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A Manganese-independent Aldolase Enables Staphylococcus aureus To Resist Host-imposed Metal Starvation. mBio 2023; 14:e0322322. [PMID: 36598285 PMCID: PMC9973326 DOI: 10.1128/mbio.03223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The preferred carbon source of Staphylococcus aureus and many other pathogens is glucose, and its consumption is critical during infection. However, glucose utilization increases the cellular demand for manganese, a nutrient sequestered by the host as a defense against invading pathogens. Therefore, bacteria must balance glucose metabolism with the increasing demand that metal-dependent processes, such as glycolysis, impose upon the cell. A critical regulator that enables S. aureus to resist nutritional immunity is the ArlRS two-component system. This work revealed that ArlRS regulates the expression of FdaB, a metal-independent fructose 1,6-bisphosphate aldolase. Further investigation revealed that when S. aureus is metal-starved by the host, FdaB functionally replaces the metal-dependent isozyme FbaA, thereby allowing S. aureus to resist host-imposed metal starvation in culture. Although metal-dependent aldolases are canonically zinc-dependent, this work uncovered that FbaA requires manganese for activity and that FdaB protects S. aureus from manganese starvation. Both FbaA and FdaB contribute to the ability of S. aureus to cause invasive disease in wild-type mice. However, the virulence defect of a strain lacking FdaB was reversed in calprotectin-deficient mice, which have defects in manganese sequestration, indicating that this isozyme contributes to the ability of this pathogen to overcome manganese limitation during infection. Cumulatively, these observations suggest that the expression of the metal-independent aldolase FdaB allows S. aureus to alleviate the increased demand for manganese that glucose consumption imposes, and highlights the cofactor flexibility of even established metalloenzyme families. IMPORTANCE Staphylococcus aureus and other pathogens consume glucose during infection. Glucose utilization increases the demand for transition metals, such as manganese, a nutrient that the host limits as a defense mechanism against invading pathogens. Therefore, pathogenic bacteria must balance glucose and manganese requirements during infection. The two-component system ArlRS is an important regulator that allows S. aureus to adapt to both glucose and manganese starvation. Among the genes regulated by ArlRS is the metal-independent fructose 1,6-bisphosphate aldolase fdaB, which functionally substitutes for the metal-dependent isoenzyme FbaA and enables S. aureus to survive host-imposed manganese starvation. Unexpectedly, and differing from most characterized metal-dependent aldolases, FbaA requires manganese for activity. Cumulatively, these findings reveal a new mechanism for overcoming nutritional immunity as well as the cofactor plasticity of even well-characterized metalloenzyme families.
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Dai Y, Zhang J, Jiang B, Zhang T, Chen J. New strategy for rare sugars biosynthesis: Aldol reactions using dihydroxyacetone phosphate (DHAP)-dependent aldolases. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
Accumulation of phosphorylated intermediates during cellular metabolism can have wide-ranging toxic effects on many organisms, including humans and the pathogens that infect them. These toxicities can be induced by feeding an upstream metabolite (a sugar, for instance) while simultaneously blocking the appropriate metabolic pathway with either a mutation or an enzyme inhibitor. Here, we survey the toxicities that can arise in the metabolism of glucose, galactose, fructose, fructose-asparagine, glycerol, trehalose, maltose, mannose, mannitol, arabinose, and rhamnose. Select enzymes in these metabolic pathways may serve as novel therapeutic targets. Some are conserved broadly among prokaryotes and eukaryotes (e.g., glucose and galactose) and are therefore unlikely to be viable drug targets. However, others are found only in bacteria (e.g., fructose-asparagine, rhamnose, and arabinose), and one is found in fungi but not in humans (trehalose). We discuss what is known about the mechanisms of toxicity and how resistance is achieved in order to identify the prospects and challenges associated with targeted exploitation of these pervasive metabolic vulnerabilities.
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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Kumar J, Chauhan AS, Gupta JA, Rathore AS. Supplementation of critical amino acids improves glycerol and lactose uptake and enhances recombinant protein production in Escherichia coli. Biotechnol J 2021; 16:e2100143. [PMID: 34047499 DOI: 10.1002/biot.202100143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Lactose-based induction strategy in E. coli cultivation has several advantages over IPTG as it is cheap, does not impart metabolic stress to cells, and is non-toxic to cells. However, complexity of lactose as an inducer limits its application in fed-batch cultivation. A mixed glycerol-lactose based induction strategy is generally opted during fed-batch cultivation of E. coli. However, slow growth of E. coli in glycerol and lactose results in slower induction of heterologous protein. MAIN METHODS AND MAJOR RESULTS In this study, initially we have demonstrated supplementation of critical amino acids (AAs) improves uptake rate of glycerol and lactose in wildtype E. coli BL21(DE3) in defined medium. A feeding strategy of mixed glycerol-lactose feed along with supplement of critical AAs enhances recombinant production of pramlintide multimer (rPramlintide). High cell density cultivation of E. coli using mixed glycerol-lactose feed and critical AAs supplement resulted in final cell density of 52.2 ± 0.90 g L-1 and rPramlintide titer of 7.8 g L-1 . RT-qPCR analysis of genes involved in glycerol and lactose metabolism of recombinant culture showed upregulation with AAs supplementation. CONCLUSIONS AND IMPLICATIONS We hypothesize that supplementation of critical AAs serves dual purpose: (i) faster assimilation of carbon sources, and (ii) combating metabolic stress arises due to AAs starvation. The substrate uptake and gene expression profiles demonstrate that AAs addition enhances glycerol and lactose assimilation due to overall improvement in their metabolism governed by global regulators of carbon metabolism.
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Affiliation(s)
- Jashwant Kumar
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Ashish S Chauhan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Jaya A Gupta
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, Delhi, India
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Zhao W, Liu H, Zhang L, Hu Z, Liu J, Hua W, Xu S, Liu J. Genome-Wide Identification and Characterization of FBA Gene Family in Polyploid Crop Brassica napus. Int J Mol Sci 2019; 20:E5749. [PMID: 31731804 PMCID: PMC6888112 DOI: 10.3390/ijms20225749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022] Open
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is a versatile metabolic enzyme involved in multiple important processes of glycolysis, gluconeogenesis, and Calvin cycle. Despite its significance in plant biology, the identity of this gene family in oil crops is lacking. Here, we performed genome-wide identification and characterization of FBAs in an allotetraploid species, oilseed rape Brassica napus. Twenty-two BnaFBA genes were identified and divided into two groups based on integrative analyses of functional domains, phylogenetic relationships, and gene structures. Twelve and ten B. napus FBAs (BnaFBAs) were predicted to be localized in the chloroplast and cytoplasm, respectively. Notably, synteny analysis revealed that Brassica-specific triplication contributed to the expansion of the BnaFBA gene family during the evolution of B. napus. Various cis-acting regulatory elements pertinent to abiotic and biotic stresses, as well as phytohormone responses, were detected. Intriguingly, each of the BnaFBA genes exhibited distinct sequence polymorphisms. Among them, six contained signatures of selection, likely having experienced breeding selection during adaptation and domestication. Importantly, BnaFBAs showed diverse expression patterns at different developmental stages and were preferentially highly expressed in photosynthetic tissues. Our data thus provided the foundation for further elucidating the functional roles of individual BnaFBA and also potential targets for engineering to improve photosynthetic productivity in B. napus.
