1
|
Sarkhel R, Priyadarsini S, Mahawar M. Nutrient limitation and oxidative stress induce the promoter of acetate operon in Salmonella Typhimurium. Arch Microbiol 2024; 206:126. [PMID: 38411730 DOI: 10.1007/s00203-024-03863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Glyoxylate shunt is an important pathway for microorganisms to survive under multiple stresses. One of its enzymes, malate synthase (encoded by aceB gene), has been widely speculated for its contribution to both the pathogenesis and virulence of various microorganisms. We have previously demonstrated that malate synthase (MS) is required for the growth of Salmonella Typhimurium (S. Typhimurium) under carbon starvation and survival under oxidative stress conditions. The aceB gene is encoded by the acetate operon in S. Typhimurium. We attempted to study the activity of acetate promoter under both the starvation and oxidative stress conditions in a heterologous system. The lac promoter of the pUC19 plasmid was substituted with the putative promoter sequence of the acetate operon of S. Typhimurium upstream to the lacZ gene and transformed the vector construct into E. coli NEBα cells. The transformed cells were subjected to the stress conditions mentioned above. We observed a fourfold increase in the β-galactosidase activity in these cells resulting from the upregulation of the lacZ gene in the stationary phase of cell growth (nutrient deprived) as compared to the mid-log phase. Following exposure of stationary phase cells to hypochlorite-induced oxidative stress, we further observed a 1.6-fold increase in β galactosidase activity. These data suggest the induction of promoter activity of the acetate operon under carbon starvation and oxidative stress conditions. Thus, these observations corroborate our previous findings regarding the upregulation of aceB expression under stressful environments.
Collapse
Affiliation(s)
- Ratanti Sarkhel
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Swagatika Priyadarsini
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
- Indian Council of Agricultural Research- National Research Centre on Camel, Bikaner, Rajasthan, India.
| | - Manish Mahawar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
| |
Collapse
|
2
|
Vinacour M, Moiana M, Forné I, Jung K, Bertea M, Calero Valdayo PM, Nikel PI, Imhof A, Palumbo MC, Fernández Do Porto D, Ruiz JA. Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16. Appl Environ Microbiol 2023; 89:e0063023. [PMID: 38054732 PMCID: PMC10734416 DOI: 10.1128/aem.00630-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Fusaric acid (FA) is an important virulence factor produced by several Fusarium species. These fungi are responsible for wilt and rot diseases in a diverse range of crops. FA is toxic for animals, humans and soil-borne microorganisms. This mycotoxin reduces the survival and competition abilities of bacterial species able to antagonize Fusarium spp., due to its negative effects on viability and the production of antibiotics effective against these fungi. FA biodegradation is not a common characteristic among bacteria, and the determinants of FA catabolism have not been identified so far in any microorganism. In this study, we identified genes, enzymes, and metabolic pathways involved in the degradation of FA in the soil bacterium Burkholderia ambifaria T16. Our results provide insights into the catabolism of a pyridine-derivative involved in plant pathogenesis by a rhizosphere bacterium.
Collapse
Affiliation(s)
- Matias Vinacour
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Moiana
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Micaela Bertea
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Patricia M. Calero Valdayo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Miranda C. Palumbo
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Fernández Do Porto
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena A. Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
3
|
Wang L, Zhang K, Gao S, Zhang M, Liu T, Cai B, Wang L, Su L, Wu J, Chen S. High-Yield Synthesis of 2'-Fucosyllactose from Glycerol and Glucose in Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15237-15248. [PMID: 37795855 DOI: 10.1021/acs.jafc.3c05015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
2'-Fucosyllactose (2'-FL) is vital for the growth and development of newborns. In this study, we developed a synthesis pathway for 2'-FL in Escherichia coli BL21 (DE3). Then, we optimized the solubility of α-1,2-fucosyltransferase, thereby enhancing the production yield of 2'-FL. Based on this finding, we further enhanced the expression of guanosine inosine kinase Gsk and knocked out the isocitrate lyase regulator gene iclR. This strategy reduced the formation of byproduct acetate during the metabolic process and alleviated carbon source overflow effects in the strain, resulting in further improvement of the yield of 2'-FL. In a 3 L bioreactor, employing fed-batch fermentation with glycerol and glucose as substrates, the engineered strain BWLAI-RSZL exhibited impressive 2'-FL titers of 121.9 and 111.56 g/L, along with productivity levels of 1.57 and 1.31 g/L/h, respectively. The reported 2'-FL titers reached a groundbreaking level, irrespective of the carbon source employed (glycerol or glucose), highlighting the significant potential for large-scale industrial synthesis of 2'-FL.
Collapse
Affiliation(s)
- Luyao Wang
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Kang Zhang
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shengqi Gao
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Mengwei Zhang
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Tongle Liu
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Bohan Cai
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lei Wang
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Resources, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| |
Collapse
|
4
|
Yang P, Liu W, Chen Y, Gong AD. Engineering the glyoxylate cycle for chemical bioproduction. Front Bioeng Biotechnol 2022; 10:1066651. [PMID: 36532595 PMCID: PMC9755347 DOI: 10.3389/fbioe.2022.1066651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 07/24/2023] Open
Abstract
With growing concerns about environmental issues and sustainable economy, bioproduction of chemicals utilizing microbial cell factories provides an eco-friendly alternative to current petro-based processes. Creating high-performance strains (with high titer, yield, and productivity) through metabolic engineering strategies is critical for cost-competitive production. Commonly, it is inevitable to fine-tuning or rewire the endogenous or heterologous pathways in such processes. As an important pathway involved in the synthesis of many kinds of chemicals, the potential of the glyoxylate cycle in metabolic engineering has been studied extensively these years. Here, we review the metabolic regulation of the glyoxylate cycle and summarize recent achievements in microbial production of chemicals through tuning of the glyoxylate cycle, with a focus on studies implemented in model microorganisms. Also, future prospects for bioproduction of glyoxylate cycle-related chemicals are discussed.
Collapse
|
5
|
Ma P, Hong Y, Liu C, Sun Y, Liu M, Yang Z, Ma P, Wu H, Xue F. Rumen microbiota responses to the enzymatic hydrolyzed cottonseed peptide supplement under high-concentrate diet feeding process. Front Vet Sci 2022; 9:984634. [PMID: 36439362 PMCID: PMC9698919 DOI: 10.3389/fvets.2022.984634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/03/2022] [Indexed: 04/09/2024] Open
Abstract
In current dairy production, dietary energy is always excessively provided with a high-concentrate diet feeding to improve milk production. However, this feeding practice disturbed the rumen microbial ecosystem and the balance between ruminal energy and nitrogen, resulting in decreased nutrient fermentability, which in turn declined the milk yield of dairy cows. Therefore, supplementation of dietary degradable nitrogen may be helpful for high dairy production. In this study, we evaluated the regulatory effects of easily utilized enzymatic hydrolyzed cottonseed peptide (EHP) supplements on rumen microbiota communities and rumen nutrient fermentability under high-concentrate feeding. For this purpose, a gradient concentrate of EHP (from 0.2 to 1.0%) was added to the high-concentrate basal substrates for an in vitro experiment. Each treatment contained three replicates, with three bottles in each replicate. Rumen fermentable parameters included microbial protein content, volatile fatty acids, and ammonia-N; the rumen nutrient degradability of dry matter, crude protein, neutral detergent fiber, acid detergent fiber, ether extracts, calcium, and phosphorus were further investigated after in vitro fermentation for 72 h. Then, rumen microbiota communities and their correlation with ruminal fermentation parameters and rumen nutritional degradability were analyzed to understand the regulatory mechanism of the EHP supplements on rumen fermentability. Results indicate that treatment with 0.6% of EHP supplements had the highest content of acetate, butyrate, and neutral detergent fiber degradability among all treatments. Furthermore, EHP supplements significantly increased the relative abundance of rumen cellulose and starch-degrading bacteria such as Ruminococcus, Bifidobacterium, and Acetitomaculum, and the high nitrogen utilizing bacteria Butyrivibrio and Pseudobutyrivibrio, which may further promote the rumen carbohydrate and nitrogen metabolism. In summary, supplementation of easily degraded small peptides helps reestablish rumen energy and nitrogen balance to promote the rumen fermentable functions and nutritional degradability under high-concentrate diet feeding circumstances. These findings may further promote dairy production.
