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De la Fuente IM, Martínez L, Carrasco-Pujante J, Fedetz M, López JI, Malaina I. Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior. Front Genet 2021; 12:644615. [PMID: 34093645 PMCID: PMC8176287 DOI: 10.3389/fgene.2021.644615] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Nutrition, CEBAS-CSIC Institute, Murcia, Spain
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Luis Martínez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Basque Center of Applied Mathematics (BCAM), Bilbao, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
| | - José I. López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
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Griffith MB, Lazorchak JM, Haring H. Uptake of Sulfate from Ambient Water by Freshwater Animals. WATER 2020; 12:1-1496. [PMID: 32704397 PMCID: PMC7376752 DOI: 10.3390/w12051496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To better understand how the sulfate (SO4 2-) anion may contribute to the adverse effects associated with elevated ionic strength or salinity in freshwaters, we measured the uptake and efflux of SO4 2- in four freshwater species: the fathead minnow (Pimephales promelas, Teleostei: Cyprinidae), paper pondshell (Utterbackia imbecillis, Bivalvia: Unionidae), red swamp crayfish (Procambarus clarkii, Crustacea: Cambaridae), and two-lined mayfly (Hexagenia bilineata, Insecta: Ephemeridae). Using δ( 34 S/ 32 S) stable isotope ratios and the concentrations of S and SO4 2-, we measured the SO4 2- influx rate (J in ), net flux (J net ), and efflux rate (Jout) during a 24 h exposure period. For all four species, the means of J in for SO4 2- were positive, and J in was significantly greater than 0 at both target SO4 2- concentrations in the fish and mollusk and at the lower SO4 2- concentration in the crayfish. The means of J out and J net were much more variable than those for J in , but several species by target SO4 2- concentration combinations for J out and J net , were negative, which suggests the net excretion of SO4 2- by the animals. The results of our experiments suggest a greater regulation of SO4 2- in freshwater animals than has been previously reported.
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Affiliation(s)
- Michael B. Griffith
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Environmental Assessment, Cincinnati, OH 45268, USA
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
| | - James M. Lazorchak
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, USA
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, Cincinnati, OH 45268, USA
| | - Herman Haring
- Pegasus Technical Services, Inc., Cincinnati, OH 45268, USA
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Abstract
Sulfur is present in the amino acids cysteine and methionine and in a large range of essential coenzymes and cofactors and is therefore essential for all organisms. It is also a constituent of sulfate esters in proteins, carbohydrates, and numerous cellular metabolites. The sulfation and desulfation reactions modifying a variety of different substrates are commonly known as sulfation pathways. Although relatively little is known about the function of most sulfated metabolites, the synthesis of activated sulfate used in sulfation pathways is essential in both animal and plant kingdoms. In humans, mutations in the genes encoding the sulfation pathway enzymes underlie a number of developmental aberrations, and in flies and worms, their loss-of-function is fatal. In plants, a lower capacity for synthesizing activated sulfate for sulfation reactions results in dwarfism, and a complete loss of activated sulfate synthesis is also lethal. Here, we review the similarities and differences in sulfation pathways and associated processes in animals and plants, and we point out how they diverge from bacteria and yeast. We highlight the open questions concerning localization, regulation, and importance of sulfation pathways in both kingdoms and the ways in which findings from these "red" and "green" experimental systems may help reciprocally address questions specific to each of the systems.
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Affiliation(s)
- Süleyman Günal
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany
| | - Rebecca Hardman
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne 50674, Germany.
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom.
