51
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Helmstetter F, Arnold P, Höger B, Petersen LM, Beitz E. Formate-nitrite transporters carrying nonprotonatable amide amino acids instead of a central histidine maintain pH-dependent transport. J Biol Chem 2018; 294:623-631. [PMID: 30455351 DOI: 10.1074/jbc.ra118.006340] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/09/2018] [Indexed: 01/25/2023] Open
Abstract
Microbial formate-nitrite transporter-type proteins (FNT) exhibit dual transport functionality. At neutral pH, electrogenic anion currents are detectable, whereas upon acidification transport of the neutral, protonated monoacid predominates. Physiologically, FNT-mediated proton co-transport is vital when monocarboxylic acid products of the energy metabolism, such as l-lactate, are released from the cell. Accordingly, Plasmodium falciparum malaria parasites can be killed by small-molecule inhibitors of PfFNT. Two opposing hypotheses on the site of substrate protonation are plausible. The proton relay mechanism postulates proton transfer from a highly conserved histidine centrally positioned in the transport path. The dielectric slide mechanism assumes decreasing acidity of substrates entering the lipophilic vestibules and protonation via the bulk water. Here, we defined the transport mechanism of the FNT from the amoebiasis parasite Entamoeba histolytica, EhFNT, and also show that BtFdhC from Bacillus thuringiensis is a functional formate transporter. Both FNTs carry a nonprotonatable amide amino acid, asparagine or glutamine, respectively, at the central histidine position. Despite having a nonprotonatable residue, EhFNT displayed the same substrate selectivity for larger monocarboxylates including l-lactate, a low substrate affinity as is typical for FNTs, and, strikingly, proton motive force-dependent transport as observed for PfFNT harboring a central histidine. These results argue against a proton relay mechanism, indicating that substrate protonation must occur outside of the central histidine region, most likely in the vestibules. Furthermore, EhFNT is the sole annotated FNT in the Entamoeba genome suggesting that it could be a putative new drug target with similar utility as that of the malarial PfFNT.
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Affiliation(s)
| | - Philipp Arnold
- the Anatomical Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Bastian Höger
- From the Department of Pharmaceutical and Medicinal Chemistry, and
| | | | - Eric Beitz
- From the Department of Pharmaceutical and Medicinal Chemistry, and
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52
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Erler H, Ren B, Gupta N, Beitz E. The intracellular parasite Toxoplasma gondii harbors three druggable FNT-type formate and l-lactate transporters in the plasma membrane. J Biol Chem 2018; 293:17622-17630. [PMID: 30237165 DOI: 10.1074/jbc.ra118.003801] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/14/2018] [Indexed: 12/31/2022] Open
Abstract
Toxoplasma gondii is a globally prevalent parasitic protist. It is well-known for its ability to infect almost all nucleated vertebrate cells, which is reflected by its unique metabolic architecture. Its fast-growing tachyzoite stage catabolizes glucose via glycolysis to yield l-lactate as a major by-product that must be exported from the cell to prevent toxicity; the underlying mechanism remains to be elucidated, however. Herein, we report three formate-nitrite transporter (FNT)-type monocarboxylate/proton symporters located in the plasma membrane of the T. gondii tachyzoite stage. We observed that all three proteins transport both l-lactate and formate in a pH-dependent manner and are inhibited by 2-hydroxy-chromanones (a class of small synthetic molecules). We also show that these compounds pharmacologically inhibit T. gondii growth. Using a chemical biology approach, we identified the critical residues in the substrate-selectivity region of the parasite transporters that determine differential specificity and sensitivity toward both substrates and inhibitors. Our findings further indicate that substrate specificity in FNT family proteins from T. gondii has evolved such that a functional repurposing of prokaryotic-type transporters helps fulfill a critical metabolic role in a clinically important parasitic protist. In summary, we have identified and characterized the lactate transporters of T. gondii and have shown that compounds blocking the FNTs in this parasite can inhibit its growth, suggesting that these transporters could have utility as potential drug targets.
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Affiliation(s)
- Holger Erler
- From the Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany and
| | - Bingjian Ren
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, 10115 Berlin, Germany
| | - Nishith Gupta
- Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, 10115 Berlin, Germany
| | - Eric Beitz
- From the Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany and
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53
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Doyle CJ, O'Toole PW, Cotter PD. Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain. Front Microbiol 2018; 9:1507. [PMID: 30026740 PMCID: PMC6041559 DOI: 10.3389/fmicb.2018.01507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/18/2018] [Indexed: 11/25/2022] Open
Abstract
Anaerobic sporeformers, specifically spoilage and pathogenic members of the genus Clostridium, are a concern for producers of dairy products, and of powdered dairy products in particular. As an alternative to testing for individual species, the traditional, and still current, approach to detecting these sporeformers, including non-spoilage/non-pathogenic species, in dairy products has involved testing for a sulphite reducing phenotype [Sulphite reducing Clostridia (SRCs)] under anaerobic conditions. This phenotype is conserved throughout the Order Clostridia. Unfortunately, however, this phenotype is exhibited by other sulphite reducing bacteria (SRBs) also, potentially leading to potential for false positives. Here, this risk was borne out through the identification of several SRBs from industry samples that were identified as Proteus mirabilis and various Bacillus/Paenibacillus sp. Genome wide comparison of a number of representative SRCs and SRBs was employed to determine phylogenetic relationships, especially among SRCs, and to characterize the genes responsible for the sulphite reducing phenotype. This screen identified two associated operons, i.e., asrABC in SRCs, and cysJI in Bacillus/Paenibacillus spp. and P. mirabilis. This screen identified spp. belonging to sensu stricto, Lachnospiraceae and Cluster XIV of the Clostridia all producing the SRC phenotype. This study highlights the inaccuracy of the industry standard SRC test but highlights the potential to generate an equivalent molecular test designed to detect the genes responsible for this phenotype in clostridia.
