATP-yielding metabolism of L. mesenteroides, dominantly controlled by the cellular redox state, could potentially aid strain design for probiotic and cell factory applications.
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Affiliation(s)
- Lokanand Koduru
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576, Singapore
| | - Yujin Kim
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jeongsu Bang
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore
| | - Nam Soo Han
- Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576, Singapore.
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore.
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The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions. Microbiol Mol Biol Rev 2015; 78:231-56. [PMID: 24847021 DOI: 10.1128/mmbr.00001-14] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The bacterial phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) carries out both catalytic and regulatory functions. It catalyzes the transport and phosphorylation of a variety of sugars and sugar derivatives but also carries out numerous regulatory functions related to carbon, nitrogen, and phosphate metabolism, to chemotaxis, to potassium transport, and to the virulence of certain pathogens. For these different regulatory processes, the signal is provided by the phosphorylation state of the PTS components, which varies according to the availability of PTS substrates and the metabolic state of the cell. PEP acts as phosphoryl donor for enzyme I (EI), which, together with HPr and one of several EIIA and EIIB pairs, forms a phosphorylation cascade which allows phosphorylation of the cognate carbohydrate bound to the membrane-spanning EIIC. HPr of firmicutes and numerous proteobacteria is also phosphorylated in an ATP-dependent reaction catalyzed by the bifunctional HPr kinase/phosphorylase. PTS-mediated regulatory mechanisms are based either on direct phosphorylation of the target protein or on phosphorylation-dependent interactions. For regulation by PTS-mediated phosphorylation, the target proteins either acquired a PTS domain by fusing it to their N or C termini or integrated a specific, conserved PTS regulation domain (PRD) or, alternatively, developed their own specific sites for PTS-mediated phosphorylation. Protein-protein interactions can occur with either phosphorylated or unphosphorylated PTS components and can either stimulate or inhibit the function of the target proteins. This large variety of signal transduction mechanisms allows the PTS to regulate numerous proteins and to form a vast regulatory network responding to the phosphorylation state of various PTS components.
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Distribution and functions of phosphotransferase system genes in the genome of the lactic acid bacterium Oenococcus oeni. Appl Environ Microbiol 2013; 79:3371-9. [PMID: 23524676 DOI: 10.1128/aem.00380-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oenococcus oeni, the lactic acid bacterium primarily responsible for malolactic fermentation in wine, is able to grow on a large variety of carbohydrates, but the pathways by which substrates are transported and phosphorylated in this species have been poorly studied. We show that the genes encoding the general phosphotransferase proteins, enzyme I (EI) and histidine protein (HPr), as well as 21 permease genes (3 isolated ones and 18 clustered into 6 distinct loci), are highly conserved among the strains studied and may form part of the O. oeni core genome. Additional permease genes differentiate the strains and may have been acquired or lost by horizontal gene transfer events. The core pts genes are expressed, and permease gene expression is modulated by the nature of the bacterial growth substrate. Decryptified O. oeni cells are able to phosphorylate glucose, cellobiose, trehalose, and mannose at the expense of phosphoenolpyruvate. These substrates are present at low concentrations in wine at the end of alcoholic fermentation. The phosphotransferase system (PTS) may contribute to the perfect adaptation of O. oeni to its singular ecological niche.
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Shimizu K. Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism. ISRN BIOCHEMISTRY 2013; 2013:645983. [PMID: 25937963 PMCID: PMC4393010 DOI: 10.1155/2013/645983] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/25/2012] [Indexed: 12/19/2022]
Abstract
It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Fukuoka, Iizuka 820-8502, Japan
- Institute of Advanced Bioscience, Keio University, Yamagata, Tsuruoka 997-0017, Japan
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Tsakraklides V, Shaw AJ, Miller BB, Hogsett DA, Herring CD. Carbon catabolite repression in Thermoanaerobacterium saccharolyticum. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:85. [PMID: 23181505 PMCID: PMC3526391 DOI: 10.1186/1754-6834-5-85] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/25/2012] [Indexed: 02/20/2024]
Abstract
BACKGROUND The thermophilic anaerobe Thermoanaerobacterium saccharolyticum is capable of directly fermenting xylan and the biomass-derived sugars glucose, cellobiose, xylose, mannose, galactose and arabinose. It has been metabolically engineered and developed as a biocatalyst for the production of ethanol. RESULTS We report the initial characterization of the carbon catabolite repression system in this organism. We find that sugar metabolism in T. saccharolyticum is regulated by histidine-containing protein HPr. We describe a mutation in HPr, His15Asp, that leads to derepression of less-favored carbon source utilization. CONCLUSION Co-utilization of sugars can be achieved by mutation of HPr in T. saccharolyticum. Further manipulation of CCR in this organism will be instrumental in achieving complete and rapid conversion of all available sugars to ethanol.