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Ortiz-Tena JG, Rühmann B, Sieber V. Colorimetric Determination of Sulfate via an Enzyme Cascade for High-Throughput Detection of Sulfatase Activity. Anal Chem 2018; 90:2526-2533. [PMID: 29307190 DOI: 10.1021/acs.analchem.7b03719] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput screening (HTS) methods have become decisive for the discovery and development of new biocatalysts and their application in numerous fields. Sulfatases, a broad class of biocatalysts that hydrolyze sulfate esters, are involved in diverse relevant cellular functions (e.g., signaling and hormonal regulation) and are therefore gaining importance, particularly in the medical field. Additionally, various technical applications have been recently devised. One of the major challenges in the field of enzyme development is the sensitive and high-throughput detection of the actual product of the biocatalyst of interest without the need for chromophore analogues. Addressing this issue, a colorimetric assay for sulfatases was developed and validated for detecting sulfate through a two-step enzymatic cascade, with a linear detection range of 3.3 (limit of detection) up to 250 μM. The procedure is compatible with relevant compounds employed in sulfatase reactions, including cosolvents, cations, and buffers. The assay was optimized and performed as part of a 96-well screening workflow that included bacterial growth, heterologous sulfatase expression, cell lysis, sulfate ester hydrolysis, inactivation of cell lysate, and colorimetric sulfate determination. With this procedure, the activity of an aryl and an alkyl sulfatase could be confirmed and validated. Overall, this assay provides a simple and fast alternative for screening and engineering sulfatases from DNA libraries (e.g., using metagenomics) with medical or synthetic relevance.
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Affiliation(s)
- Jose G Ortiz-Tena
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany.,Fraunhofer IGB , Straubing Branch BioCat, 94315 Straubing, Germany.,TUM Catalysis Research Center , Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany.,The University of Queensland , School of Chemistry and Molecular Biosciences, 68 Copper Road, St. Lucia 4072, Australia
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A Class II small heat shock protein OsHsp18.0 plays positive roles in both biotic and abiotic defense responses in rice. Sci Rep 2017; 7:11333. [PMID: 28900229 PMCID: PMC5595972 DOI: 10.1038/s41598-017-11882-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 08/31/2017] [Indexed: 11/08/2022] Open
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice. However, the molecular mechanism underpinning the Xoo resistance of rice is still not fully understood. Here, we report that a class II small heat shock protein gene, OsHsp18.0, whose expression was differentially induced between a resistant and a susceptible variety in response to Xoo infection, plays positive roles in both biotic and abiotic resistance. The molecular chaperone activity of OsHsp18.0 was confirmed by a bacterium-expressed glutathione S-transferase fusion protein. Overexpression of OsHsp18.0 in a susceptible rice variety significantly enhanced its resistance to multiple Xoo strains, whereas silencing of OsHsp18.0 in a resistant variety drastically increased its susceptibility. The enhanced Xoo resistance in OsHsp18.0-overexpressing lines was positively correlated with the sensitized salicylic acid-dependent defense responses. In addition to disease resistance, the OsHsp18.0 overexpressing and silencing lines exhibited enhanced and reduced tolerance, respectively, to heat and salt treatments. The subcellular localization study revealed that the green fluorescent protein-OsHsp18.0 was enriched on the nuclear envelope, suggesting a potential role of OsHsp18.0 in the nucleo-cytoplasmic trafficking. Together, our results reveal that the rice OsHsp18.0 is a positive regulator in both biotic and abiotic defense responses.
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Liu Y, Sun MH, Shao SK, Deng G. An affinity-based aqueous two-phase mixed micellar system and its purification of Yeast 3′,5′-bisphosphate nucleotidase. J Chromatogr B Analyt Technol Biomed Life Sci 2017. [DOI: 10.1016/j.jchromb.2017.05.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Zhang W, Cao Y, Xu L, Gong J, Sun M. A laboratory exercise for visible gel filtration chromatography using fluorescent proteins. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 43:33-8. [PMID: 25400007 DOI: 10.1002/bmb.20833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/11/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
Gel filtration chromatography (GFC) separates molecules according to size and is one of the most widely used methods for protein purification. Here, red fluorescent protein (RFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), cyan fluorescent protein (CFP), and/or their fusion proteins were prokaryotically expressed, purified, and used in a laboratory exercise to intuitively demonstrate GFC. Different bands, corresponding to RFP, RFP-CFP (RC), YFP-RFP-YFP (YRY), and pyruvate kinase II-GFP (PKG) were well separated on a Superdex 200 column from a 0.5-mL sample. Increasing the sample volume and changing the chromatographic resin to Sephadex G-100 resulted in lower resolution separation. Students enjoyed identifying combinations of colored proteins and found this exercise helpful for understanding the factors that affect GFC resolution.