Collapse
Affiliation(s)
- Peng Ma
- Nanchang Key Laboratory of Animal Health and Safety Production, Jiangxi Agricultural University, Nanchang, China
- Anyou Biotechnology Group Co. Ltd., Taicang, China
| | - Yifen Hong
- Anyou Biotechnology Group Co. Ltd., Taicang, China
| | - Chunxue Liu
- Anyou Biotechnology Group Co. Ltd., Taicang, China
| | - Yuqin Sun
- Yangxin Yiliyuan Halal Meat Co. Ltd., Yangxin, China
| | - Minze Liu
- Yangxin Yiliyuan Halal Meat Co. Ltd., Yangxin, China
| | - Zhengang Yang
- Yangxin Yiliyuan Halal Meat Co. Ltd., Yangxin, China
| | - Pengyun Ma
- Nanchang Key Laboratory of Animal Health and Safety Production, Jiangxi Agricultural University, Nanchang, China
| | - Hongxiang Wu
- Nanchang Key Laboratory of Animal Health and Safety Production, Jiangxi Agricultural University, Nanchang, China
| | - Fuguang Xue
- Nanchang Key Laboratory of Animal Health and Safety Production, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
6
|
Mutyala S, Kim JR. Recent advances and challenges in the bioconversion of acetate to value-added chemicals. BIORESOURCE TECHNOLOGY 2022; 364:128064. [PMID: 36195215 DOI: 10.1016/j.biortech.2022.128064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Acetate is a major byproduct of the bioconversion of the greenhouse gas carbon dioxide, pretreatment of lignocellulose biomass, and microbial fermentation. The utilization and valorization of acetate have been emphasized in transforming waste to clean energy and value-added platform chemicals, contributing to the development of a closed carbon loop toward a low-carbon circular bio-economy. Acetate has been used to produce several platform chemicals, including succinate, 3-hydroxypropionate, and itaconic acid, highlighting the potential of acetate to synthesize many biochemicals and biofuels. On the other hand, the yields and titers have not reached the theoretical maximum. Recently, recombinant strain development and pathway regulation have been suggested to overcome this limitation. This review provides insights into the important constraints limiting the yields and titers of the biochemical and metabolic pathways of bacteria capable of metabolizing acetate for acetate bioconversion. The current developments in recombinant strain engineering are also discussed.
Collapse
Affiliation(s)
- Sakuntala Mutyala
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
| |
Collapse
|
7
|
Sarkhel R, Apoorva S, Priyadarsini S, Sridhar HB, Bhure SK, Mahawar M. Malate synthase contributes to the survival of Salmonella Typhimurium against nutrient and oxidative stress conditions. Sci Rep 2022; 12:15979. [PMID: 36155623 PMCID: PMC9510125 DOI: 10.1038/s41598-022-20245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
To survive and replicate in the host, S. Typhimurium have evolved several metabolic pathways. The glyoxylate shunt is one such pathway that can utilize acetate for the synthesis of glucose and other biomolecules. This pathway is a bypass of the TCA cycle in which CO2 generating steps are omitted. Two enzymes involved in the glyoxylate cycle are isocitrate lyase (ICL) and malate synthase (MS). We determined the contribution of MS in the survival of S. Typhimurium under carbon limiting and oxidative stress conditions. The ms gene deletion strain (∆ms strain) grew normally in LB media but failed to grow in M9 minimal media supplemented with acetate as a sole carbon source. However, the ∆ms strain showed hypersensitivity (p < 0.05) to hypochlorite. Further, ∆ms strain has been significantly more susceptible to neutrophils. Interestingly, several folds induction of ms gene was observed following incubation of S. Typhimurium with neutrophils. Further, ∆ms strain showed defective colonization in poultry spleen and liver. In short, our data demonstrate that the MS contributes to the virulence of S. Typhimurium by aiding its survival under carbon starvation and oxidative stress conditions.
Collapse
|
8
|
Rangwala AM, Mingione VR, Georghiou G, Seeliger MA. Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome. Biomolecules 2022; 12:biom12050685. [PMID: 35625613 PMCID: PMC9138534 DOI: 10.3390/biom12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.
Collapse
|
9
|
Kim Y, Lama S, Agrawal D, Kumar V, Park S. Acetate as a potential feedstock for the production of value-added chemicals: Metabolism and applications. Biotechnol Adv 2021; 49:107736. [PMID: 33781888 DOI: 10.1016/j.biotechadv.2021.107736] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Acetate is regarded as a promising carbon feedstock in biological production owing to its possible derivation from C1 gases such as CO, CO2 and methane. To best use of acetate, comprehensive understanding of acetate metabolisms from genes and enzymes to pathways and regulations is needed. This review aims to provide an overview on the potential of acetate as carbon feedstock for industrial biotechnology. Biochemical, microbial and biotechnological aspects of acetate metabolism are described. Especially, the current state-of-the art in the production of value-added chemicals from acetate is summarized. Challenges and future perspectives are also provided.
Collapse
Affiliation(s)
- Yeonhee Kim
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield, MK430AL, United Kingdom.
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea.
| |
Collapse
|
10
|
Santala S, Santala V, Liu N, Stephanopoulos G. Partitioning metabolism between growth and product synthesis for coordinated production of wax esters in Acinetobacter baylyi ADP1. Biotechnol Bioeng 2021; 118:2283-2292. [PMID: 33666232 DOI: 10.1002/bit.27740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 02/27/2021] [Indexed: 11/11/2022]
Abstract
Microbial storage compounds, such as wax esters (WE), are potential high-value lipids for the production of specialty chemicals and medicines. Their synthesis, however, is strictly regulated and competes with cell growth, which leads to trade-offs between biomass and product formation. Here, we use metabolic engineering and synergistic substrate cofeeding to partition the metabolism of Acinetobacter baylyi ADP1 into two distinct modules, each dedicated to cell growth and WE biosynthesis, respectively. We first blocked the glyoxylate shunt and upregulated the WE synthesis pathway to direct the acetate substrate exclusively for WE synthesis, then we controlled the supply of gluconate so it could be used exclusively for cell growth and maintenance. We show that the two modules are functionally independent from each other, allowing efficient lipid accumulation while maintaining active cell growth. Our strategy resulted in 7.2- and 4.2-fold improvements in WE content and productivity, respectively, and the product titer was enhanced by 8.3-fold over the wild type strain. Notably, during a 24-h cultivation, a yield of 18% C-WE/C-total-substrates was achieved, being the highest reported for WE biosynthesis. This study provides a simple, yet powerful, means of controlling cellular operations and overcoming some of the fundamental challenges in microbial storage lipid production.
Collapse
Affiliation(s)
- Suvi Santala
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Ville Santala
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
11
|
Liao Y, Ni Z, Wu J, Li Z, Ge Y, Chen X, Yao J. Effect of acetate metabolism modulation on 2'-fucosyllactose production in engineered Escherichia coli. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1885996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Yingxue Liao
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Scinece Island Branch, Graduate School of USTC, Hefei, PR China
| | - Zhijian Ni
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Scinece Island Branch, Graduate School of USTC, Hefei, PR China
| | - Jinyong Wu
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Huainan New Energy Research Center, Institute of Plasma Physics, Chinese Academy of Sciences, Huainan, Anhui, PR China
| | - Zhongkui Li
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Scinece Island Branch, Graduate School of USTC, Hefei, PR China
| | - Yuanfei Ge
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Scinece Island Branch, Graduate School of USTC, Hefei, PR China
| | - Xiangsong Chen
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Huainan New Energy Research Center, Institute of Plasma Physics, Chinese Academy of Sciences, Huainan, Anhui, PR China
| | - Jianming Yao
- Institute of Plasma Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
- Scinece Island Branch, Graduate School of USTC, Hefei, PR China
| |
Collapse
|
12
|
Zhou S, Lama S, Jiang J, Sankaranarayanan M, Park S. Use of acetate for the production of 3-hydroxypropionic acid by metabolically-engineered Pseudomonas denitrificans. BIORESOURCE TECHNOLOGY 2020; 307:123194. [PMID: 32234590 DOI: 10.1016/j.biortech.2020.123194] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
The use of acetate as carbon feedstock can enhance sustainability and economics of the current bio-productions. This study explored the potential of acetate for the production of 3-hydroxypropionic acid by engineered Pseudomonas denitrificans. Heterologous mcr (encoding malonyl-CoA reductase) from Chloroflexus aurantiacus and endogenous accABCD (encoding acetyl-CoA carboxylase) were overexpressed in P. denitrificans. Carbon flux to 3-HP synthesis at the malonyl-CoA node was promoted by suppressing fatty acid synthesis through addition of cerulenin or deletion of fabF gene. In addition, stimulation of glyoxylate shunt and/or TCA cycle were attempted. Recombinant P. denitrificans overexpressing mcr and accABCD produced 19.3 mM 3-HP with cerulenin addition, and 14.2 mM with fabF deletion, respectively. Furthermore, the non-growing cells devoid of fabF could continuously produce 3-HP up to 40.4 mM without losing its production activity for 22 h. This study demonstrates that acetate is a good substrate for 3-HP production by recombinant P. denitrificans.