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Affiliation(s)
| | - A Joe Shaw
- Mascoma Corporation, 67 Etna Road, Suite 300, New Hampshire, 03766, Lebanon
| | - Bethany B Miller
- Mascoma Corporation, 67 Etna Road, Suite 300, New Hampshire, 03766, Lebanon
| | - David A Hogsett
- Mascoma Corporation, 67 Etna Road, Suite 300, New Hampshire, 03766, Lebanon
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Kim JH, Block DE, Mills DA. Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol 2010; 88:1077-85. [PMID: 20838789 PMCID: PMC2956055 DOI: 10.1007/s00253-010-2839-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 11/25/2022]
Abstract
Lignocellulosic biomass is an attractive carbon source for bio-based fuel and chemical production; however, its compositional heterogeneity hinders its commercial use. Since most microbes possess carbon catabolite repression (CCR), mixed sugars derived from the lignocellulose are consumed sequentially, reducing the efficacy of the overall process. To overcome this barrier, microbes that exhibit the simultaneous consumption of mixed sugars have been isolated and/or developed and evaluated for the lignocellulosic biomass utilization. Specific strains of Escherichia coli, Saccharomyces cerevisiae, and Zymomonas mobilis have been engineered for simultaneous glucose and xylose utilization via mutagenesis or introduction of a xylose metabolic pathway. Other microbes, such as Lactobacillus brevis, Lactobacillus buchneri, and Candida shehatae possess a relaxed CCR mechanism, showing simultaneous consumption of glucose and xylose. By exploiting CCR-negative phenotypes, various integrated processes have been developed that incorporate both enzyme hydrolysis of lignocellulosic material and mixed sugar fermentation, thereby enabling greater productivity and fermentation efficacy.
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Affiliation(s)
- Jae-Han Kim
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - David E. Block
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
- Department of Chemical Engineering and Materials Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - David A. Mills
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
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Kim JH, Shoemaker SP, Mills DA. Relaxed control of sugar utilization in Lactobacillus brevis. Microbiology (Reading) 2009; 155:1351-1359. [DOI: 10.1099/mic.0.024653-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prioritization of sugar consumption is a common theme in bacterial growth and a problem for complete utilization of five and six carbon sugars derived from lignocellulose. Growth studies show that Lactobacillus brevis simultaneously consumes numerous carbon sources and appears to lack normal hierarchical control of carbohydrate utilization. Analysis of several independent L. brevis isolates indicated that co-utilization of xylose and glucose is a common trait for this species. Moreover, carbohydrates that can be used as a single carbon source are simultaneously utilized with glucose. Analysis of the proteome of L. brevis cells grown on glucose, xylose or a glucose/xylose mixture revealed the constitutive expression of the enzymes of the heterofermentative pathway. In addition, fermentative mass balances between mixed sugar inputs and end-products indicated that both glucose and xylose are simultaneously metabolized through the heterofermentative pathway. Proteomic and mRNA analyses revealed that genes in the xyl operon were expressed in the cells grown on xylose or on glucose/xylose mixtures but not in those grown on glucose alone. However, the expression level of XylA and XylB proteins in cells grown on a glucose/xylose mixture was reduced 2.7-fold from that observed in cells grown solely on xylose. These results suggest that regulation of xylose utilization in L. brevis is not stringently controlled as seen in other lactic acid bacteria, where carbon catabolite repression operates to prioritize carbohydrate utilization more rigorously.