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Affiliation(s)
- Wenqiang Zhang
- Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China, 321004
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Li H, Li Z, Ma J, Sun M. Adenosine-5′-phosphosulfate kinase from Thermobifida fusca. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s000368381406009x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Xiang X, Pan G, Rong T, Zheng ZL, Leustek T. A luciferase-based method for assay of 5'-adenylylsulfate reductase. Anal Biochem 2014; 460:22-8. [PMID: 24857786 DOI: 10.1016/j.ab.2014.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 01/13/2023]
Abstract
A luciferase-based method was developed for measurement of 5'-adenylylsulfate (APS) reductase (APR), an enzyme of the reductive sulfate assimilation pathway in prokaryotes and plants. APR catalyzes the two-electron reduction of APS and forms sulfite and adenosine 5'-monophospahate (AMP). The luciferase-based assay measures AMP production using an enzyme-coupled system that generates luminescence. The method is shown to provide an accurate measurement of APR kinetic properties and can be used for both endpoint and continuous assays. APR activity can be measured from pure enzyme preparations as well as from crude protein extracts of tissues. In addition, the assay is ideally suited to high-throughput sample analysis of APR activity in a microtiter dish format. The method adds new capability to the study of the biochemistry and physiology of APR.
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Affiliation(s)
- Xiaoli Xiang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA; Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingzhao Rong
- Institute of Maize Research, Key Laboratory of Biology and Genetic Improvement of Maize in the Southwest Region, Ministry of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi-Liang Zheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY 10468, USA
| | - Thomas Leustek
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA.
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Yeast 3',5'-bisphosphate nucleotidase: an affinity tag for protein purification. Protein Expr Purif 2014; 97:81-7. [PMID: 24613729 DOI: 10.1016/j.pep.2014.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/23/2014] [Accepted: 02/25/2014] [Indexed: 11/22/2022]
Abstract
Affinity chromatography is one of the most popular methods for protein purification. Each tag method has its advantages and disadvantages, and combination of different tags and developing of new tags had been proposed and performed. Yeast 3',5'-bisphosphate nucleotidase, also known as HAL2, hydrolyzes 3'-phosphoadenosine 5'-phosphate (PAP) with submicromolar Km, which indicated the tight interactions between HAL2 and PAP. In order to explore the feasibility of HAL2 as a protein purification affinity tag, HAL2 was further characterized with PAP as substrate. Results demonstrated that KmPAP and kcatPAP were ∼0.3μM and ∼11s(-)(1), respectively. Kd for PAP was 0.008μM in the presence of Ca(2+). pH was also found to affect interactions between HAL2 and PAP, with tightest binding (Kd∼8nM) at pH 7.5 and 8. The purification protocol was rationally designed based on nanomolar affinity to PAP agarose in the presence of Ca(2+), which could satisfy the metal requirement for PAP binding, prevent hydrolysis of immobilized PAP and could be chelated by ethylene glycol tetraacetic acid (EGTA) for elution. A series of expression vectors were further constructed and Escherichia coli adenosine 5'-phosphosulfate kinase (APSK) was prokaryotically expressed, purified and characterized. Ready to use expression vector with eight commonly used restriction enzyme recognition sites in multiple cloning site was subsequently constructed. By comparing with current popular tags, HAL2 was found to be an efficient and economical tag for prokaryotic protein expression and purification.