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Affiliation(s)
- Conor J Doyle
- Teagasc Food Research Centre, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Cork, Ireland.,APC Microbiome Ireland, Cork, Ireland
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54
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Shen J, Walsh BJC, Flores-Mireles AL, Peng H, Zhang Y, Zhang Y, Trinidad JC, Hultgren SJ, Giedroc DP. Hydrogen Sulfide Sensing through Reactive Sulfur Species (RSS) and Nitroxyl (HNO) in Enterococcus faecalis. ACS Chem Biol 2018; 13:1610-1620. [PMID: 29712426 PMCID: PMC6088750 DOI: 10.1021/acschembio.8b00230] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent studies of hydrogen sulfide (H2S) signaling implicate low molecular weight (LMW) thiol persulfides and other reactive sulfur species (RSS) as signaling effectors. Here, we show that a CstR protein from the human pathogen Enterococcus faecalis ( E. faecalis), previously identified in Staphylococcus aureus ( S. aureus), is an RSS-sensing repressor that transcriptionally regulates a cst-like operon in response to both exogenous sulfide stress and Angeli's salt, a precursor of nitroxyl (HNO). E. faecalis CstR reacts with coenzyme A persulfide (CoASSH) to form interprotomer disulfide and trisulfide bridges between C32 and C61', which negatively regulate DNA binding to a consensus CstR DNA operator. A Δ cstR strain exhibits deficiency in catheter colonization in a catheter-associated urinary tract infection (CAUTI) mouse model, suggesting sulfide regulation and homeostasis is critical for pathogenicity. Cellular polysulfide metabolite profiling of sodium sulfide-stressed E. faecalis confirms an increase in both inorganic polysulfides and LMW thiols and persulfides sensed by CstR. The cst-like operon encodes two authentic thiosulfate sulfurtransferases and an enzyme we characterize here as an NADH and FAD-dependent coenzyme A (CoA) persulfide reductase (CoAPR) that harbors an N-terminal CoA disulfide reductase (CDR) domain and a C-terminal rhodanese homology domain (RHD). Both cysteines in the CDR (C42) and RHD (C508) domains are required for CoAPR activity and complementation of a sulfide-induced growth phenotype of a S. aureus strain lacking cstB, encoding a nonheme FeII persulfide dioxygenase. We propose that S. aureus CstB and E. faecalis CoAPR employ orthogonal chemistries to lower CoASSH that accumulates under conditions of cellular sulfide toxicity and signaling.
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Affiliation(s)
- Jiangchuan Shen
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Brenna J. C. Walsh
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Ana Lidia Flores-Mireles
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63011, United States
| | - Hui Peng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Yifan Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Biochemistry Graduate Program, Indiana University, Bloomington, Indiana 47405, United States
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Jonathan C. Trinidad
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Laboratory for Biological Mass Spectrometry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Scott J. Hultgren
- Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri 63011, United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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55
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Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. THE ISME JOURNAL 2018; 12:1715-1728. [PMID: 29467397 PMCID: PMC6018805 DOI: 10.1038/s41396-018-0078-0] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 11/16/2022]
Abstract
A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, Berkeley, CA, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bela Hausmann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Sean P Jungbluth
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Rose S Kantor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adi Lavy
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Lesley A Warren
- Department of Civil Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Brian C Thomas
- Department of Earth and Planetary Science, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, Berkeley, CA, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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56
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Hydrogen sulfide as a regulatory factor in kidney health and disease. Biochem Pharmacol 2018; 149:29-41. [DOI: 10.1016/j.bcp.2017.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/05/2017] [Indexed: 12/19/2022]
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57
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Shefa U, Kim MS, Jeong NY, Jung J. Antioxidant and Cell-Signaling Functions of Hydrogen Sulfide in the Central Nervous System. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1873962. [PMID: 29507650 PMCID: PMC5817206 DOI: 10.1155/2018/1873962] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/13/2017] [Accepted: 12/11/2017] [Indexed: 12/13/2022]
Abstract
Hydrogen sulfide (H2S), a toxic gaseous molecule, plays a physiological role in regulating homeostasis and cell signaling. H2S is produced from cysteine by enzymes, such as cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), cysteine aminotransferase (CAT), and 3-mercaptopyruvate sulfurtransferase (3MST). These enzymes regulate the overall production of H2S in the body. H2S has a cell-signaling function in the CNS and plays important roles in combating oxidative species such as reactive oxygen species (ROS) and reactive nitrogen species (RNS) in the body. H2S is crucial for maintaining balanced amounts of antioxidants to protect the body from oxidative stress, and appropriate amounts of H2S are required to protect the CNS in particular. The body regulates CBS, 3MST, and CSE levels in the CNS, and higher or lower levels of these enzymes cause various neurodegenerative diseases. This review discusses how H2S protects the CNS by acting as an antioxidant that reduces excessive amounts of ROS and RNS. Additionally, H2S regulates cell signaling to combat neuroinflammation and protect against central neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS).