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Affiliation(s)
- Wei Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Jun Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
| | - Shouming Xu
- Henan key laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China; (W.Z.); (H.L.); (L.Z.); (Z.H.); (J.L.); (W.H.)
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Patipong T, Ngoennet S, Honda M, Hibino T, Waditee-Sirisattha R, Kageyama H. A class I fructose-1,6-bisphosphate aldolase is associated with salt stress tolerance in a halotolerant cyanobacterium Halothece sp. PCC 7418. Arch Biochem Biophys 2019; 672:108059. [PMID: 31356779 DOI: 10.1016/j.abb.2019.07.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022]
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) is a key metabolic enzyme, which is involved in glycolysis, gluconeogenesis and the Calvin cycle. The distinct physiological roles of FBAs in various organisms have been reported; however, in cyanobacteria, the functional characterization of FBAs and investigation of the intracellular dynamics of FBAs largely remains unknown. Here, we utilized a two-step chromatographic technique to identify a class I FBA (CI-FBA), which we named H2846. H2846 was induced by salt stress in the halotolerant cyanobacterium Halothece sp. PCC 7418 (hereafter referred to as Halothece 7418). Phylogenetic analysis showed that H2846-like CI-FBAs existed mainly in cyanobacterial species that inhabit hypersaline environments. Subcellular fractionation revealed that H2846 localized in the cytosolic and periplasmic spaces and size-exclusion chromatography suggested that H2846 formed a homohexamer. The CI-FBA activity of recombinant H2846-mediated cleavage of fructose bisphosphate (FBP) was characterized using a coupled enzymatic assay. This analysis allowed us to determine the Km and Vmax values of recombinant H2846, which were then compared to previously reported Km and Vmax values of several FBAs. Our data suggested that H2846 was likely responsible for the salt stress-induced CI-FBA activity from the total soluble protein extracts derived from Halothece 7418 cells. Moreover, heterologous expression of H2846 but not H2847, a class II FBA (CII-FBA), conferred salt stress tolerance to the salt-sensitive freshwater cyanobacterium, Synechococcus elongatus PCC 7942, which only contains the CII-FBA, S1443. S. elongatus PCC 7942 with a S1443 gene deletion was complemented by H2847 expression, but was not complemented by expression of H2846. Taken together, these results indicate the functional differences between two distinct sets of FBAs in cyanobacteria. H2846 is an active CI-FBA that contributes to the mechanism of salt stress tolerance in Halothece 7418.
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Affiliation(s)
- Tanutcha Patipong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand; Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Siripat Ngoennet
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Masaki Honda
- Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | - Takashi Hibino
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan; Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Aichi, 468-8502, Japan
| | | | - Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya, Aichi, 468-8502, Japan; Department of Chemistry, Faculty of Science and Technology, Meijo University, Nagoya, Aichi, 468-8502, Japan.
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Dadinova LA, Shtykova EV, Konarev PV, Rodina EV, Snalina NE, Vorobyeva NN, Kurilova SA, Nazarova TI, Jeffries CM, Svergun DI. X-Ray Solution Scattering Study of Four Escherichia coli Enzymes Involved in Stationary-Phase Metabolism. PLoS One 2016; 11:e0156105. [PMID: 27227414 PMCID: PMC4881948 DOI: 10.1371/journal.pone.0156105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/08/2016] [Indexed: 11/21/2022] Open
Abstract
The structural analyses of four metabolic enzymes that maintain and regulate the stationary growth phase of Escherichia coli have been performed primarily drawing on the results obtained from solution small angle X-ray scattering (SAXS) and other structural techniques. The proteins are (i) class I fructose-1,6-bisphosphate aldolase (FbaB); (ii) inorganic pyrophosphatase (PPase); (iii) 5-keto-4-deoxyuronate isomerase (KduI); and (iv) glutamate decarboxylase (GadA). The enzyme FbaB, that until now had an unknown structure, is predicted to fold into a TIM-barrel motif that form globular protomers which SAXS experiments show associate into decameric assemblies. In agreement with previously reported crystal structures, PPase forms hexamers in solution that are similar to the previously reported X-ray crystal structure. Both KduI and GadA that are responsible for carbohydrate (pectin) metabolism and acid stress responses, respectively, form polydisperse mixtures consisting of different oligomeric states. Overall the SAXS experiments yield additional insights into shape and organization of these metabolic enzymes and further demonstrate the utility of hybrid methods, i.e., solution SAXS combined with X-ray crystallography, bioinformatics and predictive 3D-structural modeling, as tools to enrich structural studies. The results highlight the structural complexity that the protein components of metabolic networks may adopt which cannot be fully captured using individual structural biology techniques.
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Affiliation(s)
- Liubov A. Dadinova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- M.V. Lomonosov Moscow State University, Physics Department, Moscow, Russia
| | - Eleonora V. Shtykova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Rodina
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Natalia E. Snalina
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Natalia N. Vorobyeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- M.V. Lomonosov Moscow State University, Chemistry Department, Moscow, Russia
| | - Svetlana A. Kurilova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tatyana I. Nazarova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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Fructose-1,6-bisphosphate aldolase (FBA)-a conserved glycolytic enzyme with virulence functions in bacteria: 'ill met by moonlight'. Biochem Soc Trans 2015; 42:1792-5. [PMID: 25399608 DOI: 10.1042/bst20140203] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Moonlighting proteins constitute an intriguing class of multifunctional proteins. Metabolic enzymes and chaperones, which are often highly conserved proteins in bacteria, archaea and eukaryotic organisms, are among the most commonly recognized examples of moonlighting proteins. Fructose-1,6-bisphosphate aldolase (FBA) is an enzyme involved in the Embden-Meyerhof-Parnas (EMP) glycolytic pathway and in gluconeogenesis. Increasingly, it is also recognized that FBA has additional functions beyond its housekeeping role in central metabolism. In the present review, we summarize the current knowledge of the moonlighting functions of FBA in bacteria.
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Capodagli GC, Lee SA, Boehm KJ, Brady KM, Pegan SD. Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:7604-14. [PMID: 25390935 PMCID: PMC4263427 DOI: 10.1021/bi501141t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
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Staphylococcus aureus is one of the most common
nosocomial sources of soft-tissue and skin infections and has more
recently become prevalent in the community setting as well. Since
the use of penicillins to combat S. aureus infections
in the 1940s, the bacterium has been notorious for developing resistances
to antibiotics, such as methicillin-resistant Staphylococcus
aureus (MRSA). With the persistence of MRSA as well as many
other drug resistant bacteria and parasites, there is a growing need
to focus on new pharmacological targets. Recently, class II fructose
1,6-bisphosphate aldolases (FBAs) have garnered attention to fill
this role. Regrettably, scarce biochemical data and no structural
data are currently available for the class II FBA found in MRSA (SaFBA).
With the recent finding of a flexible active site zinc-binding loop
(Z-Loop) in class IIa FBAs and its potential for broad spectrum class
II FBA inhibition, the lack of information regarding this feature
of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop
inhibitor development. Therefore, we elucidated the crystal structure
of SaFBA to 2.1 Å allowing for a more direct structural analysis
of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate,
as well as performed mode of inhibition studies for an inhibitor that
takes advantage of the Z-loop’s flexibility. Together the data
offers insight into a class IIb FBA from a pervasively drug resistant
bacterium and a comparison of Z-loops and other features between the
different subtypes of class II FBAs.