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Prioretti L, Gontero B, Hell R, Giordano M. Diversity and regulation of ATP sulfurylase in photosynthetic organisms. FRONTIERS IN PLANT SCIENCE 2014; 5:597. [PMID: 25414712 PMCID: PMC4220642 DOI: 10.3389/fpls.2014.00597] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 05/20/2023]
Abstract
ATP sulfurylase (ATPS) catalyzes the first committed step in the sulfate assimilation pathway, the activation of sulfate prior to its reduction. ATPS has been studied in only a few model organisms and even in these cases to a much smaller extent than the sulfate reduction and cysteine synthesis enzymes. This is possibly because the latter were considered of greater regulatory importance for sulfate assimilation. Recent evidences (reported in this paper) challenge this view and suggest that ATPS may have a crucial regulatory role in sulfate assimilation, at least in algae. In the ensuing text, we summarize the current knowledge on ATPS, with special attention to the processes that control its activity and gene(s) expression in algae. Special attention is given to algae ATPS proteins. The focus on algae is the consequence of the fact that a comprehensive investigation of ATPS revealed that the algal enzymes, especially those that are most likely involved in the pathway of sulfate reduction to cysteine, possess features that are not present in other organisms. Remarkably, algal ATPS proteins show a great diversity of isoforms and a high content of cysteine residues, whose positions are often conserved. According to the occurrence of cysteine residues, the ATPS of eukaryotic algae is closer to that of marine cyanobacteria of the genera Synechococcus and Prochlorococcus and is more distant from that of freshwater cyanobacteria. These characteristics might have evolved in parallel with the radiation of algae in the oceans and the increase of sulfate concentration in seawater.
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Affiliation(s)
- Laura Prioretti
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle MarcheAncona, Italy
| | - Brigitte Gontero
- Aix-Marseille Université Centre National de la Recherche Scientifique, BL' Unité de Bioénergétique et Ingénierie des Protéines UMR 7281Marseille, France
| | - Ruediger Hell
- Centre for Organismal Studies, University of HeidelbergHeidelberg, Germany
| | - Mario Giordano
- Laboratory of Algal and Plant Physiology, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle MarcheAncona, Italy
- Institute of Microbiology Academy of Sciences of the Czech RepublicTrebon, Czech Republic
- *Correspondence: Mario Giordano, Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy e-mail:
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Yadid I, Rudolph J, Hlouchova K, Copley SD. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proc Natl Acad Sci U S A 2013; 110:E2182-90. [PMID: 23676275 PMCID: PMC3683723 DOI: 10.1073/pnas.1214052110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbes in contaminated environments often evolve new metabolic pathways for detoxification or degradation of pollutants. In some cases, intermediates in newly evolved pathways are more toxic than the initial compound. The initial step in the degradation of pentachlorophenol by Sphingobium chlorophenolicum generates a particularly reactive intermediate; tetrachlorobenzoquinone (TCBQ) is a potent alkylating agent that reacts with cellular thiols at a diffusion-controlled rate. TCBQ reductase (PcpD), an FMN- and NADH-dependent reductase, catalyzes the reduction of TCBQ to tetrachlorohydroquinone. In the presence of PcpD, TCBQ formed by pentachlorophenol hydroxylase (PcpB) is sequestered until it is reduced to the less toxic tetrachlorohydroquinone, protecting the bacterium from the toxic effects of TCBQ and maintaining flux through the pathway. The toxicity of TCBQ may have exerted selective pressure to maintain slow turnover of PcpB (0.02 s(-1)) so that a transient interaction between PcpB and PcpD can occur before TCBQ is released from the active site of PcpB.