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Affiliation(s)
- Ulfuara Shefa
- Department of Biomedical Science, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Min-Sik Kim
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Na Young Jeong
- Department of Anatomy and Cell Biology, College of Medicine, Dong-A University, 32 Daesingongwon-ro, Seo-gu, Busan 49201, Republic of Korea
| | - Junyang Jung
- Department of Biomedical Science, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
- East-West Medical Research Institute, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
- Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
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58
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Louyakis AS, Gourlé H, Casaburi G, Bonjawo RME, Duscher AA, Foster JS. A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environ Microbiol 2017; 20:842-861. [DOI: 10.1111/1462-2920.14029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Hadrien Gourlé
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
- Department of Animal Breeding and Genetics; Global Bioinformatics Centre, Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Rachelle M. E. Bonjawo
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Alexandrea A. Duscher
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Jamie S. Foster
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
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59
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Olson KR. H 2S and polysulfide metabolism: Conventional and unconventional pathways. Biochem Pharmacol 2017; 149:77-90. [PMID: 29248597 DOI: 10.1016/j.bcp.2017.12.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 12/12/2017] [Indexed: 12/13/2022]
Abstract
It is now well established that hydrogen sulfide (H2S) is an effector of a wide variety of physiological processes. It is also clear that many of the effects of H2S are mediated through reactions with cysteine sulfur on regulatory proteins and most of these are not mediated directly by H2S but require prior oxidation of H2S and the formation of per- and polysulfides (H2Sn, n = 2-8). Attendant with understanding the regulatory functions of H2S and H2Sn is an appreciation of the mechanisms that control, i.e., both increase and decrease, their production and catabolism. Although a number of standard "conventional" pathways have been described and well characterized, novel "unconventional" pathways are continuously being identified. This review summarizes our current knowledge of both the conventional and unconventional.
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Affiliation(s)
- Kenneth R Olson
- Indiana University School of Medicine - South Bend, South Bend, IN 46617, USA.
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60
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Abstract
Numerous recent developments in the biochemistry, molecular biology, and physiology of formate and H2 metabolism and of the [NiFe]-hydrogenase (Hyd) cofactor biosynthetic machinery are highlighted. Formate export and import by the aquaporin-like pentameric formate channel FocA is governed by interaction with pyruvate formate-lyase, the enzyme that generates formate. Formate is disproportionated by the reversible formate hydrogenlyase (FHL) complex, which has been isolated, allowing biochemical dissection of evolutionary parallels with complex I of the respiratory chain. A recently identified sulfido-ligand attached to Mo in the active site of formate dehydrogenases led to the proposal of a modified catalytic mechanism. Structural analysis of the homologous, H2-oxidizing Hyd-1 and Hyd-5 identified a novel proximal [4Fe-3S] cluster in the small subunit involved in conferring oxygen tolerance to the enzymes. Synthesis of Salmonella Typhimurium Hyd-5 occurs aerobically, which is novel for an enterobacterial Hyd. The O2-sensitive Hyd-2 enzyme has been shown to be reversible: it presumably acts as a conformational proton pump in the H2-oxidizing mode and is capable of coupling reverse electron transport to drive H2 release. The structural characterization of all the Hyp maturation proteins has given new impulse to studies on the biosynthesis of the Fe(CN)2CO moiety of the [NiFe] cofactor. It is synthesized on a Hyp-scaffold complex, mainly comprising HypC and HypD, before insertion into the apo-large subunit. Finally, clear evidence now exists indicating that Escherichia coli can mature Hyd enzymes differentially, depending on metal ion availability and the prevailing metabolic state. Notably, Hyd-3 of the FHL complex takes precedence over the H2-oxidizing enzymes.
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61
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Atkovska K, Hub JS. Energetics and mechanism of anion permeation across formate-nitrite transporters. Sci Rep 2017; 7:12027. [PMID: 28931899 PMCID: PMC5607303 DOI: 10.1038/s41598-017-11437-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/24/2017] [Indexed: 01/13/2023] Open
Abstract
Formate-nitrite transporters (FNTs) facilitate the translocation of monovalent polyatomic anions, such as formate and nitrite, across biological membranes. FNTs are widely distributed among pathogenic bacteria and eukaryotic parasites, but they lack human homologues, making them attractive drug targets. The mechanisms and energetics involved in anion permeation across the FNTs have remained largely unclear. Both, channel and transporter mode of function have been proposed, with strong indication of proton coupling to the permeation process. We combine molecular dynamics simulations, quantum mechanical calculations, and pK a calculations, to compute the energetics of the complete permeation cycle of an FNT. We find that anions as such, are not able to traverse the FNT pore. Instead, anion binding into the pore is energetically coupled to protonation of a centrally located histidine. In turn, the histidine can protonate the permeating anion, thereby enabling its release. Such mechanism can accommodate the functional diversity among the FNTs, as it may facilitate both, export and import of substrates, with or without proton co-transport. The mechanism excludes proton leakage via the Grotthuss mechanism, and it rationalises the selectivity for weak acids.