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Affiliation(s)
- Glenn C Capodagli
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
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Weaver DS, Keseler IM, Mackie A, Paulsen IT, Karp PD. A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. BMC SYSTEMS BIOLOGY 2014; 8:79. [PMID: 24974895 PMCID: PMC4086706 DOI: 10.1186/1752-0509-8-79] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/19/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Constraint-based models of Escherichia coli metabolic flux have played a key role in computational studies of cellular metabolism at the genome scale. We sought to develop a next-generation constraint-based E. coli model that achieved improved phenotypic prediction accuracy while being frequently updated and easy to use. We also sought to compare model predictions with experimental data to highlight open questions in E. coli biology. RESULTS We present EcoCyc-18.0-GEM, a genome-scale model of the E. coli K-12 MG1655 metabolic network. The model is automatically generated from the current state of EcoCyc using the MetaFlux software, enabling the release of multiple model updates per year. EcoCyc-18.0-GEM encompasses 1445 genes, 2286 unique metabolic reactions, and 1453 unique metabolites. We demonstrate a three-part validation of the model that breaks new ground in breadth and accuracy: (i) Comparison of simulated growth in aerobic and anaerobic glucose culture with experimental results from chemostat culture and simulation results from the E. coli modeling literature. (ii) Essentiality prediction for the 1445 genes represented in the model, in which EcoCyc-18.0-GEM achieves an improved accuracy of 95.2% in predicting the growth phenotype of experimental gene knockouts. (iii) Nutrient utilization predictions under 431 different media conditions, for which the model achieves an overall accuracy of 80.7%. The model's derivation from EcoCyc enables query and visualization via the EcoCyc website, facilitating model reuse and validation by inspection. We present an extensive investigation of disagreements between EcoCyc-18.0-GEM predictions and experimental data to highlight areas of interest to E. coli modelers and experimentalists, including 70 incorrect predictions of gene essentiality on glucose, 80 incorrect predictions of gene essentiality on glycerol, and 83 incorrect predictions of nutrient utilization. CONCLUSION Significant advantages can be derived from the combination of model organism databases and flux balance modeling represented by MetaFlux. Interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database.
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Affiliation(s)
- Daniel S Weaver
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
| | - Ingrid M Keseler
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
| | - Amanda Mackie
- Department of Chemistry and Biomolecular Science, Macquarie University, Balaclava Rd, North Ryde NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Science, Macquarie University, Balaclava Rd, North Ryde NSW 2109, Australia
| | - Peter D Karp
- Bioinformatics Research Group, SRI International, 333 Ravenswood Ave., 94025 Menlo Park, CA, USA
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Capodagli GC, Sedhom WG, Jackson M, Ahrendt KA, Pegan SD. A noncompetitive inhibitor for Mycobacterium tuberculosis's class IIa fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:202-13. [PMID: 24325645 PMCID: PMC4167715 DOI: 10.1021/bi401022b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Class II fructose 1,6-bisphosphate aldolase (FBA) is an enzyme critical for bacterial, fungal, and protozoan glycolysis/gluconeogenesis. Importantly, humans lack this type of aldolase, having instead a class I FBA that is structurally and mechanistically distinct from class II FBAs. As such, class II FBA is considered a putative pharmacological target for the development of novel antibiotics against pathogenic bacteria such as Mycobacterium tuberculosis, the causative agent for tuberculosis (TB). To date, several competitive class II FBA substrate mimic-styled inhibitors have been developed; however, they lack either specificity, potency, or properties that limit their potential as possible therapeutics. Recently, through the use of enzymatic and structure-based assisted screening, we identified 8-hydroxyquinoline carboxylic acid (HCA) that has an IC50 of 10 ± 1 μM for the class II FBA present in M. tuberculosis (MtFBA). As opposed to previous inhibitors, HCA behaves in a noncompetitive manner, shows no inhibitory properties toward human and rabbit class I FBAs, and possesses anti-TB properties. Furthermore, we were able to determine the crystal structure of HCA bound to MtFBA to 2.1 Å. HCA also demonstrates inhibitory effects for other class II FBAs, including pathogenic bacteria such as methicillin-resistant Staphylococcus aureus. With its broad-spectrum potential, unique inhibitory characteristics, and flexibility of functionalization, the HCA scaffold likely represents an important advancement in the development of class II FBA inhibitors that can serve as viable preclinical candidates.
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Affiliation(s)
- Glenn C. Capodagli
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Wafik G. Sedhom
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kateri A. Ahrendt
- Department of Chemistry, Regis University, Denver, Colorado 80221, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
| | - Scott D. Pegan
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States,Eleanor Roosevelt Institute, University of Denver, Denver, Colorado 80208, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
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DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications. Extremophiles 2013; 18:1-13. [DOI: 10.1007/s00792-013-0593-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022]
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14
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García-Contreras R, Vos P, Westerhoff HV, Boogerd FC. Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions. FEBS J 2012; 279:4145-59. [PMID: 22978366 DOI: 10.1111/febs.12007] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 08/09/2012] [Accepted: 09/10/2012] [Indexed: 01/10/2023]
Abstract
Does the understanding of the dynamics of biochemical networks in vivo, in terms of the properties of their components determined in vitro, require the latter to be determined all under the same conditions? An in vivo-like assay medium for enzyme activity determination was designed based on the concentrations of the major ionic constituents of the Escherichia coli cytosol: K(+), Na(+), Mg(2+), phosphate, glutamate, sulfate and Cl(-). The maximum capacities (V(max)) of the extracted enzymes of two pathways were determined using both this in vivo-like assay medium and the assay medium specific for each enzyme. The enzyme activities differed between the two assay conditions. Most of the differences could be attributed to unsuspected, pleiotropic effects of K(+) and phosphate. K(+) activated some enzymes (aldolase, enolase and glutamate dehydrogenase) and inhibited others (phosphoglucose isomerase, phosphofructokinase, triosephosphate isomerase, glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase), whereas phosphate inhibited all glycolytic enzymes and glutamine synthetase but only activated glutamine 2-oxoglutarate amidotransferase. Neither a high glutamate concentration, nor macromolecular crowding affected the glycolytic or nitrogen assimilation enzymes, other than through the product inhibition of glutamate dehydrogenase by glutamate. This strategy of assessing all pathway enzymes kinetically under the same conditions may be necessary to avoid inadvertent differences between in vivo and in vitro biochemistry. It may also serve to reveal otherwise unnoticed pleiotropic regulation, such as that demonstrated in the present study by K(+) and phosphate.