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Affiliation(s)
| | | | | | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
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Paritala H, Carroll KS. A continuous spectrophotometric assay for adenosine 5'-phosphosulfate reductase activity with sulfite-selective probes. Anal Biochem 2013; 440:32-9. [PMID: 23711725 DOI: 10.1016/j.ab.2013.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/06/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) adenosine 5'-phosphosulfate (APS) reductase (APR) catalyzes the first committed step in sulfate reduction for the biosynthesis of essential reduced sulfur-containing biomolecules, such as cysteine, and is essential for survival in the latent phase of tuberculosis (TB) infection. Despite the importance of APR to Mtb and other bacterial pathogens, current assay methods depend on the use of (35)S-labeled APS or shunt adenosine 5'-monophosphate (AMP) to a coupled-enzyme system. Both methods are cumbersome and require the use of expensive reagents. Here, we report the development of a continuous spectrophotometric method for measuring APR activity by using novel sulfite-selective colorimetric or "off-on" fluorescent levulinate-based probes. Thus, the APR activity can be followed by monitoring the increase in absorbance or fluorescence of the resulting phenolate product. Using this assay, we determined Michaelis-Menten kinetic constants (K(m), k(cat), and k(cat)/K(m)) and the apparent inhibition constant (Ki) for adenosine 5'-diphosphate (ADP), which compared favorably with values obtained in the "gold standard" radioactive assay. The newly developed assay is robust and easy to perform with a simple spectrophotometer.
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Mueller JW, Shafqat N. Adenosine-5'-phosphosulfate--a multifaceted modulator of bifunctional 3'-phospho-adenosine-5'-phosphosulfate synthases and related enzymes. FEBS J 2013; 280:3050-7. [PMID: 23517310 PMCID: PMC3734648 DOI: 10.1111/febs.12252] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/13/2013] [Accepted: 03/18/2013] [Indexed: 12/17/2022]
Abstract
All sulfation reactions rely on active sulfate in the form of 3′-phospho-adenosine-5′-phosphosulfate (PAPS). In fungi, bacteria, and plants, the enzymes responsible for PAPS synthesis, ATP sulfurylase and adenosine-5′-phosphosulfate (APS) kinase, reside on separate polypeptide chains. In metazoans, however, bifunctional PAPS synthases catalyze the consecutive steps of sulfate activation by converting sulfate to PAPS via the intermediate APS. This intricate molecule and the related nucleotides PAPS and 3′-phospho-adenosine-5′-phosphate modulate the function of various enzymes from sulfation pathways, and these effects are summarized in this review. On the ATP sulfurylase domain that initially produces APS from sulfate and ATP, APS acts as a potent product inhibitor, being competitive with both ATP and sulfate. For the APS kinase domain that phosphorylates APS to PAPS, APS is an uncompetitive substrate inhibitor that can bind both at the ATP/ADP-binding site and the PAPS/APS-binding site. For human PAPS synthase 1, the steady-state concentration of APS has been modelled to be 1.6 μm, but this may increase up to 60 μm under conditions of sulfate excess. It is noteworthy that the APS concentration for maximal APS kinase activity is 15 μm. Finally, we recognized APS as a highly specific stabilizer of bifunctional PAPS synthases. APS most likely stabilizes the APS kinase part of these proteins by forming a dead-end enzyme–ADP–APS complex at APS concentrations between 0.5 and 5 μm; at higher concentrations, APS may bind to the catalytic centers of ATP sulfurylase. Based on the assumption that cellular concentrations of APS fluctuate within this range, APS can therefore be regarded as a key modulator of PAPS synthase functions.
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Affiliation(s)
- Jonathan W Mueller
- Centre for Endocrinology, Diabetes, and Metabolism (CEDAM), School of Clinical and Experimental Medicine, University of Birmingham, Institute of Biomedical Research, Birmingham, UK.