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Affiliation(s)
- Kalina Atkovska
- University of Goettingen, Institute for Microbiology and Genetics, Goettingen, 37077, Germany.,University of Goettingen, Göttingen Center for Molecular Biosciences, Goettingen, 37077, Germany
| | - Jochen S Hub
- University of Goettingen, Institute for Microbiology and Genetics, Goettingen, 37077, Germany. .,University of Goettingen, Göttingen Center for Molecular Biosciences, Goettingen, 37077, Germany.
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62
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Gerritsen J, Hornung B, Renckens B, van Hijum SA, Martins dos Santos VA, Rijkers GT, Schaap PJ, de Vos WM, Smidt H. Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine. PeerJ 2017; 5:e3698. [PMID: 28924494 PMCID: PMC5598433 DOI: 10.7717/peerj.3698] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. METHODS The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. RESULTS We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. DISCUSSION This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
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Affiliation(s)
- Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Winclove Probiotics, Amsterdam, The Netherlands
| | - Bastian Hornung
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bernadette Renckens
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
| | - Sacha A.F.T. van Hijum
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Vitor A.P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Ger T. Rijkers
- Laboratory for Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, The Netherlands
- Department of Science, University College Roosevelt, Middelburg, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Departments of Microbiology and Immunology and Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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63
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Motl N, Skiba MA, Kabil O, Smith JL, Banerjee R. Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation. J Biol Chem 2017; 292:14026-14038. [PMID: 28684420 PMCID: PMC5572905 DOI: 10.1074/jbc.m117.790170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/26/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide (H2S) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts H2S to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium Burkholderia phytofirmans The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The B. phytofirmans PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that B. phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the Staphylococcus aureus PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.
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Affiliation(s)
- Nicole Motl
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Meredith A Skiba
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Omer Kabil
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600
| | - Janet L Smith
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, Michigan 48109-0600.
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64
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Hunger D, Röcker M, Falke D, Lilie H, Sawers RG. The C-terminal Six Amino Acids of the FNT Channel FocA Are Required for Formate Translocation But Not Homopentamer Integrity. Front Microbiol 2017; 8:1616. [PMID: 28878762 PMCID: PMC5572259 DOI: 10.3389/fmicb.2017.01616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/08/2017] [Indexed: 01/27/2023] Open
Abstract
FocA is the archetype of the pentameric formate-nitrite transporter (FNT) superfamily of channels, members of which translocate small organic and inorganic anions across the cytoplasmic membrane of microorganisms. The N- and C-termini of each protomer are cytoplasmically oriented. A Y-L-R motif is found immediately after transmembrane helix 6 at the C-terminus of FNT proteins related to FocA, or those with a role in formate translocation. Previous in vivo studies had revealed that formate translocation through FocA was controlled by interaction with the formate-producing glycyl-radical enzyme pyruvate formate-lyase (PflB) or its structural and functional homolog, TdcE. In this study we analyzed the effect on in vivo formate export and import, as well as on the stability of the homopentamer in the membrane, of successively removing amino acid residues from the C-terminus of FocA. Removal of up to five amino acids was without consequence for either formate translocation or oligomer stability. Removal of a sixth residue (R280) prevented formate uptake by FocA in a strain lacking PflB and significantly reduced, but did not prevent, formate export. Sensitivity to the toxic formate analog hypophosphite, which is also transported into the cell by FocA, was also relieved. Circular dichroism spectroscopy and blue-native PAGE analysis revealed, however, that this variant had near identical secondary and quaternary structural properties to those of native FocA. Interaction with the glycyl radical enzyme, TdcE, was also unaffected by removal of the C-terminal 6 amino acid residues, indicating that impaired interaction with TdcE was not the reason for impaired formate translocation. Removal of a further residue (L279) severely restricted formate export, the stability of the protein and its ability to form homopentamers. Together, these studies revealed that the Y278-L279-R280 motif at the C-terminus is essential for bidirectional formate translocation by FocA, but that L279 is both necessary and sufficient for homopentamer integrity.