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Affiliation(s)
- Rodolfo García-Contreras
- Section of Molecular Cell Physiology, Netherlands Institute for Systems Biology, VU University Amsterdam, The Netherlands
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15
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Jain R, Yan Y. Dehydratase mediated 1-propanol production in metabolically engineered Escherichia coli. Microb Cell Fact 2011; 10:97. [PMID: 22074179 PMCID: PMC3245452 DOI: 10.1186/1475-2859-10-97] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/10/2011] [Indexed: 11/28/2022] Open
Abstract
Background With the increasing consumption of fossil fuels, the question of meeting the global energy demand is of great importance in the near future. As an effective solution, production of higher alcohols from renewable sources by microorganisms has been proposed to address both energy crisis and environmental concerns. Higher alcohols contain more than two carbon atoms and have better physiochemical properties than ethanol as fuel substitutes. Results We designed a novel 1-propanol metabolic pathway by expanding the well-known 1,2-propanediol pathway with two more enzymatic steps catalyzed by a 1,2-propanediol dehydratase and an alcohol dehydrogenase. In order to engineer the pathway into E. coli, we evaluated the activities of eight different methylglyoxal synthases which play crucial roles in shunting carbon flux from glycolysis towards 1-propanol biosynthesis, as well as two secondary alcohol dehydrogenases of different origins that reduce both methylglyoxal and hydroxyacetone. It is evident from our results that the most active enzymes are the methylglyoxal synthase from Bacillus subtilis and the secondary alcohol dehydrogenase from Klebsiella pneumoniae, encoded by mgsA and budC respectively. With the expression of these two genes and the E. coli ydjG encoding methylglyoxal reductase, we achieved the production of 1,2-propanediol at 0.8 g/L in shake flask experiments. We then characterized the catalytic efficiency of three different diol dehydratases on 1,2-propanediol and identified the optimal one as the 1,2-propanediol dehydratase from Klebsiella oxytoca, encoded by the operon ppdABC. Co-expressing this enzyme with the above 1,2-propanediol pathway in wild type E. coli resulted in the production of 1-propanol at a titer of 0.25 g/L. Conclusions We have successfully established a new pathway for 1-propanol production by shunting the carbon flux from glycolysis. To our knowledge, it is the first time that this pathway has been utilized to produce 1-propanol in E. coli. The work presented here forms a basis for further improvement in production. We speculate that dragging more carbon flux towards methylglyoxal by manipulating glycolytic pathway and eliminating competing pathways such as lactate generation can further enhance the production of 1-propanol.
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Affiliation(s)
- Rachit Jain
- Biochemical Engineering Program, University of Georgia, Athens, GA 30602, USA
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Macomber L, Elsey SP, Hausinger RP. Fructose-1,6-bisphosphate aldolase (class II) is the primary site of nickel toxicity in Escherichia coli. Mol Microbiol 2011; 82:1291-300. [PMID: 22014167 DOI: 10.1111/j.1365-2958.2011.07891.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nickel is toxic to all forms of life, but the mechanisms of cell damage are unknown. Indeed, environmentally relevant nickel levels (8 µM) inhibit wild-type Escherichia coli growth on glucose minimal medium. The same concentration of nickel also inhibits growth on fructose, but not succinate, lactate or glycerol; these results suggest that fructose-1,6-bisphosphate aldolase (FbaA) is a target of nickel toxicity. Cells stressed by 8 µM Ni(II) for 20 min lost 75% of their FbaA activity, demonstrating that FbaA is inactivated during nickel stress. Furthermore, overexpression of fbaA restored growth of an rcnA mutant in glucose minimal medium supplemented with 4 µM Ni(II), thus confirming that FbaA is a primary target of nickel toxicity. This class II aldolase has an active site zinc and a non-catalytic zinc nearby. Purified FbaA lost 80 % of its activity within 2 min when challenged with 8 µM Ni(II). Nickel-challenged FbaA lost 0.8 zinc and gained 0.8 nickel per inactivated monomer. FbaA mutants (D144A and E174A) affecting the non-catalytic zinc were resistant to nickel inhibition. These results define the primary site of nickel toxicity in E. coli as the class II aldolase FbaA through binding to the non-catalytic zinc site.
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Affiliation(s)
- Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA
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17
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Identification of new protein complexes of Escherichia coli inorganic pyrophosphatase using pull-down assay. Biochimie 2011; 93:1576-83. [DOI: 10.1016/j.biochi.2011.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 05/10/2011] [Indexed: 11/20/2022]
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18
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Labbé G, de Groot S, Rasmusson T, Milojevic G, Dmitrienko GI, Guillemette JG. Evaluation of four microbial Class II fructose 1,6-bisphosphate aldolase enzymes for use as biocatalysts. Protein Expr Purif 2011; 80:224-33. [PMID: 21763425 DOI: 10.1016/j.pep.2011.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/28/2011] [Accepted: 06/29/2011] [Indexed: 12/01/2022]
Abstract
Fructose 1,6-bisphosphate (FBP) aldolase has been used as biocatalyst in the synthesis of several pharmaceutical compounds such as monosaccharides and analogs. Is has been suggested that microbial metal-dependant Class II aldolases could be better industrial catalysts than mammalian Class I enzyme because of their greater stability. The Class II aldolases from four microbes were subcloned into the Escherichia coli vector pT7-7, expressed and purified to near homogeneity. The kinetic parameters, temperature stability, pH profile, and tolerance to organic solvents of the Class II enzymes were determined, and compared with the properties of the Class I aldolase from rabbit muscle. Contrary to results obtained previously with the E. coli Class II aldolase, which was reported to be more stable than the mammalian enzyme, other recombinant Class II aldolases were found to be generally less stable than the Class I enzyme, especially in the presence of organic solvents. Class II aldolase from Bacillus cereus showed higher temperature stability than the other enzymes tested, but only the Mycobacterium tuberculosis Class II aldolase had a stability comparable to the Class I mammalian enzyme under assay conditions. The turnover number of the recombinant M. tuberculosis and Magnaporthe grisea Class II type A aldolases was comparable or higher than that of the Class I enzyme. The recombinant B. cereus and Pseudomonas aeruginosa Class II type B aldolases had very low turnover numbers and low metal content, indicating that the E. coli overexpression system may not be suitable for the Class II type B aldolases from these microorganisms.
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Affiliation(s)
- Geneviève Labbé
- Department of Chemistry, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L3G1, Canada
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19
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Fan W, Zhang Z, Zhang Y. Cloning and molecular characterization of fructose-1,6-bisphosphate aldolase gene regulated by high-salinity and drought in Sesuvium portulacastrum. PLANT CELL REPORTS 2009; 28:975-84. [PMID: 19381641 DOI: 10.1007/s00299-009-0702-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 03/08/2009] [Accepted: 04/02/2009] [Indexed: 05/19/2023]
Abstract
Sesuvium portulacastrum, a mangrove plant from seashore, is a halophyte species well adapted to salinity and drought. Some efforts have been made to describe its physiological and structural characteristics on salt and drought-tolerance, but the underlying molecular mechanism and key components have not yet been identified. Here, a fructose-1,6-bisphosphate aldolase gene, designated SpFBA, was isolated and characterized from S. portulacastrum roots in response to seawater. The SpFBA cDNA has a total length of 1452 bp with an open reading frame of 1071 bp, and is predicted to encode a precursor protein of 357 amino acid residues sharing high degree of homology with class I FBAs from other plants. Semi-quantitative RT-PCR analysis indicated that the SpFBA was more strongly expressed in roots than in leaves and stems, and the abiotic stimuli such as Seawater, NaCl, ABA, and PEG, could trigger a significant induction of SpFBA in S. portulacastrum roots within 2-12 h. Overproduction of Recombinant SpFBA resulted in an increased tolerance to salinity in transgenic Escherichia coli. All these results suggest that the SpFBA plays very important roles in responding to salt stress and related abiotic stimuli, and in improving the survival ability of S. portulacastrum under high salinity and drought.