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Affiliation(s)
- Jae-Han Kim
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Sharon P. Shoemaker
- California Institute of Food and Agricultural Research, University of California, Davis, CA 95616, USA
| | - David A. Mills
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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Görke B, Stülke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 2008; 6:613-24. [PMID: 18628769 DOI: 10.1038/nrmicro1932] [Citation(s) in RCA: 1065] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Most bacteria can selectively use substrates from a mixture of different carbon sources. The presence of preferred carbon sources prevents the expression, and often also the activity, of catabolic systems that enable the use of secondary substrates. This regulation, called carbon catabolite repression (CCR), can be achieved by different regulatory mechanisms, including transcription activation and repression and control of translation by an RNA-binding protein, in different bacteria. Moreover, CCR regulates the expression of virulence factors in many pathogenic bacteria. In this Review, we discuss the most recent findings on the different mechanisms that have evolved to allow bacteria to use carbon sources in a hierarchical manner.
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Affiliation(s)
- Boris Görke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr 8, D-37077 Göttingen, Germany
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Abstract
The increasing number of genomic and post-genomic studies on Gram-positive organisms and especially on lactic acid bacteria brings a lot of information on sugar catabolism in these bacteria. Like for many other bacteria, glucose is the most preferred source of carbon and energy for Lactococcus lactis. Other carbon sources can induce their own utilization in the absence of well-metabolized sugar. These processes engage numbers of genes and undergo complex mechanisms of regulation. In this review, we discuss various biochemical and genetic control mechanisms involved in sugar catabolism, like regulation by repressors, activators, antiterminators or carbon catabolite repression control.
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Affiliation(s)
- Magdalena Kowalczyk
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics PAS, Pawinskiego, Warszawa, Poland.
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Yebra MJ, Zúñiga M, Beaufils S, Pérez-Martínez G, Deutscher J, Monedero V. Identification of a gene cluster enabling Lactobacillus casei BL23 to utilize myo-inositol. Appl Environ Microbiol 2007; 73:3850-8. [PMID: 17449687 PMCID: PMC1932728 DOI: 10.1128/aem.00243-07] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome analysis of Lactobacillus casei BL23 revealed that, compared to L. casei ATCC 334, it carries a 12.8-kb DNA insertion containing genes involved in the catabolism of the cyclic polyol myo-inositol (MI). Indeed, L. casei ATCC 334 does not ferment MI, whereas strain BL23 is able to utilize this carbon source. The inserted DNA consists of an iolR gene encoding a DeoR family transcriptional repressor and a divergently transcribed iolTABCDG1G2EJK operon, encoding a complete MI catabolic pathway, in which the iolK gene probably codes for a malonate semialdehyde decarboxylase. The presence of iolK suggests that L. casei has two alternative pathways for the metabolism of malonic semialdehyde: (i) the classical MI catabolic pathway in which IolA (malonate semialdehyde dehydrogenase) catalyzes the formation of acetyl-coenzyme A from malonic semialdehyde and (ii) the conversion of malonic semialdehyde to acetaldehyde catalyzed by the product of iolK. The function of the iol genes was verified by the disruption of iolA, iolT, and iolD, which provided MI-negative strains. By contrast, the disruption of iolK resulted in a strain with no obvious defect in MI utilization. Transcriptional analyses conducted with different mutant strains showed that the iolTABCDG1G2EJK cluster is regulated by substrate-specific induction mediated by the inactivation of the transcriptional repressor IolR and by carbon catabolite repression mediated by the catabolite control protein A (CcpA). This is the first example of an operon for MI utilization in lactic acid bacteria and illustrates the versatility of carbohydrate utilization in L. casei BL23.