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Affiliation(s)
- Doreen Hunger
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Marie Röcker
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Dörte Falke
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-WittenbergHalle, Germany
| | - R Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-WittenbergHalle, Germany
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65
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Anion-selective Formate/nitrite transporters: taxonomic distribution, phylogenetic analysis and subfamily-specific conservation pattern in prokaryotes. BMC Genomics 2017; 18:560. [PMID: 28738779 PMCID: PMC5525234 DOI: 10.1186/s12864-017-3947-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/16/2017] [Indexed: 11/10/2022] Open
Abstract
Background The monovalent anions formate, nitrite and hydrosulphide are main metabolites of bacterial respiration during anaerobic mixed-acid fermentation. When accumulated in the cytoplasm, these anions become cytotoxic. Membrane proteins that selectively transport these monovalent anions across the membrane have been identified and they belong to the family of Formate/Nitrite Transporters (FNTs). Individual members that selectively transport formate, nitrite and hydrosulphide have been investigated. Experimentally determined structures of FNTs indicate that they share the same hourglass helical fold with aquaporins and aquaglyceroporins and have two constriction regions, namely, cytoplasmic slit and central constriction. Members of FNTs are found in bacteria, archaea, fungi and protists. However, no FNT homolog has been identified in mammals. With FNTs as potential drug targets for many bacterial diseases, it is important to understand the mechanism of selectivity and transport across these transporters. Results We have systematically searched the sequence databases and identified 2206 FNT sequences from bacteria, archaea and eukaryotes. Although FNT sequences are very diverse, homology modeling followed by structure-based sequence alignment revealed that nearly one third of all the positions within the transmembrane region exhibit high conservation either as a group or at the level of individual residues across all three kingdoms. Phylogenetic analysis of prokaryotic FNT sequences revealed eight different subgroups. Formate, nitrite and hydrosulphide transporters respectively are clustered into two (FocA and FdhC), three (NirC-α, NirC-β and NirC-γ) and one (HSC) subfamilies. We have also recognized two FNT subgroups (YfdC-α and YfdC-β) with unassigned function. Analysis of taxonomic distribution indicates that each subfamily prefers specific taxonomic groups. Structure-based sequence alignment of individual subfamily members revealed that certain positions in the two constriction regions and some residues facing the interior show subfamily-specific conservation. We have also identified examples of FNTs with the two constriction regions formed by residues that are less frequently observed. We have developed dbFNT, a database of FNT models and associated details. dbFNT is freely available to scientific community. Conclusions Taxonomic distribution and sequence conservation of FNTs exhibit subfamily-specific features. The conservation pattern in the central constriction and cytoplasmic slit in the open and closed states are distinct for YfdC and NirC subfamilies. The same is true for some residues facing the interior of the transporters. The specific residues in these positions can exert influence on the type of solutes that are transported by these proteins. With FNTs found in many disease-causing bacteria, the knowledge gained in this study can be used in the development and design of anti-bacterial drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3947-4) contains supplementary material, which is available to authorized users.
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66
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Wiechert M, Erler H, Golldack A, Beitz E. A widened substrate selectivity filter of eukaryotic formate-nitrite transporters enables high-level lactate conductance. FEBS J 2017; 284:2663-2673. [PMID: 28544379 DOI: 10.1111/febs.14117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/05/2017] [Accepted: 05/18/2017] [Indexed: 12/24/2022]
Abstract
Bacterial formate-nitrite transporters (FNT) regulate the metabolic flow of small weak mono-acids derived from anaerobic mixed-acid fermentation, such as formate, and further transport nitrite and hydrosulfide. The eukaryotic Plasmodium falciparumFNT is vital for the malaria parasite by its ability to release the larger l-lactate substrate as the metabolic end product of anaerobic glycolysis in symport with protons preventing cytosolic acidification. However, the molecular basis for substrate discrimination by FNTs has remained unclear. Here, we identified a size-selective FNT substrate filter region around an invariant lysine at the bottom of the periplasmic/extracellular vestibule. The selectivity filter is reminiscent of the aromatic/arginine constriction of aquaporin water and solute channels regarding composition, location in the protein, and the size-selection principle. Bioinformatics support an adaptation of the eukaryotic FNT selectivity filter to accommodate larger physiologically relevant substrates. Mutations that affect the diameter at the filter site predictably modulated substrate selectivity. The shape of the vestibule immediately above the filter region further affects selectivity. This study indicates that eukaryotic FNTs evolved to transport larger mono-acid substrates, especially l-lactic acid as a product of energy metabolism.
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Affiliation(s)
- Marie Wiechert
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Germany
| | - Holger Erler
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Germany
| | - André Golldack
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Germany
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67
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Wiechert M, Beitz E. Mechanism of formate-nitrite transporters by dielectric shift of substrate acidity. EMBO J 2017; 36:949-958. [PMID: 28250043 DOI: 10.15252/embj.201695776] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/25/2017] [Accepted: 01/30/2017] [Indexed: 11/09/2022] Open
Abstract
Bacterial formate-nitrite transporters (FNTs) regulate the metabolic flow of small, weak mono-acids. Recently, the eukaryotic PfFNT was identified as the malaria parasite's lactate transporter and novel drug target. Despite crystal data, central mechanisms of FNT gating and transport remained unclear. Here, we show elucidation of the FNT transport mechanism by single-step substrate protonation involving an invariant lysine in the periplasmic vestibule. Opposing earlier gating hypotheses and electrophysiology reports, quantification of total uptake by radiolabeled substrate indicates a permanently open conformation of the bacterial formate transporter, FocA, irrespective of the pH Site-directed mutagenesis, heavy water effects, mathematical modeling, and simulations of solvation imply a general, proton motive force-driven FNT transport mechanism: Electrostatic attraction of the acid anion into a hydrophobic vestibule decreases substrate acidity and facilitates protonation by the bulk solvent. We define substrate neutralization by proton transfer for transport via a hydrophobic transport path as a general theme of the Amt/Mep/Rh ammonium and formate-nitrite transporters.