Collapse
Affiliation(s)
- Shengfang Zhou
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Suman Lama
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mugesh Sankaranarayanan
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Avadi, Chennai 600062, India
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| |
Collapse
|
13
|
Sigala JC, Quiroz L, Arteaga E, Olivares R, Lara AR, Martinez A. Physiological and transcriptional comparison of acetate catabolism between Acinetobacter schindleri ACE and Escherichia coli JM101. FEMS Microbiol Lett 2019; 366:5529389. [DOI: 10.1093/femsle/fnz151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 07/04/2019] [Indexed: 01/12/2023] Open
Abstract
ABSTRACTAcinetobacter bacteria preferentially use gluconeogenic substrates instead of hexoses or pentoses. Accordingly, Acinetobacter schindleri ACE reaches a high growth rate on acetate but is unable to grow on glucose, xylose or arabinose. In this work, we compared the physiology of A. schindleri ACE and Escherichia coli JM101 growing on acetate as the carbon source. In contrast to JM101, ACE grew on acetate threefold faster, had a twofold higher biomass yield, and a 45% higher specific acetate consumption rate. Transcriptional analysis revealed that genes like ackA, pta, aceA, glcB, fumA, tktA and talA were overexpressed while acsA, sfcA, ppc and rpiA were underexpressed in ACE relative to JM101. This transcriptional profile together with carbon flux balance analysis indicated that ACE forms acetyl-CoA preferentially by the AckA-Pta (acetate kinase-phosphotransacetylase) pathway instead of Acs (acetyl-CoA synthetase) and that the glyoxylate shunt and tricarboxylic acid cycle are more active in ACE than in JM101. Moreover, in ACE, ribose 5-phosphate and erythrose 4-phosphate are formed from trioses, and NADPH is mainly produced by isocitrate dehydrogenase. This knowledge will contribute to an understanding of the carbon metabolism of Acinetobacter species of medical, biotechnological and microbiological relevance.
Collapse
Affiliation(s)
- Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Lucy Quiroz
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México 05348, México
| | - Eduardo Arteaga
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México 05348, México
| | - Roberto Olivares
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor. 62210, México
| |
Collapse
|
14
|
Wang P, Liu T, Zhou X, Zhu G. Evaluation of the Potential Phosphorylation Effect on Isocitrate Dehydrogenases from Saccharomyces cerevisiae and Yarrowia lipolytica. Appl Biochem Biotechnol 2019; 187:1131-1142. [PMID: 30903384 DOI: 10.1007/s12010-019-02974-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 02/01/2019] [Indexed: 11/28/2022]
Abstract
Escherichia coli isocitrate dehydrogenase (IDH) is regulated by reversible phosphorylation on Ser113. Latest phosphoproteomic studies revealed that eukaryotic IDHs can also be phosphorylated on the analogous Ser site. So as to understand the possible phosphorylation mechanism, the equivalent Ser of NADP-IDHs from yeast Saccharomyces cerevisiae (ScIDH) and Yarrowia lipolytica(YlIDH) were investigated by site-directed mutagenesis. ScIDH Ser110 and YlIDH Ser103 were replaced by Asp or Glu to mimic a continuous phosphorylation state. Meanwhile, the effects of another four amino acids (Thr, Tyr, Gly, Ala) with various side chain on IDH activity were determined as well. Enzymatic analysis showed that replacement of Ser with Asp or Glu nearly inactivated ScIDH and YlIDH. Four other mutant enzymes of ScIDH, S110T, S110G, S110A, and S110Y, retained 38.07%, 3.24%, 2.65%, and 0.01% of its original activity, and four other mutant enzymes of YlIDH, S103T, S103G, S103A, and S103Y retained 44.26%, 27.99%, 16.29%, and 0.01% of its original activity, respectively. These results suggested that phosphorylation on eukaryotic IDHs has identical consequence to that on the bacterial IDHs. We thus presume that phosphorylation on the substrate-binding Ser shall be a common regulatory mechanism among IDHs.
Collapse
Affiliation(s)
- Peng Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, China
| | - Tingting Liu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, China
| | - Xinxin Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, No.1 Beijing East Road, Wuhu, 241000, Anhui, China.
| |
Collapse
|
15
|
Nitta K, Laviña WA, Pontrelli S, Liao JC, Putri SP, Fukusaki E. Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli. J Biosci Bioeng 2019; 127:301-308. [DOI: 10.1016/j.jbiosc.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
|
16
|
Studies on the activation of isocitrate dehydrogenase kinase/phosphatase (AceK) by Mn 2+ and Mg 2. Biometals 2018; 31:991-1002. [PMID: 30311020 DOI: 10.1007/s10534-018-0144-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
Abstract
Isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme with both kinase and phosphatase activities that are activated by Mg2+. We have studied the interactions of Mn2+and Mg2+ with AceK using isothermal titration calorimetry (ITC) combined with molecular docking simulations and show for the first time that Mn2+ also activates the enzyme activities. However, Mn2+ and Mg2+ exert their effects by different mechanisms. Although they have similar binding constants (of 1.11 × 105 and 0.98 × 105 M-1, respectively) for AceK and induce conformational changes of the enzyme, they do not compete for the same binding site. Instead Mn2+ appears to bind to the regulatory domain of AceK, and its effect is transmitted to the active site of the enzyme by the conformational change that it induces. The information in this study should be very useful for understanding the molecular mechanism underlying the interaction between AceK and metal ions, especially Mn2+ and Mg2+.
Collapse
|
17
|
Dong H, Bai L, Zhang Y, Zhang G, Mao Y, Min L, Xiang F, Qian D, Zhu X, Song CP. Modulation of Guard Cell Turgor and Drought Tolerance by a Peroxisomal Acetate-Malate Shunt. MOLECULAR PLANT 2018; 11:1278-1291. [PMID: 30130577 DOI: 10.1016/j.molp.2018.07.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 07/13/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
In plants, stomatal movements are tightly controlled by changes in cellular turgor pressure. Carbohydrates produced by glycolysis and the tricarboxylic acid cycle play an important role in regulating turgor pressure. Here, we describe an Arabidopsis mutant, bzu1, isolated in a screen for elevated leaf temperature in response to drought stress, which displays smaller stomatal pores and higher drought resistance than wild-type plants. BZU1 encodes a known acetyl-coenzyme A synthetase, ACN1, which acts in the first step of a metabolic pathway converting acetate to malate in peroxisomes. We showed that BZU1/ACN1-mediated acetate-to-malate conversion provides a shunt that plays an important role in osmoregulation of stomatal turgor. We found that the smaller stomatal pores in the bzu1 mutant are a consequence of reduced accumulation of malate, which acts as an osmoticum and/or a signaling molecule in the control of turgor pressure within guard cells, and these results provided new genetic evidence for malate-regulated stomatal movement. Collectively, our results indicate that a peroxisomal BZU1/ACN1-mediated acetate-malate shunt regulates drought resistance by controlling the turgor pressure of guard cells in Arabidopsis.