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Affiliation(s)
- Wei Fan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, China
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20
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Pegan SD, Rukseree K, Franzblau SG, Mesecar AD. Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. J Mol Biol 2009; 386:1038-53. [PMID: 19167403 PMCID: PMC2654403 DOI: 10.1016/j.jmb.2009.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 01/05/2009] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), currently infects one-third of the world's population in its latent form. The emergence of multidrug-resistant and extensive drug-resistant strains has highlighted the need for new pharmacological targets within M. tuberculosis. The class IIa fructose 1,6-bisphosphate aldolase (FBA) enzyme from M. tuberculosis (MtFBA) has been proposed as one such target since it is upregulated in latent TB. Since the structure of MtFBA has not been determined and there is little information available on its reaction mechanism, we sought to determine the X-ray structure of MtFBA in complex with its substrates. By lowering the pH of the enzyme in the crystalline state, we were able to determine a series of high-resolution X-ray structures of MtFBA bound to dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, and fructose 1,6-bisphosphate at 1.5, 2.1, and 1.3 A, respectively. Through these structures, it was discovered that MtFBA belongs to a novel tetrameric class of type IIa FBAs. The molecular details at the interface of the tetramer revealed important information for better predictability of the quaternary structures among the FBAs based on their primary sequences. These X-ray structures also provide interesting and new details on the reaction mechanism of class II FBAs. Substrates and products were observed in geometries poised for catalysis; in addition, unexpectedly, the hydroxyl-enolate intermediate of dihydroxyacetone phosphate was also captured and resolved structurally. These concise new details offer a better understanding of the reaction mechanisms for FBAs in general and provide a structural basis for inhibitor design efforts aimed at this class of enzymes.
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Affiliation(s)
- Scott D Pegan
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA
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21
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Rukseree K, Thammarongtham C, Palittapongarnpim P. One-step purification and characterization of a fully active histidine-tagged Class II fructose-1,6-bisphosphate aldolase from Mycobacterium tuberculosis. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Erales J, Avilan L, Lebreton S, Gontero B. Exploring CP12 binding proteins revealed aldolase as a new partner for the phosphoribulokinase/glyceraldehyde 3-phosphate dehydrogenase/CP12 complex - purification and kinetic characterization of this enzyme from Chlamydomonas reinhardtii. FEBS J 2008; 275:1248-59. [DOI: 10.1111/j.1742-4658.2008.06284.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vallee BL, Galdes A. The metallobiochemistry of zinc enzymes. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 56:283-430. [PMID: 6364704 DOI: 10.1002/9780470123027.ch5] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
Central metabolism of carbohydrates uses the Embden-Meyerhof-Parnas (EMP), pentose phosphate (PP), and Entner-Doudoroff (ED) pathways. This review reviews the biological roles of the enzymes and genes of these three pathways of E. coli. Glucose, pentoses, and gluconate are primarily discussed as the initial substrates of the three pathways, respectively. The genetic and allosteric regulatory mechanisms of glycolysis and the factors that affect metabolic flux through the pathways are considered here. Despite the fact that a lot of information on each of the reaction steps has been accumulated over the years for E. coli, surprisingly little quantitative information has been integrated to analyze glycolysis as a system. Therefore, the review presents a detailed description of each of the catalytic steps by a systemic approach. It considers both structural and kinetic aspects. Models that include kinetic information of the reaction steps will always contain the reaction stoichiometry and therefore follow the structural constraints, but in addition to these also kinetic rate laws must be fulfilled. The kinetic information obtained on isolated enzymes can be integrated using computer models to simulate behavior of the reaction network formed by these enzymes. Successful examples of such approaches are the modeling of glycolysis in S. cerevisiae, the parasite Trypanosoma brucei, and the red blood cell. With the rapid developments in the field of Systems Biology many new methods have been and will be developed, for experimental and theoretical approaches, and the authors expect that these will be applied to E. coli glycolysis in the near future.
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Affiliation(s)
- Tony Romeo
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa, and Department of Molecular Cell Physiology, Vrije Universiteit, Amsterdam, The Netherlands
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25
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Carneiro LC, de Faria FP, Felipe MSS, Pereira M, de Almeida Soares CM. Paracoccidioides brasiliensis presents two different cDNAs encoding homologues of the fructose 1,6-biphosphate aldolase: protein isolation, cloning of the cDNAs and genes, structural, phylogenetic, and expression analysis. Fungal Genet Biol 2005; 42:51-60. [PMID: 15588996 DOI: 10.1016/j.fgb.2004.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Accepted: 10/06/2004] [Indexed: 10/26/2022]
Abstract
A proteomic approach was used to identify a 39 kDa antigen of Paracoccidioides brasiliensis. Amino acid sequences of the N-terminal and of endoproteinase Lys-C digested peptides revealed the protein to be a fructose 1,6-biphosphate aldolase (FBA) Class II of P. brasiliensis. Two cDNA homologues, Pbfba1 and Pbfba2, were cloned and characterized. Pbfba1 encoded a predicted polypeptide of 360 amino acids that was highly homologous in the primary structure to the same enzyme from fungi and bacteria. The other DNA, Pbfba2, encoded a polypeptide predicted to be 363 amino acids. The sequence of Pbfba2 differed significantly from Pbfba1. Phylogenetic and molecular analysis supports the concept of gene duplication for FBAs in P. brasiliensis, constituting a two-member family. Expression analysis demonstrated differential expression for both fbas genes in P. brasiliensis cells.
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Affiliation(s)
- Lílian Carla Carneiro
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
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26
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Ramsaywak PC, Labbé G, Siemann S, Dmitrienko GI, Guillemette JG. Molecular cloning, expression, purification, and characterization of fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis—a novel Class II A tetramer. Protein Expr Purif 2004; 37:220-8. [PMID: 15294302 DOI: 10.1016/j.pep.2004.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 05/14/2004] [Indexed: 11/19/2022]
Abstract
The Class II fructose 1,6-bisphosphate aldolase (fda, Rv0363c) from the pathogen Mycobacterium tuberculosis H37RV was subcloned in the Escherichia coli vector pT7-7 and purified to near homogeneity. The specific activity (35 U/mg) is approximately 9 times higher than previously reported for the enzyme partially purified from the pathogen. Attempts to express the enzyme with an N-terminal fusion tag yielded inactive, mostly insoluble protein. The native recombinant enzyme is zinc-dependent and has a catalytic efficiency for fructose 1,6-bisphosphate cleavage higher than most Class II aldolases characterized to date. The aldolase has a Km of 20 microM, a kcat of 21 s(-1), and a pH optimum of 7.8. The molecular mass of the enzyme subunits as determined by mass spectrometry is in agreement with the mass calculated on the basis of its gene sequence minus the terminal methionine, 36,413 Da. The enzyme is a homotetramer and retains only two zinc ions per tetramer when transferred to a metal-free buffer, as determined by ICP-MS and by a colorimetric assay using 4-(2-pyridylazo)-resorcinol (PAR) as a chelator. The E. coli expression system reported in this study will facilitate the further characterization of this enzyme and the screening for potential inhibitors.