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Affiliation(s)
- Marie Wiechert
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel, Kiel, Germany
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68
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Ishibashi K, Morishita Y, Tanaka Y. The Evolutionary Aspects of Aquaporin Family. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 969:35-50. [PMID: 28258564 DOI: 10.1007/978-94-024-1057-0_2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aquaporins (AQPs ) are a family of transmembrane proteins present in almost all species including virus. They are grossly divided into three subfamilies based on the sequence around a highly conserved pore-forming NPA motif: (1) classical water -selective AQP (CAQP), (2) glycerol -permeable aquaglyceroporin (AQGP) and (3) AQP super-gene channel, superaquaporin (SAQP). AQP is composed of two tandem repeats of conserved three transmembrane domains and a NPA motif. AQP ancestors probably started in prokaryotes by the duplication of half AQP genes to be diversified into CAQPs or AQGPs by evolving a subfamily-specific carboxyl-terminal NPA motif. Both AQP subfamilies may have been carried over to unicellular eukaryotic ancestors, protists and further to multicellular organisms. Although fungus lineage has kept both AQP subfamilies, the plant lineage has lost AQGP after algal ancestors with extensive diversifications of CAQPs into PIP, TIP, SIP, XIP, HIP and LIP with a possible horizontal transfer of NIP from bacteria. Interestingly, the animal lineage has obtained new SAQP subfamily with highly deviated NPA motifs, especially at the amino-terminal halves in both prostomial and deuterostomial animals. The prostomial lineage has lost AQGP after hymenoptera, while the deuterostomial lineage has kept all three subfamilies up to the vertebrate with diversified CAQPs (AQP0, 1, 2, 4, 5, 6, 8) and AQGPs (AQP3, 7, 9, 10) with limited SAQPs (AQP11, 12) in mammals. Whole-genome duplications, local gene duplications and horizontal gene transfers may have produced the AQP diversity with adaptive selections and functional alternations in response to environment changes. With the above evolutionary perspective in mind, the function of each AQP could be speculated by comparison among species to get new insights into physiological roles of AQPs . This evolutionary guidance in AQP research will lead to deeper understandings of water and solute homeostasis.
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Affiliation(s)
- Kenichi Ishibashi
- Division of Pathophysiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan.
| | - Yoshiyuki Morishita
- Division of Nephrology, Saitama Medical Center, Jichi Medical University, 1-847 Ohmiya, Saitama-City, Saitama, 330-8503, Japan
| | - Yasuko Tanaka
- Division of Pathophysiology, Meiji Pharmaceutical University, Kiyose, Tokyo, 204-8588, Japan
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69
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Shen J, Peng H, Zhang Y, Trinidad JC, Giedroc DP. Staphylococcus aureus sqr Encodes a Type II Sulfide:Quinone Oxidoreductase and Impacts Reactive Sulfur Speciation in Cells. Biochemistry 2016; 55:6524-6534. [PMID: 27806570 DOI: 10.1021/acs.biochem.6b00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent studies implicate hydrogen sulfide (H2S) oxidation as an important aspect of bacterial antibiotic resistance and sulfide homeostasis. The cst operon of the major human pathogen Staphylococcus aureus is induced by exogenous H2S stress and encodes enzymes involved in sulfide oxidation, including a group I flavoprotein disulfide oxidoreductase sulfide:quinone oxidoreductase (SQR). In this work, we show that S. aureus SQR catalyzes the two-electron oxidation of sodium sulfide (Na2S) into sulfane sulfur (S0) when provided flavin adenine dinucleotide and a water-soluble quinone acceptor. Cyanide, sulfite, and coenzyme A (CoA) are all capable of functioning as the S0 acceptor in vitro. This activity requires a C167-C344 disulfide bond in the resting enzyme, with the intermediacy of a C344 persulfide in the catalytic cycle, verified by mass spectrometry of sulfide-reacted SQR. Incubation of purified SQR and S. aureus CstB, a known FeII persulfide dioxygenase-sulfurtransferase also encoded by the cst operon, yields thiosulfate from sulfide, in a CoA-dependent manner, thus confirming the intermediacy of CoASSH as a product and substrate of SQR and CstB, respectively. Sulfur metabolite profiling of wild-type, Δsqr, and Δsqr::pSQR strains reveals a marked and specific elevation in endogenous levels of CoASSH and inorganic tetrasulfide in the Δsqr strain. We conclude that SQR impacts the cellular speciation of these reactive sulfur species but implicates other mechanisms not dependent on SQR in the formation of low-molecular weight thiol persulfides and inorganic polysulfides during misregulation of sulfide homeostasis.