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Affiliation(s)
- María Jesús Yebra
- Laboratorio de Bacterias Lácticas y Probióticos, IATA-CSIC, P.O. Box 73, 46100 Burjassot, Valencia, Spain
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Zhang Z, Ma C, Pornillos O, Xiu X, Chang G, Saier MH. Functional characterization of the heterooligomeric EbrAB multidrug efflux transporter of Bacillus subtilis. Biochemistry 2007; 46:5218-25. [PMID: 17417881 DOI: 10.1021/bi7001604] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Bacillus subtilis genome contains two tandem genes, ebrA and ebrB, which encode two homologues of the SMR family of multidrug efflux transporters. The sequences of EbrA and EbrB are highly similar to each other and to that of EmrE, the prototypical SMR transporter of Escherichia coli. Drug resistance profiling and drug binding experiments showed that the presence of both EbrA and EbrB is required for proper transport function. EbrA and EbrB directly interact and combine to form a functional transporter. They likely form a heterodimer in analogy to the EmrE homodimer. Mutagenesis experiments indicate that the conserved membrane-embedded glutamates in the first transmembrane helices of both EbrA and EbrB are required for multidrug efflux activity. However, the two glutamates are nonequivalent since EbrA E15 is required for substrate binding while EbrB E14 is not. Our studies support a model in which functional residues in EbrAB are relegated to at least two sets that participate in distinct steps of the active drug transport process.
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Affiliation(s)
- Zhongge Zhang
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
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16
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 967] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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Monedero V, Mazé A, Boël G, Zúñiga M, Beaufils S, Hartke A, Deutscher J. The Phosphotransferase System of Lactobacillus casei: Regulation of Carbon Metabolism and Connection to Cold Shock Response. J Mol Microbiol Biotechnol 2006; 12:20-32. [PMID: 17183208 DOI: 10.1159/000096456] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genome sequencing of two different Lactobacillus casei strains (ATCC334 and BL23) is presently going on and preliminary data revealed that this lactic acid bacterium possesses numerous carbohydrate transport systems probably reflecting its capacity to proliferate under varying environmental conditions. Many carbohydrate transporters belong to the phosphoenolpyruvate:sugar phosphotransferase system (PTS), but all different kinds of non-PTS transporters are present as well and their substrates are known in a few cases. In L. casei regulation of carbohydrate transport and carbon metabolism is mainly achieved by PTS proteins. Carbon catabolite repression (CCR) is mediated via several mechanisms, including the major P-Ser-HPr/catabolite control protein A (CcpA)-dependent mechanism. Catabolite response elements, the target sites for the P-Ser-HPr/CcpA complex, precede numerous genes and operons. PTS regulation domain-containing antiterminators and transcription activators are also present in both L. casei strains. Their activity is usually controlled by two PTS-mediated phosphorylation reactions exerting antagonistic effects on the transcription regulators: P~EIIB-dependent phosphorylation regulates induction of the corresponding genes and P~His-HPr-mediated phosphorylation plays a role in CCR. Carbohydrate transport of L. casei is also regulated via inducer exclusion and inducer expulsion. The presence of glucose, fructose, etc. leads to inhibition of the transport or metabolism of less favorable carbon sources (inducer exclusion) or to the export of accumulated non-metabolizable carbon sources (inducer expulsion). While P-Ser-HPr is essential for inducer exclusion of maltose, it is not necessary for the expulsion of accumulated thio-methyl-beta-D-galactopyranoside. Surprisingly, recent evidence suggests that the PTS of L. casei also plays a role in cold shock response.
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Affiliation(s)
- Vicente Monedero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Burjassot, Spain
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Yebra MJ, Monedero V, Zúñiga M, Deutscher J, Pérez-Martínez G. Molecular analysis of the glucose-specific phosphoenolpyruvate : sugar phosphotransferase system from Lactobacillus casei and its links with the control of sugar metabolism. Microbiology (Reading) 2006; 152:95-104. [PMID: 16385119 DOI: 10.1099/mic.0.28293-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus caseitransports glucose preferentially by a mannose-class phosphoenolpyruvate : sugar phosphotransferase system (PTS). The genomic analysis ofL. caseiallowed the authors to find a gene cluster (manLMNO) encoding the IIAB (manL), IIC (manM) and IID (manN) proteins of a mannose-class PTS, and a putative 121 aa protein of unknown function (encoded bymanO), homologues of which are also present inmanclusters that encode glucose/mannose transporters in other Gram-positive bacteria. TheL. casei manoperon is constitutively expressed into amanLMNOmessenger, but an additionalmanOtranscript was also detected. Upstream of themanoperon, two genes (upsRandupsA) were found which encode proteins resembling a transcriptional regulator and a membrane protein, respectively. Disruption of eitherupsRorupsAdid not affectmanLMNOtranscription, and had no effect on glucose uptake. Cells carrying amanOdeletion transported glucose at a rate similar to that of the wild-type strain. By contrast, amanMdisruption resulted in cells unable to transport glucose by the PTS, thus confirming the functional role of themangenes. In addition, themanMmutant exhibited neither inducer exclusion of maltose nor glucose repression. This result confirms the need for glucose transport through the PTS to trigger these regulatory processes inL. casei.