Collapse
Affiliation(s)
- Huan Dong
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Ling Bai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yu Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Guozeng Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Yanqing Mao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Lulu Min
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Fuyou Xiang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Dongdong Qian
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Xiaohong Zhu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Chun-Peng Song
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng 475001, China.
| |
Collapse
|
18
|
Cao ZL, Tan TT, Zhang YL, Han L, Hou XY, Ma HY, Cai J. NagR Bt Is a Pleiotropic and Dual Transcriptional Regulator in Bacillus thuringiensis. Front Microbiol 2018; 9:1899. [PMID: 30254611 PMCID: PMC6141813 DOI: 10.3389/fmicb.2018.01899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
NagR, belonging to the GntR/HutC family, is a negative regulator that directly represses the nagP and nagAB genes, which are involved in GlcNAc transport and utilization in Bacillus subtilis. Our previous work confirmed that the chitinase B gene (chiB) of Bacillus thuringiensis strain Bti75 is also negatively controlled by YvoABt, the ortholog of NagR from B. subtilis. In this work, we investigated its regulatory network in Bti75 and found that YvoABt is an N-acetylglucosamine utilization regulator primarily involved in GlcNAc catabolism; therefore YvoABt is renamed as NagRBt. The RNA-seq data revealed that 27 genes were upregulated and 14 genes were downregulated in the ΔnagR mutant compared with the wild-type strain. The regulon (exponential phase) was characterized by RNA-seq, bioinformatics software, electrophoretic mobility shift assays, and quantitative real-time reverse transcription PCR. In the Bti75 genome, 19 genes that were directly regulated and 30 genes that were indirectly regulated by NagRBt were identified. We compiled in silico, in vitro, and in vivo evidence that NagRBt behaves as a repressor and activator to directly or indirectly influence major biological processes involved in amino sugar metabolism, nucleotide metabolism, fatty acid metabolism, phosphotransferase system, and the Embden-Meyerhof-Parnas pathway.
Collapse
Affiliation(s)
- Zhang-Lei Cao
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tong-Tong Tan
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yan-Li Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Lu Han
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Yue Hou
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Hui-Yong Ma
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China.,Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China
| |
Collapse
|
19
|
Abstract
2017 marks the 60th anniversary of Krebs’ seminal paper on the glyoxylate shunt (and coincidentally, also the 80th anniversary of his discovery of the citric acid cycle). Sixty years on, we have witnessed substantial developments in our understanding of how flux is partitioned between the glyoxylate shunt and the oxidative decarboxylation steps of the citric acid cycle. The last decade has shown us that the beautifully elegant textbook mechanism that regulates carbon flux through the shunt in E. coli is an oversimplification of the situation in many other bacteria. The aim of this review is to assess how this new knowledge is impacting our understanding of flux control at the TCA cycle/glyoxylate shunt branch point in a wider range of genera, and to summarize recent findings implicating a role for the glyoxylate shunt in cellular functions other than metabolism.
Collapse
Affiliation(s)
- Stephen K. Dolan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
| |
Collapse
|
20
|
Takeo M, Kimura K, Mayilraj S, Inoue T, Tada S, Miyamoto K, Kashiwa M, Ikemoto K, Baranwal P, Kato D, Negoro S. Biosynthetic Pathway and Genes of Chitin/Chitosan-Like Bioflocculant in the Genus Citrobacter. Polymers (Basel) 2018; 10:polym10030237. [PMID: 30966272 PMCID: PMC6414854 DOI: 10.3390/polym10030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
Chitin/chitosan, one of the most abundant polysaccharides in nature, is industrially produced as a powder or flake form from the exoskeletons of crustaceans such as crabs and shrimps. Intriguingly, many bacterial strains in the genus Citrobacter secrete a soluble chitin/chitosan-like polysaccharide into the culture medium during growth in acetate. Because this polysaccharide shows strong flocculation activity for suspended solids in water, it can be used as a bioflocculant (BF). The BF synthetic pathway of C. freundii IFO 13545 is expected from known bacterial metabolic pathways to be as follows: acetate is metabolized in the TCA cycle and the glyoxylate shunt via acetyl-CoA. Next, fructose 6-phosphate is generated from the intermediates of the TCA cycle through gluconeogenesis and enters into the hexosamine synthetic pathway to form UDP-N-acetylglucosamine, which is used as a direct precursor to extend the BF polysaccharide chain. We conducted the draft genome sequencing of IFO 13545 and identified all of the candidate genes corresponding to the enzymes in this pathway in the 5420-kb genome sequence. Disruption of the genes encoding acetyl-CoA synthetase and isocitrate lyase by homologous recombination resulted in little or no growth on acetate, indicating that the cell growth depends on acetate assimilation via the glyoxylate shunt. Disruption of the gene encoding glucosamine 6-phosphate synthase, a key enzyme for the hexosamine synthetic pathway, caused a significant decrease in flocculation activity, demonstrating that this pathway is primarily used for the BF biosynthesis. A gene cluster necessary for the polymerization and secretion of BF, named bfpABCD, was also identified for the first time. In addition, quantitative RT-PCR analysis of several key genes in the expected pathway was conducted to know their expression in acetate assimilation and BF biosynthesis. Based on the data obtained in this study, an overview of the BF synthetic pathway is discussed.
Collapse
Affiliation(s)
- Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kazuyuki Kimura
- Hyogo Analysis Center Co., Ltd., 4-10-8 Seimondori, Hirohata, Himeji, Hyogo 671-1116, Japan.
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh-160 036, India.
| | - Takuya Inoue
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Shohei Tada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kouki Miyamoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Masami Kashiwa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Keishi Ikemoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Priyanka Baranwal
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Daiichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima 890-8580, Japan.
| | - Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| |
Collapse
|
21
|
Sarkhel R, Rajan P, Gupta AK, Kumawat M, Agarwal P, Shome A, Puii L, Mahawar M. Methionine sulfoxide reductase A of Salmonella Typhimurium interacts with several proteins and abets in its colonization in the chicken. Biochim Biophys Acta Gen Subj 2017; 1861:3238-3245. [DOI: 10.1016/j.bbagen.2017.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 11/25/2022]
|
22
|
Hong CY, Ryu SH, Jeong H, Lee SS, Kim M, Choi IG. Phanerochaete chrysosporium Multienzyme Catabolic System for in Vivo Modification of Synthetic Lignin to Succinic Acid. ACS Chem Biol 2017; 12:1749-1759. [PMID: 28463479 DOI: 10.1021/acschembio.7b00046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Whole cells of the basidiomycete fungus Phanerochaete chrysosporium (ATCC 20696) were applied to induce the biomodification of lignin in an in vivo system. Our results indicated that P. chrysosporium has a catabolic system that induces characteristic biomodifications of synthetic lignin through a series of redox reactions, leading not only to the degradation of lignin but also to its polymerization. The reducing agents ascorbic acid and α-tocopherol were used to stabilize the free radicals generated from the ligninolytic process. The application of P. chrysosporium in combination with reducing agents produced aromatic compounds and succinic acid as well as degraded lignin polymers. P. chrysosporium selectively catalyzed the conversion of lignin to succinic acid, which has an economic value. A transcriptomic analysis of P. chrysosporium suggested that the bond cleavage of synthetic lignin was caused by numerous enzymes, including extracellular enzymes such as lignin peroxidase and manganese peroxidase, and that the aromatic compounds released were metabolized in both the short-cut and classical tricarboxylic acid cycles of P. chrysosporium. In conclusion, P. chrysosporium is suitable as a biocatalyst for lignin degradation to produce a value-added product.
Collapse
Affiliation(s)
- Chang-Young Hong
- Division of Wood Chemistry & Microbiology, Department of Forest Products, National Institute of Forest Science, Seoul, Republic of Korea
| | - Sun-Hwa Ryu
- Division of Wood Chemistry & Microbiology, Department of Forest Products, National Institute of Forest Science, Seoul, Republic of Korea
| | - Hanseob Jeong
- Division of Wood Chemistry & Microbiology, Department of Forest Products, National Institute of Forest Science, Seoul, Republic of Korea
| | - Sung-Suk Lee
- Division of Wood Chemistry & Microbiology, Department of Forest Products, National Institute of Forest Science, Seoul, Republic of Korea
| | - Myungkil Kim
- Division of Wood Chemistry & Microbiology, Department of Forest Products, National Institute of Forest Science, Seoul, Republic of Korea
| | - In-Gyu Choi
- Department
of Forest Sciences, Seoul National University, Seoul, Republic of Korea
- Research
Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Institutes
of Green Bio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea
| |
Collapse
|
23
|
Campilongo R, Fung RKY, Little RH, Grenga L, Trampari E, Pepe S, Chandra G, Stevenson CEM, Roncarati D, Malone JG. One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet 2017; 13:e1006839. [PMID: 28658302 PMCID: PMC5489143 DOI: 10.1371/journal.pgen.1006839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG, an Entner Doudoroff (ED) pathway intermediate. KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR. RccR inversely controls the glyoxylate shunt, gluconeogenesis and pyruvate metabolism, suppressing the first two pathways as pyruvate metabolism genes are expressed, and vice versa. This complex regulation is enabled by two distinct RccR-binding consensus sequences in the RccR regulon promoters. KDPG binding simultaneously increases RccR affinity for the glyoxylate shunt and gluconeogenesis promoters, and releases repression of pyruvate metabolism. This elegant two-regulator circuit allows Pseudomonas to rapidly respond to carbon source availability by sensing a single key intermediate, KDPG.