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Affiliation(s)
- Jiangchuan Shen
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Biochemistry Graduate Program, Indiana University , Bloomington, Indiana 47405, United States
| | - Hui Peng
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Biochemistry Graduate Program, Indiana University , Bloomington, Indiana 47405, United States
| | - Yixiang Zhang
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Laboratory for Biological Mass Spectrometry, Indiana University , Bloomington, Indiana 47405, United States
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Laboratory for Biological Mass Spectrometry, Indiana University , Bloomington, Indiana 47405, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States.,Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
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Hartle MD, Hansen RJ, Tresca BW, Prakel SS, Zakharov LN, Haley MM, Pluth MD, Johnson DW. A Synthetic Supramolecular Receptor for the Hydrosulfide Anion. Angew Chem Int Ed Engl 2016; 55:11480-4. [PMID: 27510286 DOI: 10.1002/anie.201605757] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Indexed: 12/11/2022]
Abstract
Hydrogen sulfide (H2 S) has emerged as a crucial biomolecule in physiology and cellular signaling. Key challenges associated with developing new chemical tools for understanding the biological roles of H2 S include developing platforms that enable reversible binding of this important biomolecule. The first synthetic small molecule receptor for the hydrosulfide anion, HS(-) , using only reversible, hydrogen-bonding interactions in a series of bis(ethynylaniline) derivatives, is reported. Binding constants of up to 90 300±8700 m(-1) were obtained in MeCN. The fundamental science of reversible sulfide binding, in this case featuring a key CH⋅⋅⋅S hydrogen bond, will expand the possibility for discovery of sulfide protein targets and molecular recognition agents.
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Affiliation(s)
- Matthew D Hartle
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Ryan J Hansen
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Blakely W Tresca
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Samuel S Prakel
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA
| | - Lev N Zakharov
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.,CAMCOR-Center for Advanced Materials Characterization in Oregon, University of Oregon, Eugene, OR, 97403-1443, USA
| | - Michael M Haley
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
| | - Michael D Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
| | - Darren W Johnson
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403-1253, USA.
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71
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Hartle MD, Hansen RJ, Tresca BW, Prakel SS, Zakharov LN, Haley MM, Pluth MD, Johnson DW. A Synthetic Supramolecular Receptor for the Hydrosulfide Anion. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew D. Hartle
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Ryan J. Hansen
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Blakely W. Tresca
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Samuel S. Prakel
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Lev N. Zakharov
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
- CAMCOR—Center for Advanced Materials Characterization in Oregon University of Oregon Eugene OR 97403-1443 USA
| | - Michael M. Haley
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Michael D. Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
| | - Darren W. Johnson
- Department of Chemistry & Biochemistry, Materials Science Institute, and Institute of Molecular Biology University of Oregon Eugene OR 97403-1253 USA
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72
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Kimura H. Hydrogen polysulfide (H 2S n ) signaling along with hydrogen sulfide (H 2S) and nitric oxide (NO). J Neural Transm (Vienna) 2016; 123:1235-1245. [PMID: 27484215 DOI: 10.1007/s00702-016-1600-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/19/2016] [Indexed: 01/22/2023]
Abstract
Hydrogen sulfide (H2S) is a physiological mediator with various roles, including neuro-modulation, vascular tone regulation, and cytoprotection against ischemia-reperfusion injury, angiogenesis, and oxygen sensing. Hydrogen polysulfide (H2S n ), which possesses a higher number of sulfur atoms than H2S, recently emerged as a potential signaling molecule that regulates the activity of ion channels, a tumor suppressor, transcription factors, and protein kinases. Some of the previously reported effects of H2S are now attributed to the more potent H2S n . H2S n is produced by 3-mercaptopyruvate sulfurtransferase (3MST) from 3-mercaptopyruvate (3MP) and is generated by the chemical interaction of H2S with nitric oxide (NO). H2S n sulfhydrates (sulfurates) cysteine residues of target proteins and modifies their activity, whereas H2S sulfurates oxidized cysteine residues as well as reduces cysteine disulfide bonds. This review focuses on the recent progress made in studies concerning the production and physiological roles of H2S n and H2S.
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Affiliation(s)
- Hideo Kimura
- Department of Molecular Pharmacology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.
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73
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Holm-Bertelsen J, Bock S, Helmstetter F, Beitz E. High-level cell-free production of the malarial lactate transporter PfFNT as a basis for crystallization trials and directional transport studies. Protein Expr Purif 2016; 126:109-114. [PMID: 27345711 DOI: 10.1016/j.pep.2016.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 01/10/2023]
Abstract
The malaria parasite Plasmodium falciparum relies on the function of channel and transport proteins for the uptake of nutrients and the release of metabolic waste products. Inhibition of vital transport processes is an unexploited means for developing novel antimalarial drugs. The recently discovered plasmodial lactate transporter, PfFNT, represents a promising new drug target since the parasite's energy generation by anaerobic glycolysis depends on the rapid secretion of lactate. Yet, membrane proteins, in particular those of malaria parasites, are notoriously difficult to produce and purify in the native, functional form hampering crystallization and biophysical studies. Here, we show synthesis of milligram quantities of correctly folded PfFNT in a cell-free system. Solubilized PfFNT maintained its oligomeric, largely SDS-resistant quaternary structure and appears suitable for setting up crystallization trials. After reconstitution into proteoliposomes, PfFNT was functional as a transporter for formate, acetate, and lactate as determined by a light-scattering assay. Analysis of the accessibility of a protease cleavage site at the N-terminus revealed an even outside-in orientation of the total proteoliposomal PfFNT population that may be due to membrane curvature restrictions. Contrary to previous studies using heterologous expression in cell systems with oppositely oriented PfFNT, the proteoliposomes eventually allow for biophysical transport studies in the native, physiological direction.