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15
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Paritala H, Carroll KS. New targets and inhibitors of mycobacterial sulfur metabolism. Infect Disord Drug Targets 2013; 13:85-115. [PMID: 23808874 PMCID: PMC4332622 DOI: 10.2174/18715265113139990022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022]
Abstract
The identification of new antibacterial targets is urgently needed to address multidrug resistant and latent tuberculosis infection. Sulfur metabolic pathways are essential for survival and the expression of virulence in many pathogenic bacteria, including Mycobacterium tuberculosis. In addition, microbial sulfur metabolic pathways are largely absent in humans and therefore, represent unique targets for therapeutic intervention. In this review, we summarize our current understanding of the enzymes associated with the production of sulfated and reduced sulfur-containing metabolites in Mycobacteria. Small molecule inhibitors of these catalysts represent valuable chemical tools that can be used to investigate the role of sulfur metabolism throughout the Mycobacterial lifecycle and may also represent new leads for drug development. In this light, we also summarize recent progress made in the development of inhibitors of sulfur metabolism enzymes.
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Affiliation(s)
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, 33458, USA
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16
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The cysteine regulatory complex from plants and microbes: what was old is new again. Curr Opin Struct Biol 2013; 23:302-10. [DOI: 10.1016/j.sbi.2013.02.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 01/16/2013] [Accepted: 02/26/2013] [Indexed: 11/20/2022]
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18
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Sun M, Leyh TS. The human estrogen sulfotransferase: a half-site reactive enzyme. Biochemistry 2010; 49:4779-85. [PMID: 20429582 DOI: 10.1021/bi902190r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The affinity of 17beta-estradiol (E(2)) for the estrogen receptor is weakened beyond the point of physiological relevance by the transfer of the sulfuryl moiety (-SO(3)) from PAPS (3'-phosphoadenosine 5'-phosphosulfate) to the 3'-hydroxyl of E(2). The mechanism of this transfer reaction, catalyzed by estrogen sulfotransferase (EST), is investigated here in detail. The enzyme (a dimer of identical protomers) presents a clear example of half-sites reactivity--only one of the subunits of the dimer produces product during the catalytic cycle. This is the first example of half-sites reactivity in the sulfotransferase family. A burst of product, with an amplitude that corresponds to one-half of the available active sites, reveals that the mechanism is rate-limited by product release. The equilibrium constant governing interconversion of the substrate (E.PAPS.E(2)) and product (E.PAP.E(2)S) central complexes was determined and is strongly biased toward product (K(eq int) approximately 49). Slow product release allows the interconversion of the central complexes to approach equilibrium, with the result that K(eq int) becomes nearly linearly coupled to K(m) and contributes a factor of approximately 30 to the steady-state affinity of the enzyme for substrate. Typical of its family, estrogen sulfotransferase is partially k(cat)-inhibited by its acceptor substrate, E(2). This inhibition does not influence the burst kinetics and thus occurs after formation of the product central complex, a finding consistent with the slow escape of PAP from the nonreactive E.PAP.E(2) complex.
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Affiliation(s)
- Meihao Sun
- Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461-1926, USA
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Grum D, van den Boom J, Neumann D, Matena A, Link NM, Mueller JW. A heterodimer of human 3'-phospho-adenosine-5'-phosphosulphate (PAPS) synthases is a new sulphate activating complex. Biochem Biophys Res Commun 2010; 395:420-5. [PMID: 20382111 DOI: 10.1016/j.bbrc.2010.04.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 04/06/2010] [Indexed: 11/25/2022]
Abstract
3'-Phospho-adenosine-5'-phosphosulphate (PAPS) synthases are fundamental to mammalian sulphate metabolism. These enzymes have recently been linked to a rising number of human diseases. Despite many studies, it is not yet understood how the mammalian PAPS synthases 1 and 2 interact with each other. We provide first evidence for heterodimerisation of these two enzymes by pull-down assays and Förster resonance energy transfer (FRET) measurements. Kinetics of dimer dissociation/association indicates that these heterodimers form as soon as PAPSS1 and -S2 encounter each other in solution. Affinity of the homo- and heterodimers were found to be in the low nanomolar range using anisotropy measurements employing proteins labelled with the fluorescent dye IAEDANS that--in spite of its low quantum yield--is well suited for anisotropy due to its large Stokes shift. Within its kinase domain, the PAPS synthase heterodimer displays similar substrate inhibition by adenosine-5'-phosphosulphate (APS) as the homodimers. Due to divergent catalytic efficacies of PAPSS1 and -S2, the heterodimer might be a way of regulating PAPS synthase function within mammalian cells.