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Affiliation(s)
- María J Yebra
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Apdo. Correos 73, 46100 Burjassot, Spain
| | - Vicente Monedero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Apdo. Correos 73, 46100 Burjassot, Spain
| | - Manuel Zúñiga
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Apdo. Correos 73, 46100 Burjassot, Spain
| | - Josef Deutscher
- Microbiologie et Génétique Moléculaire, CNRS/INRA/INA-PG, UMR2585, 78850 Thiverval-Grignon, France
| | - Gaspar Pérez-Martínez
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Apdo. Correos 73, 46100 Burjassot, Spain
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Ehrmann MA, Vogel RF. Molecular taxonomy and genetics of sourdough lactic acid bacteria. Trends Food Sci Technol 2005. [DOI: 10.1016/j.tifs.2004.06.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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The bacterial phosphotransferase system: a perfect link of sugar transport and signal transduction. ACTA ACUST UNITED AC 2004. [DOI: 10.1007/b95776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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21
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Abstract
The sgaTBA genes of Escherichia coli encode a putative 12-transmembrane alpha-helical segment (12 TMS) transporter, an enzyme IIB-like protein and an enzyme IIA-like protein of the phosphotransferase system (PTS), respectively. We show that all three proteins as well as the energy-coupling PTS proteins, enzyme I and HPr, are required for the anaerobic utilization and uptake of L-ascorbate in vivo and its phosphoenolpyruvate-dependent phosphorylation in vitro. The transporter exhibits an apparent K(m) for L-ascorbate of 9 micro M and is highly specific. The sgaTBA genes are regulated at the transcriptional level by the yjfQ gene product, as well as by Crp and Fnr. The yjfR gene product is essential for L-ascorbate utilization and probably encodes a cytoplasmic L-ascorbate 6-phosphate lactonase. We conclude that SgaT represents a novel prototypical enzyme IIC that functions with SgaA and SgaB to allow phosphoryl transfer from HPr(his-P) to L-ascorbate via the phosphoryl transfer pathway: [pathway: see text].
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Affiliation(s)
- Zhongge Zhang
- Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116, USA
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Grossiord BP, Luesink EJ, Vaughan EE, Arnaud A, de Vos WM. Characterization, expression, and mutation of the Lactococcus lactis galPMKTE genes, involved in galactose utilization via the Leloir pathway. J Bacteriol 2003; 185:870-8. [PMID: 12533462 PMCID: PMC142802 DOI: 10.1128/jb.185.3.870-878.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2002] [Accepted: 11/06/2002] [Indexed: 11/20/2022] Open
Abstract
A cluster containing five similarly oriented genes involved in the metabolism of galactose via the Leloir pathway in Lactococcus lactis subsp. cremoris MG1363 was cloned and characterized. The order of the genes is galPMKTE, and these genes encode a galactose permease (GalP), an aldose 1-epimerase (GalM), a galactokinase (GalK), a hexose-1-phosphate uridylyltransferase (GalT), and a UDP-glucose 4-epimerase (GalE), respectively. This genetic organization reflects the order of the metabolic conversions during galactose utilization via the Leloir pathway. The functionality of the galP, galK, galT, and galE genes was shown by complementation studies performed with both Escherichia coli and L. lactis mutants. The GalP permease is a new member of the galactoside-pentose-hexuronide family of transporters. The capacity of GalP to transport galactose was demonstrated by using galP disruption mutant strains of L. lactis MG1363. A galK deletion was constructed by replacement recombination, and the mutant strain was not able to ferment galactose. Disruption of the galE gene resulted in a deficiency in cell separation along with the appearance of a long-chain phenotype when cells were grown on glucose as the sole carbon source. Recovery of the wild-type phenotype for the galE mutant was obtained either by genetic complementation or by addition of galactose to the growth medium.