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Affiliation(s)
- Peggy C Ramsaywak
- Department of Chemistry, University of Waterloo, 200 University Avenue W, Waterloo, Ont., N2L 3G1, Canada
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27
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Rashid N, Imanaka H, Fukui T, Atomi H, Imanaka T. Presence of a novel phosphopentomutase and a 2-deoxyribose 5-phosphate aldolase reveals a metabolic link between pentoses and central carbon metabolism in the hyperthermophilic archaeon Thermococcus kodakaraensis. J Bacteriol 2004; 186:4185-91. [PMID: 15205420 PMCID: PMC421627 DOI: 10.1128/jb.186.13.4185-4191.2004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Numerous bacteria and mammalian cells harbor two enzymes, phosphopentomutase (PPM) and 2-deoxyribose 5-phosphate aldolase (DERA), involved in the interconversion between nucleosides and central carbon metabolism. In this study, we have examined the presence of this metabolic link in the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1. A search of the genome sequence of this strain revealed the presence of a closely related orthologue (TK2104) of bacterial DERA genes while no orthologue related to previously characterized PPM genes could be detected. Expression, purification, and characterization of the TK2104 protein product revealed that this gene actually encoded a DERA, catalyzing the reaction through a class I aldolase mechanism. As PPM activity was detected in T. kodakaraensis cells, we partially purified the protein to examine its N-terminal amino acid sequence. The sequence corresponded to a gene (TK1777) similar to phosphomannomutases within COG1109 but not COG1015, which includes all previously identified PPMs. Heterologous gene expression of TK1777 and characterization of the purified recombinant protein clearly revealed that the gene indeed encoded a PPM. Both enzyme activities could be observed in T. kodakaraensis cells under glycolytic and gluconeogenic growth conditions, whereas the addition of ribose, 2-deoxyribose, and 2'-deoxynucleosides in the medium did not lead to a significant induction of these activities. Our results clearly indicate the presence of a metabolic link between pentoses and central carbon metabolism in T. kodakaraensis, providing an alternative route for pentose biosynthesis through the functions of DERA and a structurally novel PPM.
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Affiliation(s)
- Naeem Rashid
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Gene cloning and characterization of fructose-1,6-bisphosphate aldolase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Biosci Bioeng 2002. [DOI: 10.1016/s1389-1723(02)80156-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Dhar NM, Altekar W. A class I (Schiff base) fructose-1,6-bisphosphate aldolase of halophilic archaebacterial origin. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)80469-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Altekar W, Dhar NM. Archaebacterial class I and class II aldolases from extreme halophiles. ORIGINS LIFE EVOL B 2001; 18:59-64. [PMID: 11536602 DOI: 10.1007/bf01808780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Both, class I (Schiff-base forming) and class II (metal requiring) fructose biphosphate aldolases were found to be distributed among halophilic archaebacteria. The aldolase activity from Halobacteriium halobium, H. salinarium, H. cutirubrum, H. mediterranei and H. volcanii exhibited properties of a bacterial class II aldolase as it was metal-dependent for activity and therefore inhibited by EDTA. In contrast, aldolase from H. saccharovorum, Halobacterium R-113, H. vallismortis and Halobacterium CH-1 formed a Schiff-base intermediate with the substrate and therefore resembled to eukaryotic class I type. The type of aldolase did not vary by changes in the growth medium.
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Affiliation(s)
- W Altekar
- Biochemistry Division, Bhabha Atomic Research Centre, Bombay, India
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31
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Plater AR, Zgiby SM, Thomson GJ, Qamar S, Wharton CW, Berry A. Conserved residues in the mechanism of the E. coli Class II FBP-aldolase. J Mol Biol 1999; 285:843-55. [PMID: 9878448 DOI: 10.1006/jmbi.1998.2376] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The two classes of fructose-1,6-bisphosphate aldolase both catalyse the reversible cleavage of fructose 1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The Class I aldolases use Schiff base formation as part of their catalytic mechanism, whereas the Class II enzymes are zinc-containing metalloproteins. The mechanism of the Class II enzymes is less well understood than their Class I counterparts. We have combined sequence alignments of the Class II family of enzymes with examination of the crystal structure of the enzyme to highlight potentially important aspartate and asparagine residues in the enzyme mechanism. Asp109, Asp144, Asp288, Asp290, Asp329 and Asn286 were targeted for site-directed mutagenesis and the resulting proteins purified and characterised by steady-state kinetics using either a coupled assay system to study the overall cleavage reaction or using the hexacyanoferrate (III) oxidation of the enzyme bound intermediate carbanion to investigate partial reactions. The results showed only minor changes in the kinetic parameters for the Asp144, Asp288, Asp290 and Asp329 mutants, suggesting that these residues play only minor or indirect roles in catalysis. By contrast, mutation of Asp109 or Asn286 caused 3000-fold and 8000-fold decreases in the kcat of the reaction, respectively. Coupled with the kinetics measured for the partial reactions the results clearly demonstrate a role for Asn286 in catalysis and in binding the ketonic end of the substrate. Fourier transform infra-red spectroscopy of the wild-type and mutant enzymes has further delineated the role of Asp109 as being critically involved in the polarisation of the carbonyl group of glyceraldehyde 3-phosphate.
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Affiliation(s)
- A R Plater
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds, LS2 9JT, England
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32
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Thomson GJ, Howlett GJ, Ashcroft AE, Berry A. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem J 1998; 331 ( Pt 2):437-45. [PMID: 9531482 PMCID: PMC1219373 DOI: 10.1042/bj3310437] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gene encoding the Escherichia coli Class I fructose-1, 6-bisphosphate aldolase (FBP aldolase) has been cloned and the protein overproduced in high amounts. This gene sequence has previously been identified as encoding an E. coli dehydrin in the GenBanktrade mark database [gene dhnA; entry code U73760; Close and Choi (1996) Submission to GenBanktrade mark]. However, the purified protein overproduced from the dhnA gene shares all its properties with those known for the E. coli Class I FBP aldolase. The protein is an 8-10-mer with a native molecular mass of approx. 340 kDa, each subunit consisting of 349 amino acids. The Class I enzyme shows low sequence identity with other known FBP aldolases, both Class I and Class II (in the order of 20%), which may be reflected by some novel properties of this FBP aldolase. The active-site peptide has been isolated and the Schiff-base-forming lysine residue (Lys236) has been identified by a combination of site-directed mutagenesis, kinetics and electrospray-ionization MS. A second lysine residue (Lys238) has been implicated in substrate binding. The cloning of this gene and the high levels of overexpression obtained will facilitate future structure-function studies.
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Affiliation(s)
- G J Thomson
- Department of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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De Montigny C, Sygusch J. Functional characterization of an extreme thermophilic class II fructose-1,6-bisphosphate aldolase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:243-8. [PMID: 8898912 DOI: 10.1111/j.1432-1033.1996.0243t.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fructose-1,6-bisphosphate aldolase activity has been isolated and purified to homogeneity from the extreme thermophile eubacteria Thermus aquaticus. The homogeneous enzyme is a class II aldolase as fructose-1,6-bisphosphate cleavage activity was strongly inhibited by EDTA, and activated by Co2+ metal ion. Taq aldolase is a stable tetramer with estimated molecular mass of 165 kDa. The enzyme is thermostable and is not inactived after heating at 90 degrees C for 2 h but looses 80% of activity after 1 h at 97 degrees C. The pH profile corresponding to maximal aldolase activity is displaced to more acidic values compared to other class II aldolases. Enzyme activation by both detergents and alcohols and chromatographic behaviour on hydrophobic stationary phases is consistent with presence of hydrophobic surface regions on the soluble enzyme. Kinetic behaviour of T. aquaticus aldolase at high fructose-1,6-bisphosphate concentrations indicates significant negative cooperativity. The Taq aldolase NH2-terminal sequence was determined and compared with available sequences from other class II aldolases. Significant sequence similarity was found between Taq aldolase and the thermostable aldolase from Bacillus stearothermophilus.