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Affiliation(s)
- Daniel Grum
- Structural and Medicinal Biochemistry, Centre for Medical Biotechnology - ZMB, Faculty of Biology and Geography, University of Duisburg-Essen, 45117 Essen, Germany.
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Yi H, Galant A, Ravilious GE, Preuss ML, Jez JM. Sensing sulfur conditions: simple to complex protein regulatory mechanisms in plant thiol metabolism. MOLECULAR PLANT 2010; 3:269-79. [PMID: 20080815 DOI: 10.1093/mp/ssp112] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sulfur is essential for plant growth and development, and the molecular systems for maintaining sulfur and thiol metabolism are tightly controlled. From a biochemical perspective, the regulation of plant thiol metabolism highlights nature's ability to engineer pathways that respond to multiple inputs and cellular demands under a range of conditions. In this review, we focus on the regulatory mechanisms that form the molecular basis of biochemical sulfur sensing in plants by translating the intracellular concentration of sulfur-containing compounds into control of key metabolic steps. These mechanisms range from the simple (substrate availability, thermodynamic properties of reactions, feedback inhibition, and organelle localization) to the elaborate (formation of multienzyme complexes and thiol-based redox switches). Ultimately, the dynamic interplay of these regulatory systems is critical for sensing and maintaining sulfur assimilation and thiol metabolism in plants.
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Affiliation(s)
- Hankuil Yi
- Department of Biology, Washington University, St Louis, MO 63130, USA
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Hong JA, Bhave DP, Carroll KS. Identification of critical ligand binding determinants in Mycobacterium tuberculosis adenosine-5'-phosphosulfate reductase. J Med Chem 2009; 52:5485-95. [PMID: 19678707 DOI: 10.1021/jm900728u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis adenosine-5'-phosphosulfate (APS) reductase is an iron-sulfur protein and a validated target to develop new antitubercular agents, particularly for the treatment of latent infection. To facilitate the development of potent and specific inhibitors of APS reductase, we have probed the molecular determinants that underlie binding and specificity through a series of substrate and product analogues. Our study highlights the importance of specific substitutent groups for substrate binding and provides functional evidence for ligand-specific conformational states. An active site model has been developed for M. tuberculosis APS reductase that is in accord with the results presented here as well as prior structural data reported for Pseudomonas aeruginosa APS reductase and related enzymes. This model illustrates the functional features required for the interaction of APS reductase with a ligand and provides a pharmacological roadmap for the rational design of small molecules as potential inhibitors of APS reductase present in human pathogens, including M. tuberculosis.
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Affiliation(s)
- Jiyoung A Hong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
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22
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Sulfate Activation Enzymes: Phylogeny and Association with Pyrophosphatase. J Mol Evol 2008; 68:1-13. [DOI: 10.1007/s00239-008-9181-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 07/10/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022]
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Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies. Biophys J 2008; 95:4659-67. [PMID: 18689458 PMCID: PMC2576392 DOI: 10.1529/biophysj.108.140038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes required for sulfur metabolism have been suggested to gain efficiency by restricted diffusion (i.e., channeling) of an intermediate APS(2-) between active sites. This article describes modeling of the whole channeling process by numerical solution of the Smoluchowski diffusion equation, as well as by coarse-grained Brownian dynamics. The results suggest that electrostatics plays an essential role in the APS(2-) channeling. Furthermore, with coarse-grained Brownian dynamics, the substrate channeling process has been studied with reactions in multiple active sites. Our simulations provide a bridge for numerical modeling with Brownian dynamics to simulate the complicated reaction and diffusion and raise important questions relating to the electrostatically mediated substrate channeling in vitro, in situ, and in vivo.
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