Collapse
Affiliation(s)
- Rosaria Campilongo
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- Istituto Pasteur- Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘C. Darwin”, Sapienza Universita`di Roma, Roma, Italy
| | - Rowena K. Y. Fung
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Richard H. Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Eleftheria Trampari
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Simona Pepe
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Davide Roncarati
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
| |
Collapse
|
24
|
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean. mSphere 2017; 2:mSphere00359-16. [PMID: 28261669 PMCID: PMC5332604 DOI: 10.1128/msphere.00359-16] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/02/2017] [Indexed: 11/27/2022] Open
Abstract
Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes. Metagenomics has revealed the existence of numerous uncharacterized viral lineages, which are referred to as viral “dark matter.” However, our knowledge regarding viral genomes is biased toward culturable viruses. In this study, we analyzed 1,600 (1,352 nonredundant) complete double-stranded DNA viral genomes (10 to 211 kb) assembled from 52 marine viromes. Together with 244 previously reported uncultured viral genomes, a genome-wide comparison delineated 617 genus-level operational taxonomic units (OTUs) for these environmental viral genomes (EVGs). Of these, 600 OTUs contained no representatives from known viruses, thus putatively corresponding to novel viral genera. Predicted hosts of the EVGs included major groups of marine prokaryotes, such as marine group II Euryarchaeota and SAR86, from which no viruses have been isolated to date, as well as Flavobacteriaceae and SAR116. Our analysis indicates that marine cyanophages are already well represented in genome databases and that one of the EVGs likely represents a new cyanophage lineage. Several EVGs encode many enzymes that appear to function for an efficient utilization of iron-sulfur clusters or to enhance host survival. This suggests that there is a selection pressure on these marine viruses to accumulate genes for specific viral propagation strategies. Finally, we revealed that EVGs contribute to a 4-fold increase in the recruitment of photic-zone viromes compared with the use of current reference viral genomes. IMPORTANCE Viruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds of putative novel viral genera. Predicted hosts include dominant groups of marine bacteria and archaea with no isolated viruses to date. Some of the viral genomes encode many functionally related enzymes, suggesting a strong selection pressure on these marine viruses to control cellular metabolisms by accumulating genes.
Collapse
|
25
|
Lethal Consequences of Overcoming Metabolic Restrictions Imposed on a Cooperative Bacterial Population. mBio 2017; 8:mBio.00042-17. [PMID: 28246357 PMCID: PMC5347341 DOI: 10.1128/mbio.00042-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Quorum sensing (QS) controls cooperative activities in many Proteobacteria. In some species, QS-dependent specific metabolism contributes to the stability of the cooperation. However, the mechanism by which QS and metabolic networks have coevolved to support stable public good cooperation and maintenance of the cooperative group remains unknown. Here we explored the underlying mechanisms of QS-controlled central metabolism in the evolutionary aspects of cooperation. In Burkholderia glumae, the QS-dependent glyoxylate cycle plays an important role in cooperativity. A bifunctional QS-dependent transcriptional regulator, QsmR, rewired central metabolism to utilize the glyoxylate cycle rather than the tricarboxylic acid cycle. Defects in the glyoxylate cycle caused metabolic imbalance and triggered high expression of the stress-responsive chaperonin GroEL. High-level expression of GroEL in glyoxylate cycle mutants interfered with the biosynthesis of a public resource, oxalate, by physically interrupting the oxalate biosynthetic enzyme ObcA. Under such destabilized cooperativity conditions, spontaneous mutations in the qsmR gene in glyoxylate cycle mutants occurred to relieve metabolic stresses, but these mutants lost QsmR-mediated pleiotropy. Overcoming the metabolic restrictions imposed on the population of cooperators among glyoxylate cycle mutants resulted in the occurrence and selection of spontaneous qsmR mutants despite the loss of other important functions. These results provide insight into how QS bacteria have evolved to maintain stable cooperation via QS-mediated metabolic coordination. We address how quorum sensing (QS) has coevolved with metabolic networks to maintain bacterial sociality. We found that QS-mediated metabolic rewiring is critical for sustainable bacterial cooperation in Burkholderia glumae. The loss of the glyoxylate cycle triggered the expression of the stress-responsive molecular chaperonin GroEL. Excessive biosynthesis of GroEL physically hampered biosynthesis of a public good, oxalate. This is one good example of how molecular chaperones play critical roles in bacterial cooperation. In addition, we showed that metabolic restrictions in the glyoxylate cycle acted as a selection pressure on metabolic networks; there were spontaneous mutations in the qsmR gene to relieve such stresses. However, the presence of spontaneous qsmR mutants had tragic consequences for a cooperative population of B. glumae due to failure of qsmR-dependent activation of public good biosynthesis. These results provide a good example of a bacterial strategy for robust cooperation via QS-mediated metabolic rewiring.
Collapse
|
26
|
Adi PJ, Yellapu NK, Matcha B. Modeling, molecular docking, probing catalytic binding mode of acetyl-CoA malate synthase G in Brucella melitensis 16M. Biochem Biophys Rep 2016; 8:192-199. [PMID: 28955956 PMCID: PMC5613768 DOI: 10.1016/j.bbrep.2016.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 10/29/2022] Open
Abstract
There are enormous evidences and previous reports standpoint that the enzyme of glyoxylate pathway malate synthase G (MSG) is a potential virulence factor in several pathogenic organisms, including Brucella melitensis 16M. Where the lack of crystal structures for best candidate proteins like MSG of B. melitensis 16M creates big lacuna to understand the molecular pathogenesis of brucellosis. In the present study, we have constructed a 3-D structure of MSG of Brucella melitensis 16M in MODELLER with the help of crystal structure of Mycobacterium tuberculosis malate synthase (PDB ID: 2GQ3) as template. The stereo chemical quality of the restrained model was evaluated by SAVES server; remarkably we identified the catalytic functional core domain located at 4th cleft with conserved catalytic amino acids, start at ILE 59 to VAL 586 manifest the function of the protein. Furthermore, virtual screening and docking results reveals that best leadmolecules binds at the core domain pocket of MSG catalytic residues and these ligand leads could be the best prospective inhibitors to treat brucellosis.
Collapse
Affiliation(s)
- Pradeepkiran Jangampalli Adi
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, Andhra Pradesh, India
| | - Nanda Kumar Yellapu
- Biomedical Informatics Centre, Vector Control Research Centre, Puducherry 605006, India
| | - Bhaskar Matcha
- Division of Animal Biotechnology, Department of Zoology, Sri Venkateswara University, Tirupati 517502, Andhra Pradesh, India
| |
Collapse
|
27
|
Yin Y, Li S, Gao Y, Tong L, Zheng J, Jia Z, Jiang G, Wei Q. Loopβ3αC plays an important role in the structure and function of isocitrate dehydrogenase kinase/phosphatase. FEBS Lett 2016; 590:3144-54. [PMID: 27528271 DOI: 10.1002/1873-3468.12355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/02/2016] [Accepted: 08/08/2016] [Indexed: 11/08/2022]
Abstract
This work aims to investigate the role of the loopβ3αC amino acids in the structure and function of isocitrate dehydrogenase kinase/phosphatase (AceK). The results demonstrate that the precise configuration of loopβ3αC is very important for AceK structure and function: structural changes alter the affinity of the enzyme for the isocitrate dehydrogenase (ICDH), which modifies enzyme activity. Intriguingly, D340 is significant for the retention of kinase and phosphatase activities, for the conformational stability of AceK and for binding ICDH. The deletion Δ341-345 increases enzyme activity by increasing the maximum velocity and affinity for ICDH. The β3αC loop is thus critical for the structure and function of AceK.