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Affiliation(s)
- C De Montigny
- Department of Biochemistry, Université de Montréal, Canada
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34
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35
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Qamar S, Marsh K, Berry A. Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli. Protein Sci 1996; 5:154-61. [PMID: 8771208 PMCID: PMC2143241 DOI: 10.1002/pro.5560050119] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Treatment of the Class II fructose-1,6-bisphosphate aldolase of Escherichia coli with the arginine-specific alpha-dicarbonyl reagents, butanedione or phenylglyoxal, results in inactivation of the enzyme. The enzyme is protected from inactivation by the substrate, fructose 1,6-bisphosphate, or by inorganic phosphate. Modification with [7-14C] phenylglyoxal in the absence of substrate demonstrates that enzyme activity is abolished by the incorporation of approximately 2 moles of reagent per mole of enzyme. Sequence alignment of the eight known Class II FBP-aldolases shows that only one arginine residue is conserved in all the known sequences. This residue, Arg-331, was mutated to either alanine or glutamic acid. The mutant enzymes were much less susceptible to inactivation by phenylglyoxal. Measurement of the steady-state kinetic parameters revealed that mutation of Arg-331 dramatically increased the K(m) for fructose 1,6-bisphosphate. Comparatively small differences in the inhibitor constant Ki for dihydroxyacetone phosphate or its analogue, 2-phosphoglycolate, were found between the wild-type and mutant enzymes. In contrast, the mutation caused large changes in the kinetic parameters when glyceraldehyde 3-phosphate was used as an inhibitor. Kinetic analysis of the oxidation of the carbanionic aldolase-substrate intermediate of the reaction by hexacyanoferrate (III) revealed that the K(m) for dihydroxyacetone phosphate was again unaffected, whereas that for fructose 1,6-bisphosphate was dramatically increased. Taken together, these results show that Arg-331 is critically involved in the binding of fructose bisphosphate by the enzyme and demonstrate that it interacts with the C-6 phosphate group of the substrate.
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Affiliation(s)
- S Qamar
- Department of Biochemistry, University of Cambridge, United Kingdom
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36
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Witke C, Götz F. Cloning, sequencing, and characterization of the gene encoding the class I fructose-1,6-bisphosphate aldolase of Staphylococcus carnosus. J Bacteriol 1993; 175:7495-9. [PMID: 8226699 PMCID: PMC206899 DOI: 10.1128/jb.175.22.7495-7499.1993] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
fda from Staphylococcus carnosus TM300, encoding the class I fructose-1,6-bisphosphate aldolase, was cloned in Escherichia coli and sequenced. The 888-nucleotide open reading frame encoding a protein with an M(r) of 32,855 had an E. coli-like promoter sequence. Plasmids containing fda complemented E. coli NP315 (Fda-). Expression of fda in S. carnosus led to a six- to eightfold increase in aldolase production and activity; low levels of glucose in the growth medium stimulated activity.
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Affiliation(s)
- C Witke
- Universität Tübingen, Germany
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37
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A chemoenzymic synthesis of 1,5-dideoxy-1,5-imino-l-mannitol and l-rhamnitol and investigation of their effects on glycosidases. Carbohydr Res 1993. [DOI: 10.1016/0008-6215(93)84211-n] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Fothergill-Gilmore LA, Michels PA. Evolution of glycolysis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1993; 59:105-235. [PMID: 8426905 DOI: 10.1016/0079-6107(93)90001-z] [Citation(s) in RCA: 348] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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39
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Abstract
Two mechanistically distinct forms of fructose-bisphosphate aldolase are known to exist. It has been assumed that the Class II (metallo) aldolases are evolutionary more primitive than their Class I (Schiff-base) analogs since the latter had only been found in eukaryotes. With the identification of prokaryotic Class I aldolases, we present here an alternative scheme of aldolase evolution. This scheme proposes that both aldolase classes are evolutionarily ancient and rationalizes the observed highly variable expression of both enzyme types in contemporary file forms.
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Affiliation(s)
- J J Marsh
- Department of Chemistry, San Diego State University, CA 92182-0328
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40
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Singer M, Rossmiessl P, Cali BM, Liebke H, Gross CA. The Escherichia coli ts8 mutation is an allele of fda, the gene encoding fructose-1,6-diphosphate aldolase. J Bacteriol 1991; 173:6242-8. [PMID: 1917856 PMCID: PMC208376 DOI: 10.1128/jb.173.19.6242-6248.1991] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The ts8 mutant of Escherichia coli has previously been shown to preferentially inhibit stable RNA synthesis when shifted to the nonpermissive temperature. We demonstrate in this report that the ts8 mutation is an allele of fda, the gene that encodes the glycolytic enzyme fructose-1,6-diphosphate aldolase. We show that ts8 and a second fda mutation, h8, isolated and characterized by A. Böck and F. C. Neidhardt, are dominant mutations and that they encode a thermolabile aldolase activity.
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Affiliation(s)
- M Singer
- Department of Bacteriology, University of Wisconsin-Madison 53706
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41
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von der Osten CH, Barbas CF, Wong CH, Sinskey AJ. Molecular cloning, nucleotide sequence and fine-structural analysis of the Corynebacterium glutamicum fda gene: structural comparison of C. glutamicum fructose-1,6-biphosphate aldolase to class I and class II aldolases. Mol Microbiol 1989; 3:1625-37. [PMID: 2615658 DOI: 10.1111/j.1365-2958.1989.tb00148.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Corynebacterium glutamicum fda gene encoding fructose-1,6-biphosphate (FBP) aldolase has been isolated by complementation of an Escherichia coli mutant. The nucleotide sequence of a 3371 bp chromosomal fragment containing the C. glutamicum fda gene was determined. The N-terminal amino acid sequence of C. glutamicum FBP aldolase identified the correct initiation site for the fda gene, and a molecular weight of 37,092 was predicted for the fda polypeptide. S1 nuclease mapping identified the transcriptional start site, and Northern hybridization analysis indicated that the fda gene encodes a single 1.3 kb transcript. The primary structure of C. glutamicum FBP aldolase shows strong homology to class II FBP aldolases. Conservation of primary structure was observed between class I and class II aldolases, but several residues essential for catalytic activity in class I aldolases were absent from class II aldolases.
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Affiliation(s)
- C H von der Osten
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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42
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Alefounder PR, Perham RN. Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli. Mol Microbiol 1989; 3:723-32. [PMID: 2546007 DOI: 10.1111/j.1365-2958.1989.tb00221.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To investigate a possible chromosomal clustering of glycolytic enzyme genes, the complete nucleotide sequence of the 8029 bp insert of Escherichia coli DNA in the ColE1 plasmid pLC33-5 of the Clarke and Carbon collection (Clark and Carbon, 1976) was determined. Genes (pgk, fda) encoding the phosphoglycerate kinase and Class II fructose 1,6-bisphosphate aldolase, respectively, of E. coli were identified. The phosphoglycerate kinase was found to be highly homologous in primary structure to the same enzyme from eukaryotic organisms. A further large open reading frame, designated gapB, was also identified, which on the basis of sequence homology, appears to encode another glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase. This putative gene differs significantly from that (designated gapA) already identified as coding for this enzyme in E. coli and which maps elsewhere on the chromosome. The products, if any, of several other open reading frames remain to be identified.