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Affiliation(s)
- Benoît P Grossiord
- NIZO Food Research, 6710 BA Ede. Laboratory of Microbiology, Wageningen University, 6703 CT Wageningen, The Netherlands.
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Aboulwafa M, Saier MH. Dependency of sugar transport and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system on membranous phosphatidyl glycerol in Escherichia coli: studies with a pgsA mutant lacking phosphatidyl glycerophosphate synthase. Res Microbiol 2002; 153:667-77. [PMID: 12558186 DOI: 10.1016/s0923-2508(02)01376-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
It has been reported that phosphatidyl glycerol (PG) is specifically required for the in vitro activities of the hexose-phosphorylating Enzymes II of the Escherichia coli phosphoenolpyruvate-dependent sugar transporting phosphotransferase system (PTS). We have examined this possibility by measuring the properties of a null pgsA mutant that lacks detectable PG. The mutant showed lower in vitro phosphorylation activities towards several sugars when both PEP-dependent and sugar-phosphate-dependent [14C]sugar phosphorylation reactions were measured. The order of dependency on PG for the different enzymes II was: IIMannose > IIGlucose > IIFructose > IIMannitol. Nonsedimentable (40000 rpm for 2 h) Enzymes II exhibited a greater dependency on PG than pelletable Enzymes II. Western blot analyses showed that the glucose Enzyme II is present in normal amounts. Transport and fermentation measurements revealed diminished activities for all Enzymes II. Thermal stability of all of these enzymes except the mannitol-specific Enzyme II was significantly decreased by the pgsA mutation, and sensitivity to detergent treatments was enhanced. Sugar transport proved to be the most sensitive indicator of proper Enzyme II-phospholipid association. Our results show that PG stimulates but is not required for Enzyme II function in E. coli.
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Affiliation(s)
- Mohammad Aboulwafa
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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Hu KY, Saier MH. Phylogeny of phosphoryl transfer proteins of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system. Res Microbiol 2002; 153:405-15. [PMID: 12405346 DOI: 10.1016/s0923-2508(02)01339-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Some bacteria lack sugar permeases of the bacterial phosphotransferase system (PTS) but encode within their genomes phosphoryl transfer proteins of the PTS that probably function in regulation. These proteins include homologues of HPr (PtsH), the ATP-dependent HPr(ser) kinase/phosphatase (PtsK) and the PEP-dependent HPr(his) kinase known as Enzyme I (PtsI). We identify all currently sequenced homologues of these proteins, multiply align their sequences and construct phylogenetic trees in order to derive functional, structural and evolutionary conclusions. We show that no bacterium possesses more than one HPr kinase and that these proteins are probably all orthologous. alpha-Proteobacteria possess truncated HPr kinases which probably serve a unified regulatory function together with other PTS proteins. The Enzymes I are orthologous in all Gram-positive bacteria and some Gram-negative bacteria, but other Gram-negative bacteria exhibit paralogues that fall into 5 functional types. No bacterium with a fully sequenced genome exhibits all of these types. With the exception of the classical Enzymes I, each of these functional types exhibits a distinctive set of accompanying domains, usually with a characteristic domain order. One functional type, the fructose-specific type, includes two phylogenetically different subgroups with different domain orders. The results establish that domain associations occurred early during evolutionary history of the PTS, and that subsequent domain rearrangements occurred rarely. Our findings define the evolutionary histories of these important bacterial proteins and provide guides for functional assignment of PTS-related proteins encoded by genes revealed by genome sequencing.
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Affiliation(s)
- Kuang-Yu Hu
- Division of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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