Collapse
Affiliation(s)
- Yanxia Yin
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Shanze Li
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Yadan Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Li Tong
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, China
| | - Zongchao Jia
- College of Chemistry, Beijing Normal University, China
| | - Guohua Jiang
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China.
| | - Qun Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Beijing Key Laboratory, China.
| |
Collapse
|
28
|
Erkut C, Gade VR, Laxman S, Kurzchalia TV. The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast. eLife 2016; 5. [PMID: 27090086 PMCID: PMC4880444 DOI: 10.7554/elife.13614] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/18/2016] [Indexed: 02/04/2023] Open
Abstract
Many organisms, including species from all kingdoms of life, can survive desiccation by entering a state with no detectable metabolism. To survive, C. elegans dauer larvae and stationary phase S. cerevisiae require elevated amounts of the disaccharide trehalose. We found that dauer larvae and stationary phase yeast switched into a gluconeogenic mode in which metabolism was reoriented toward production of sugars from non-carbohydrate sources. This mode depended on full activity of the glyoxylate shunt (GS), which enables synthesis of trehalose from acetate. The GS was especially critical during preparation of worms for harsh desiccation (preconditioning) and during the entry of yeast into stationary phase. Loss of the GS dramatically decreased desiccation tolerance in both organisms. Our results reveal a novel physiological role for the GS and elucidate a conserved metabolic rewiring that confers desiccation tolerance on organisms as diverse as worm and yeast.
Collapse
Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Vamshidhar R Gade
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sunil Laxman
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | | |
Collapse
|
29
|
Chaudhary N, Tøndel K, Bhatnagar R, Martins dos Santos VAP, Puchałka J. Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling. MOLECULAR BIOSYSTEMS 2016; 12:994-1005. [DOI: 10.1039/c5mb00457h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sampling of the optimal flux space using modified LHS gives a more uniform coverage than Monte-Carlo Sampling. Analysis of the flux data shows that majority of variation in the flux distribution pattern within the space arises due to the presence of few alternate pathways.
Collapse
Affiliation(s)
- Neha Chaudhary
- Laboratory of Genetic Engineering and Molecular Biology
- School of Biotechnology
- Jawaharlal Nehru University
- New Delhi -110067
- India
| | - Kristin Tøndel
- Department of Mathematical Sciences and Technology
- Norwegian University of Life Sciences
- 1432 Ås
- Norway
| | - Rakesh Bhatnagar
- Laboratory of Genetic Engineering and Molecular Biology
- School of Biotechnology
- Jawaharlal Nehru University
- New Delhi -110067
- India
| | - Vítor A. P. Martins dos Santos
- Chair of Systems and Synthetic Biology
- Wageningen University Dreijenplein 10
- 6703 HB Wageningen
- The Netherlands
- Synthetic and Systems Biology Research Group
| | - Jacek Puchałka
- Synthetic and Systems Biology Research Group
- Helmholtz Centre for Infection Research
- Braunschweig
- Germany
| |
Collapse
|
30
|
Zhao L, Zhang H, Wang L, Chen H, Chen YQ, Chen W, Song Y. (13)C-metabolic flux analysis of lipid accumulation in the oleaginous fungus Mucor circinelloides. BIORESOURCE TECHNOLOGY 2015; 197:23-29. [PMID: 26318243 DOI: 10.1016/j.biortech.2015.08.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 06/04/2023]
Abstract
The oleaginous fungus Mucor circinelloides is of industrial interest because it can produce high levels of polyunsaturated fatty acid γ-linolenic acid. M. circinelloides CBS 277.49 is able to accumulate less than 15% of cell dry weight as lipids, while M. circinelloides WJ11 can accumulate lipid up to 36%. In order to better understand the mechanisms behind the differential lipid accumulation in these two strains, tracer experiments with (13)C-glucose were performed with the growth of M. circinelloides and subsequent gas chromatography-mass spectrometric detection of (13)C-patterns in proteinogenic amino acids was carried out to identify the metabolic network topology and estimate intracellular fluxes. Our results showed that the high oleaginous strain WJ11 had higher flux of pentose phosphate pathway and malic enzyme, lower flux in tricarboxylic acid cycle, higher flux in glyoxylate cycle and ATP: citrate lyase, together, it might provide more NADPH and substrate acetyl-CoA for fatty acid synthesis.
Collapse
Affiliation(s)
- Lina Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Huaiyuan Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Liping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Synergistic Innovation Center for Food Safety and Nutrition, Wuxi 214122, PR China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Synergistic Innovation Center for Food Safety and Nutrition, Wuxi 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; Synergistic Innovation Center for Food Safety and Nutrition, Wuxi 214122, PR China
| | - Yuanda Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China.
| |
Collapse
|
31
|
Crousilles A, Maunders E, Bartlett S, Fan C, Ukor EF, Abdelhamid Y, Baker Y, Floto A, Spring DR, Welch M. Which microbial factors really are important in Pseudomonas aeruginosa infections? Future Microbiol 2015; 10:1825-36. [DOI: 10.2217/fmb.15.100] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Over the last two decades, tens of millions of dollars have been invested in understanding virulence in the human pathogen, Pseudomonas aeruginosa. However, the top ‘hits’ obtained in a recent TnSeq analysis aimed at identifying those genes that are conditionally essential for infection did not include most of the known virulence factors identified in these earlier studies. Instead, it seems that P. aeruginosa faces metabolic challenges in vivo, and unless it can overcome these, it fails to thrive and is cleared from the host. In this review, we look at the kinds of metabolic pathways that the pathogen seems to find essential, and comment on how this knowledge might be therapeutically exploited.
Collapse
Affiliation(s)
- Audrey Crousilles
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Eve Maunders
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Sean Bartlett
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Catherine Fan
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Emem-Fong Ukor
- Department of Respiratory Medicine, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Yassmin Abdelhamid
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Ysobel Baker
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Andres Floto
- Department of Respiratory Medicine, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - David R Spring
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Martin Welch
- Department of Biochemistry (Hopkins Building), Tennis Court Road, Cambridge, CB2 1QW, UK
| |
Collapse
|
32
|
Rajput MS, Iyer B, Pandya M, Jog R, G NK, Rajkumar S. Derepression of Mineral Phosphate Solubilization Phenotype by Insertional Inactivation of iclR in Klebsiella pneumoniae. PLoS One 2015; 10:e0138235. [PMID: 26381651 PMCID: PMC4575152 DOI: 10.1371/journal.pone.0138235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/26/2015] [Indexed: 11/24/2022] Open
Abstract
The mode of succinate mediated repression of mineral phosphate solubilization and the role of repressor in suppressing phosphate solubilization phenotype of two free-living nitrogen fixing Klebsiella pneumoniae strains was studied. Organic acid mediated mineral phosphate solubilization phenotype of oxalic acid producing Klebsiella pneumoniae SM6 and SM11 were transcriptionally repressed by IclR in presence of succinate as carbon source. Oxalic acid production and expression of genes of the glyoxylate shunt (aceBAK) was found only in glucose but not in succinate- and glucose+succinate-grown cells. IclR, repressor of aceBAK operon, was inactivated using an allelic exchange system resulting in derepressed mineral phosphate solubilization phenotype through constitutive expression of the glyoxylate shunt. Insertional inactivation of iclR resulted in increased activity of the glyoxylate shunt enzymes even in succinate-grown cells. An augmented phosphate solubilization up to 54 and 59% soluble phosphate release was attained in glucose+succinate-grown SM6Δ and SM11Δ strains respectively, compared to glucose-grown cells, whereas phosphate solubilization was absent or negligible in wildtype cells grown in glucose+succinate. Both wildtype and iclR deletion strains showed similar indole-3-acetic acid production. Wheat seeds inoculated with wildtype SM6 and SM11 improved both root and shoot length by 1.2 fold. However, iclR deletion SM6Δ and SM11Δ strains increased root and shoot length by 1.5 and 1.4 folds, respectively, compared to uninoculated controls. The repressor inactivated phosphate solubilizers better served the purpose of constitutive phosphate solubilization in pot experiments, where presence of other carbon sources (e.g., succinate) might repress mineral phosphate solubilization phenotype of wildtype strains.