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43
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Schwelberger HG, Kohlwein SD, Paltauf F. Molecular cloning, primary structure and disruption of the structural gene of aldolase from Saccharomyces cerevisiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 180:301-8. [PMID: 2647491 DOI: 10.1111/j.1432-1033.1989.tb14648.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A yeast cDNA genetic library in a bacteriophage expression vector was screened using an antiserum reacting with fructose 1,6-bisphosphate aldolase from Saccharomyces cerevisiae. Radio-labelled probes of selected immunopositive clones were used for screening of a yeast genomic library. From the genomic clones a yeast/Escherichia coli shuttle plasmid was constructed containing on a 1990-base-pair fragment the entire structural gene FBA1 coding for yeast aldolase. The primary structure of the FBA1 gene was determined. An open reading frame comprises 1077 base pairs coding for a protein of 359 amino acids with a predicted molecular mass of 39,608 Da. As observed for other strongly expressed yeast genes, codon usage is extremely biased. The 810 base pairs at the 5' end and the 90 base pairs at the 3' end of the coding region of the cloned FBA1 gene are sufficient for normal expression and show characteristic elements present in the noncoding sequences of other yeast genes. Aldolase is the major protein in yeast cells transformed with a high-copy-number plasmid containing the FBA1 gene. The aldolase gene was disrupted by insertion of the yeast URA3 gene into the coding region of one FBA1 allele in a homozygous diploid ura3 strain. The haploid offsprings with the defective aldolase allele fba1::URA3 lack aldolase enzymatic activity and fail to grow in media containing as a carbon source metabolites of only one side of the aldolase reaction.
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Affiliation(s)
- H G Schwelberger
- Institut für Biochemie und Lebensmittelchemie, Technische Universität Graz
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44
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Alefounder PR, Baldwin SA, Perham RN, Short NJ. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. Biochem J 1989; 257:529-34. [PMID: 2649077 PMCID: PMC1135610 DOI: 10.1042/bj2570529] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleotide sequence analysis of the Escherichia coli chromosomal DNA inserted in the plasmid pLC33-5 of the Clarke and Carbon library [Clarke & Carbon (1976) Cell 9, 91-99] revealed the existence of the gene, fda, encoding the Class II (metal-dependent) fructose 1,6-bisphosphate aldolase of E. coli. The primary structure of the polypeptide chain inferred from the DNA sequence of the fda gene comprises 359 amino acids, including the initiating methionine residue, from which an Mr of 39,146 could be calculated. This value is in good agreement with that of 40,000 estimated from sodium dodecyl sulphate-polyacrylamide gel electrophoresis of the purified dimeric enzyme. The amino acid sequence of the Class II aldolase from E. coli showed no homology with the known amino acid sequences of Class I (imine-forming) fructose 1,6-bisphosphate aldolases from a wide variety of sources. On the other hand, there was obvious homology with the N-terminal sequence of 40 residues already established for the Class II fructose 1,6-bisphosphate aldolase of Saccharomyces cerevisiae. These Class II aldolases, one from a prokaryote and one from a eukaryote, evidently are structurally and evolutionarily related. A 1029 bp-fragment of DNA incorporating the fda gene was excised from plasmid pLC33-5 by digestion with restriction endonuclease HaeIII and subcloned into the expression plasmid pKK223-3, where the gene came under the control of the tac promoter. When grown in the presence of the inducer isopropyl-beta-D-thiogalactopyranoside, E. coli JM101 cells transformed with this recombinant expression plasmid generated the Class II fructose 1,6-bisphosphate aldolase as approx. 70% of their soluble protein. This unusually high expression of an E. coli gene should greatly facilitate purification of the enzyme for any future structural or mechanistic studies.
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Affiliation(s)
- P R Alefounder
- Department of Biochemistry, University of Cambridge, U.K
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45
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Jacobshagen S, Schnarrenberger C. Two Class I Aldolases in the Green Alga Chara foetida (Charophyceae). PLANT PHYSIOLOGY 1988; 87:78-82. [PMID: 16666130 PMCID: PMC1054702 DOI: 10.1104/pp.87.1.78] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Aldolase activity of Chara foetida (Braun) could be separated into a minor (peak I) and a major peak (peak II) by ion-exchange chromatography on DEAE-cellulose. Affinity chromatography on P-cellulose resulted in highly purified aldolase preparations with specific activities of 3.2 and 4.8 units per milligram protein and molecular subunit masses of 37 and 35 kilodalton, as shown by SDS-PAGE, for the aldolase of peak I and peak II, respectively. Both aldolases belong to class I aldolase since the activity is not inhibited by 1 millimolar EDTA. The K(m) (fructose-1,6-bisphosphate) values were 0.64 and 13.4 micromolar, respectively. The aldolase of peak I showed a 6.7 times stronger crossreaction with a specific antiserum against the cytosol aldolase of spinach than with an antiserum against the chloroplast aldolase of spinach. On the other hand the aldolase of peak II showed a 5.1 times stronger cross-reaction with the alpha-plastidaldolase antiserum than with the alpha-cytosol-aldolase antiserum. For algae this is the first separation of two class I aldolases. They are similar to the cytosol and chloroplast aldolases in higher plants, but different from a reported class I (Me(2+) independent) and class II (Me(2+) dependent) aldolase in other algae.
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Affiliation(s)
- S Jacobshagen
- Institut für Pflanzenphysiologie, Zellbiologie und Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16a, D-1000 Berlin 33 (West)
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46
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Danson MJ. Archaebacteria: the comparative enzymology of their central metabolic pathways. Adv Microb Physiol 1988; 29:165-231. [PMID: 3132816 DOI: 10.1016/s0065-2911(08)60348-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- M J Danson
- Department of Biochemistry, University of Bath, England
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47
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Dhar N, Altekar W. Distribution of class I and class II fructose biphosphate aldolases in halophilic archaebacteria. FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01523.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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48
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Abstract
Six mutants lacking the glycolytic enzyme fructose 1,6-bisphosphate aldolase have been isolated in the yeast Saccharomyces cerevisiae by inositol starvation. The mutants grown on gluconeogenic substrates, such as glycerol or alcohol, and show growth inhibition by glucose and related sugars. The mutations are recessive, segregate as one gene in crosses, and fall in a single complementation group. All of the mutants synthesize an antigen cross-reacting to the antibody raised against yeast aldolase. The aldolase activity in various mutant alleles measured as fructose 1,6-bisphosphate cleavage is between 1 to 2% and as condensation of triose phosphates to fructose 1,6-bisphosphate is 2 to 5% that of the wild-type. The mutants accumulate fructose 1,6-bisphosphate from glucose during glycolysis and dihydroxyacetone phosphate during gluconeogenesis. This suggests that the aldolase activity is absent in vivo.
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49
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Davis EO, Jones-Mortimer MC, Henderson PJ. Location of a structural gene for xylose-H+ symport at 91 min on the linkage map of Escherichia coli K12. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43439-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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50
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Lebherz HG, Leadbetter MM, Bradshaw RA. Isolation and characterization of the cytosolic and chloroplast forms of spinach leaf fructose diphosphate aldolase. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43558-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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