Collapse
Affiliation(s)
| | - Bhagya Iyer
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Maharshi Pandya
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Rahul Jog
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
- Environmental Molecular Biology Laboratory, Division of Biosphere, Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Naresh Kumar G
- Molecular Microbial Biochemistry Laboratory, Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Shalini Rajkumar
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| |
Collapse
|
33
|
Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions. J Proteomics 2015; 126:24-33. [DOI: 10.1016/j.jprot.2015.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/13/2015] [Accepted: 05/20/2015] [Indexed: 12/25/2022]
|
34
|
Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
Collapse
Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| |
Collapse
|
35
|
Oxalobacter formigenes Colonization and Oxalate Dynamics in a Mouse Model. Appl Environ Microbiol 2015; 81:5048-54. [PMID: 25979889 DOI: 10.1128/aem.01313-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/12/2015] [Indexed: 11/20/2022] Open
Abstract
Animal and human studies have provided compelling evidence that colonization of the intestine with Oxalobacter formigenes reduces urinary oxalate excretion and lowers the risk of forming calcium oxalate kidney stones. The mechanism providing protection appears to be related to the unique ability of O. formigenes to rely on oxalate as a major source of carbon and energy for growth. However, much is not known about the factors that influence colonization and host-bacterium interactions. We have colonized mice with O. formigenes OxCC13 and systematically investigated the impacts of diets with different levels of calcium and oxalate on O. formigenes intestinal densities and urinary and intestinal oxalate levels. Measurement of intestinal oxalate levels in mice colonized or not colonized with O. formigenes demonstrated the highly efficient degradation of soluble oxalate by O. formigenes relative to other microbiota. The ratio of calcium to oxalate in diets was important in determining colonization densities and conditions where urinary oxalate and fecal oxalate excretion were modified, and the results were consistent with those from studies we have performed with colonized and noncolonized humans. The use of low-oxalate purified diets showed that 80% of animals retained O. formigenes colonization after a 1-week dietary oxalate deprivation. Animals not colonized with O. formigenes excreted two times more oxalate in feces than they had ingested. This nondietary source of oxalate may play an important role in the survival of O. formigenes during periods of dietary oxalate deprivation. These studies suggest that the mouse will be a useful model to further characterize interactions between O. formigenes and the host and factors that impact colonization.
Collapse
|
36
|
Cappelletti M, Presentato A, Milazzo G, Turner RJ, Fedi S, Frascari D, Zannoni D. Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes. Front Microbiol 2015; 6:393. [PMID: 26029173 PMCID: PMC4428276 DOI: 10.3389/fmicb.2015.00393] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/16/2015] [Indexed: 11/16/2022] Open
Abstract
Rhodococcus sp. strain BCP1 was initially isolated for its ability to grow on gaseous n-alkanes, which act as inducers for the co-metabolic degradation of low-chlorinated compounds. Here, both molecular and metabolic features of BCP1 cells grown on gaseous and short-chain n-alkanes (up to n-heptane) were examined in detail. We show that propane metabolism generated terminal and sub-terminal oxidation products such as 1- and 2-propanol, whereas 1-butanol was the only terminal oxidation product detected from n-butane metabolism. Two gene clusters, prmABCD and smoABCD—coding for Soluble Di-Iron Monooxgenases (SDIMOs) involved in gaseous n-alkanes oxidation—were detected in the BCP1 genome. By means of Reverse Transcriptase-quantitative PCR (RT-qPCR) analysis, a set of substrates inducing the expression of the sdimo genes in BCP1 were assessed as well as their transcriptional repression in the presence of sugars, organic acids, or during the cell growth on rich medium (Luria–Bertani broth). The transcriptional start sites of both the sdimo gene clusters were identified by means of primer extension experiments. Finally, proteomic studies revealed changes in the protein pattern induced by growth on gaseous- (n-butane) and/or liquid (n-hexane) short-chain n-alkanes as compared to growth on succinate. Among the differently expressed protein spots, two chaperonins and an isocytrate lyase were identified along with oxidoreductases involved in oxidation reactions downstream of the initial monooxygenase reaction step.
Collapse
Affiliation(s)
- Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | | | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary Calgary, Alberta, Canada
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Dario Frascari
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| |
Collapse
|
37
|
Dhamankar H, Tarasova Y, Martin CH, Prather KL. Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) and 3,4-dihydroxybutyric acid (3,4-DHBA) as value-added chemicals from glucose as a sole carbon source. Metab Eng 2014; 25:72-81. [DOI: 10.1016/j.ymben.2014.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 04/18/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
|
38
|
Liu J, Wang QL, Chang Q, Han LN, Pei GL, Xue YQ, Jia LM, Zhang K, Duan YY, Kang ZS. Isocitrate lyase is required for urediniospore germination of Puccinia striiformis f. sp. tritici. Mol Biol Rep 2014; 41:7797-806. [DOI: 10.1007/s11033-014-3672-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 07/31/2014] [Indexed: 12/22/2022]
|
39
|
Hayashi T, Matsuzaki W, Takada Y. Characterization of chimeric and mutated isocitrate lyases of a mesophilic nitrogen-fixing bacterium, Azotobacter vinelandii, and a psychrophilic bacterium, Colwellia maris. Biosci Biotechnol Biochem 2014; 78:195-201. [DOI: 10.1080/09168451.2014.882744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Chimeric enzymes between a cold-adapted isocitrate lyase (ICL) of a psychrophilic bacterium, Colwellia maris, (CmICL) and a mesophilic ICL of a nitrogen-fixing bacterium, Azotobacter vinelandii, (AvICL) were constructed by dividing the ICL genes into four regions of almost equal length and exchanging regions in various combinations. The chimeric ICL, which was replaced C-terminal region 4 of AvICL by the corresponding region of CmICL, showed much lower specific activity and lower optimum temperature and thermostability for activity than wild-type AvICL, indicating that region 4 is involved in its thermal properties. Furthermore, mutual substitution between the Met501 residue in region 4 of CmICL and the corresponding Ile504 residue of AvICL influenced the temperature dependence of their activities, suggesting that these amino acid residues are important to the respective mesophilic and cold-adapted properties of AvICL and CmICL.
Collapse
Affiliation(s)
- Tomofumi Hayashi
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Wataru Matsuzaki
- Division of Biology, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, Japan
| | - Yasuhiro Takada
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
40
|
Strack RL, Song W, Jaffrey SR. Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. Nat Protoc 2013; 9:146-55. [PMID: 24356773 DOI: 10.1038/nprot.2014.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically encoded fluorescent sensors can be valuable tools for studying the abundance and flux of molecules in living cells. We recently developed a novel class of sensors composed of RNAs that can be used to detect diverse small molecules and untagged proteins. These sensors are based on Spinach, an RNA mimic of GFP, and they have successfully been used to image several metabolites and proteins in living bacteria. Here we discuss the generation and optimization of these Spinach-based sensors, which, unlike most currently available genetically encoded reporters, can be readily generated to any target of interest. We also provide a detailed protocol for imaging ADP dynamics in living Escherichia coli after a change from glucose-containing medium to other carbon sources. The entire procedure typically takes ∼4 d including bacteria transformation and image analysis. The majority of this protocol is applicable to sensing other metabolites and proteins in living bacteria.
Collapse
Affiliation(s)
- Rita L Strack
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York, USA
| |
Collapse
|
41
|
Abstract
In the present paper we describe a new carboxylic acid transporter in Escherichia coli encoded by the gene yaaH. In contrast to what had been described for other YaaH family members, the E. coli transporter is highly specific for acetic acid (a monocarboxylate) and for succinic acid (a dicarboxylate), with affinity constants at pH 6.0 of 1.24±0.13 mM for acetic acid and 1.18±0.10 mM for succinic acid. In glucose-grown cells the ΔyaaH mutant is compromised for the uptake of both labelled acetic and succinic acids. YaaH, together with ActP, described previously as an acetate transporter, affect the use of acetic acid as sole carbon and energy source. Both genes have to be deleted simultaneously to abolish acetate transport. The uptake of acetate and succinate was restored when yaaH was expressed in trans in ΔyaaH ΔactP cells. We also demonstrate the critical role of YaaH amino acid residues Leu131 and Ala164 on the enhanced ability to transport lactate. Owing to its functional role in acetate and succinate uptake we propose its assignment as SatP: the Succinate–Acetate Transporter Protein.
Collapse
|
42
|
Mainguet SE, Gronenberg LS, Wong SS, Liao JC. A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli. Metab Eng 2013; 19:116-27. [PMID: 23938029 DOI: 10.1016/j.ymben.2013.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/11/2013] [Accepted: 06/21/2013] [Indexed: 11/25/2022]
Abstract
Most central metabolic pathways such as glycolysis, fatty acid synthesis, and the TCA cycle have complementary pathways that run in the reverse direction to allow flexible storage and utilization of resources. However, the glyoxylate shunt, which allows for the synthesis of four-carbon TCA cycle intermediates from acetyl-CoA, has not been found to be reversible to date. As a result, glucose can only be converted to acetyl-CoA via the decarboxylation of the three-carbon molecule pyruvate in heterotrophs. A reverse glyoxylate shunt (rGS) could be extended into a pathway that converts C4 carboxylates into two molecules of acetyl-CoA without loss of CO2. Here, as a proof of concept, we engineered in Escherichia coli such a pathway to convert malate and succinate to oxaloacetate and two molecules of acetyl-CoA. We introduced ATP-coupled heterologous enzymes at the thermodynamically unfavorable steps to drive the pathway in the desired direction. This synthetic pathway in essence reverses the glyoxylate shunt at the expense of ATP. When integrated with central metabolism, this pathway has the potential to increase the carbon yield of acetate and biofuels from many carbon sources in heterotrophic microorganisms, and could be the basis of novel carbon fixation cycles.
Collapse
Affiliation(s)
- Samuel E Mainguet
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | | | | | | |
Collapse
|
43
|
A platform pathway for production of 3-hydroxyacids provides a biosynthetic route to 3-hydroxy-γ-butyrolactone. Nat Commun 2013; 4:1414. [DOI: 10.1038/ncomms2418] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 12/19/2012] [Indexed: 11/08/2022] Open
|
44
|
Zheng J, Yates SP, Jia Z. Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK. Philos Trans R Soc Lond B Biol Sci 2012; 367:2656-68. [PMID: 22889914 DOI: 10.1098/rstb.2011.0426] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.
Collapse
Affiliation(s)
- Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | | | | |
Collapse
|
45
|
Rudi K, Sekelja M. High or low correlation between co-occuring gene clusters and 16S rRNA gene phylogeny. FEMS Microbiol Lett 2012; 339:23-9. [DOI: 10.1111/1574-6968.12042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/01/2012] [Accepted: 11/01/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Knut Rudi
- Department of Chemistry, Biotechnology and Food Science; Norwegian University for Life Sciences; Ås; Norway
| | | |
Collapse
|
46
|
Maeda T, Wachi M. 3' Untranslated region-dependent degradation of the aceA mRNA, encoding the glyoxylate cycle enzyme isocitrate lyase, by RNase E/G in Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:8753-61. [PMID: 23042181 PMCID: PMC3502937 DOI: 10.1128/aem.02304-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/02/2012] [Indexed: 11/20/2022] Open
Abstract
We previously reported that the Corynebacterium glutamicum RNase E/G encoded by the rneG gene (NCgl2281) is required for the 5' maturation of 5S rRNA. In the search for the intracellular target RNAs of RNase E/G other than the 5S rRNA precursor, we detected that the amount of isocitrate lyase, an enzyme of the glyoxylate cycle, increased in rneG knockout mutant cells grown on sodium acetate as the sole carbon source. Rifampin chase experiments showed that the half-life of the aceA mRNA was about 4 times longer in the rneG knockout mutant than in the wild type. Quantitative real-time PCR analysis also confirmed that the level of aceA mRNA was approximately 3-fold higher in the rneG knockout mutant strain than in the wild type. Such differences were not observed in other mRNAs encoding enzymes involved in acetate metabolism. Analysis by 3' rapid amplification of cDNA ends suggested that RNase E/G cleaves the aceA mRNA at a single-stranded AU-rich region in the 3' untranslated region (3'-UTR). The lacZ fusion assay showed that the 3'-UTR rendered lacZ mRNA RNase E/G dependent. These findings indicate that RNase E/G is a novel regulator of the glyoxylate cycle in C. glutamicum.
Collapse
Affiliation(s)
- Tomoya Maeda
- Department of Bioengineering, Tokyo Institute of Technology, Yokohama, Japan
| | | |
Collapse
|
47
|
Thaker TM, Tanabe M, Fowler ML, Preininger AM, Ingram-Smith C, Smith KS, Iverson TM. Crystal structures of acetate kinases from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans. J Struct Biol 2012; 181:185-9. [PMID: 23159802 DOI: 10.1016/j.jsb.2012.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Acetate kinases (ACKs) are members of the acetate and sugar kinase/hsp70/actin (ASKHA) superfamily and catalyze the reversible phosphorylation of acetate, with ADP/ATP the most common phosphoryl acceptor/donor. While prokaryotic ACKs have been the subject of extensive biochemical and structural characterization, there is a comparative paucity of information on eukaryotic ACKs, and prior to this report, no structure of an ACK of eukaryotic origin was available. We determined the structures of ACKs from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans. Each active site is located at an interdomain interface, and the acetate and phosphate binding pockets display sequence and structural conservation with their prokaryotic counterparts. Interestingly, the E. histolytica ACK has previously been shown to be pyrophosphate (PP(i))-dependent, and is the first ACK demonstrated to have this property. Examination of its structure demonstrates how subtle amino acid substitutions within the active site have converted cosubstrate specificity from ATP to PP(i) while retaining a similar backbone conformation. Differences in the angle between domains surrounding the active site suggest that interdomain movement may accompany catalysis. Taken together, these structures are consistent with the eukaryotic ACKs following a similar reaction mechanism as is proposed for the prokaryotic homologs.
Collapse
Affiliation(s)
- Tarjani M Thaker
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Repression of oxalic acid-mediated mineral phosphate solubilization in rhizospheric isolates of Klebsiella pneumoniae by succinate. Arch Microbiol 2012; 195:81-8. [PMID: 23124768 DOI: 10.1007/s00203-012-0850-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/17/2012] [Accepted: 10/23/2012] [Indexed: 10/27/2022]
Abstract
Two strains of Klebsiella (SM6 and SM11) were isolated from rhizospheric soil that solubilized mineral phosphate by secretion of oxalic acid from glucose. Activities of enzymes for periplasmic glucose oxidation (glucose dehydrogenase) and glyoxylate shunt (isocitrate lyase and glyoxylate oxidase) responsible for oxalic acid production were estimated. In presence of succinate, phosphate solubilization was completely inhibited, and the enzymes glucose dehydrogenase and glyoxylate oxidase were repressed. Significant activity of isocitrate lyase, the key enzyme for carbon flux through glyoxylate shunt and oxalic acid production during growth on glucose suggested that it could be inducible in nature, and its inhibition by succinate appeared to be similar to catabolite repression.
Collapse
|
49
|
Paige JS, Nguyen-Duc T, Song W, Jaffrey SR. Fluorescence imaging of cellular metabolites with RNA. Science 2012; 335:1194. [PMID: 22403384 DOI: 10.1126/science.1218298] [Citation(s) in RCA: 391] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetically encoded sensors are powerful tools for imaging intracellular metabolites and signaling molecules. However, developing sensors is challenging because they require proteins that undergo conformational changes upon binding the desired target molecule. We describe an approach for generating fluorescent sensors based on Spinach, an RNA sequence that binds and activates the fluorescence of a small-molecule fluorophore. We show that these sensors can detect a variety of different small molecules in vitro and in living cells. These RNAs constitute a versatile approach for fluorescence imaging of small molecules and have the potential to detect essentially any cellular biomolecule.
Collapse
Affiliation(s)
- Jeremy S Paige
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | | | | | | |
Collapse
|
50
|
Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D. Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 2012; 7:e43401. [PMID: 22952675 PMCID: PMC3432047 DOI: 10.1371/journal.pone.0043401] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022] Open
Abstract
We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.
Collapse
Affiliation(s)
- Thomas Ulas
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - S. Alexander Riemer
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Zaparty
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Bettina Siebers
- Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
| |
Collapse
|