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Affiliation(s)
- Julia Holm-Bertelsen
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Sinja Bock
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Folknand Helmstetter
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Eric Beitz
- Christian-Albrechts-University of Kiel, Department of Medicinal and Pharmaceutical Chemistry, Gutenbergstraße 76, 24118 Kiel, Germany.
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74
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Karpowich NK, Song J, Wang DN. An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin. J Mol Biol 2016; 428:3118-30. [PMID: 27312125 DOI: 10.1016/j.jmb.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
Abstract
ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.
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Affiliation(s)
- Nathan K Karpowich
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
| | - Jinmei Song
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Da-Neng Wang
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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Bañares-España E, del Mar Fernández-Arjona M, García-Sánchez MJ, Hernández-López M, Reul A, Mariné MH, Flores-Moya A. Sulphide Resistance in the Cyanobacterium Microcystis aeruginosa: a Comparative Study of Morphology and Photosynthetic Performance Between the Sulphide-Resistant Mutant and the Wild-Type Strain. MICROBIAL ECOLOGY 2016; 71:860-872. [PMID: 26677166 DOI: 10.1007/s00248-015-0715-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The cyanobacterium Microcystis aeruginosa is a mesophilic freshwater organism, which cannot tolerate sulphide. However, it was possible to isolate a sulphide-resistant (S(r)) mutant strain that was able to survive in a normally lethal medium sulphide. In order to evaluate the cost of the mutation conferring sulphide resistance in the S(r) strain of M. aeruginosa, the morphology and the photosynthetic performance were compared to that found in the wild-type, sulphide-sensitive (S(s)) strain. An increase in size and a disrupted morphology was observed in S(r) cells in comparison to the S(s) counterpart. Phycoerythrin and phycocyanin levels were higher in the S(r) than in the S(s) cells, whereas a higher carotenoid content, per unit volume, was found in the S(s) strain. The irradiance-saturated photosynthetic oxygen-production rate (GPR max) and the photosynthetic efficiency (measured both by oxygen production and fluorescence, α(GPR) and α(ETR)) were lower in the S(r) strain than in the wild-type. These results appear to be the result of package effect. On the other hand, the S(r) strain showed higher quantum yield of non-photochemical quenching, especially those regulated mechanisms (estimated throughout qN and Y(NPQ)) and a significantly lower slope in the maximum quantum yield of light-adapted samples (Fv'/Fm') compared to the S(s) strain. These findings point to a change in the regulation of the quenching of the transition states (qT) in the S(r) strain which may be generated by a change in the distribution of thylakoidal membranes, which somehow could protect metalloenzymes of the electron transport chain from the lethal effect of sulphide.
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Affiliation(s)
- Elena Bañares-España
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain.
| | - María del Mar Fernández-Arjona
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - María Jesús García-Sánchez
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Miguel Hernández-López
- Departamento de Química Analítica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Andreas Reul
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
| | - Mariona Hernández Mariné
- Departamento de Productos Naturales, Biología Vegetal y Edafología, Facultad de Farmacia, Universidad de Barcelona, Av. Joan XXIII s/n, 08028, Barcelona, Spain
| | - Antonio Flores-Moya
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
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76
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Leavitt WD, Bradley AS, Santos AA, Pereira IAC, Johnston DT. Sulfur Isotope Effects of Dissimilatory Sulfite Reductase. Front Microbiol 2015; 6:1392. [PMID: 26733949 PMCID: PMC4690157 DOI: 10.3389/fmicb.2015.01392] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/23/2015] [Indexed: 12/01/2022] Open
Abstract
The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S, 36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in 34S/32S (hereafter, 34εDsrAB) to be 15.3 ± 2‰, 2σ. The accompanying minor isotope effect in 33S, described as 33λDsrAB, is calculated to be 0.5150 ± 0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3–0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in 34εDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of 34εDsrAB is similar to the median value of experimental observations compiled from all known published work, where 34εr−p = 16.1‰ (r–p indicates reactant vs. product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34εSO4−H2S = 17.3 ± 1.5‰, 2σ) and in modern marine sediments (34εSO4−H2S = 17.3 ± 3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments.
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Affiliation(s)
- William D Leavitt
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA; Department of Earth and Planetary Sciences, Washington University in St. LouisSt. Louis, MO, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis St. Louis, MO, USA
| | - André A Santos
- Bacterial Energy Metabolism Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Inês A C Pereira
- Bacterial Energy Metabolism Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
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77
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Abstract
This review is focused on formation and biological significance of hydropersulfides, i.e. S-sulfhydration process. Biogenesis and properties of reactive sulfur species and their role in redox signaling are presented. The effect of S-sulfhydration on protein function is discussed. For many years reactive oxygen and nitrogen species (ROS and RNS) have been recognized as key messengers in the process of thiol-based redox regulation. Relatively recently, literature reports began to mention reactive sulfur species (RSS) and their role in thiol regulation. This review is focused on biogenesis and biological properties of RSS, including: hydropersulfides, polysulfides and hydrogen sulfide (H2S). Based on the most up-to-date literature data, the paper presents biological significance of S-sulfhydration process. In this reaction, sulfane sulfur is transferred to the–SH groups forming hydropersulfides. Protein cysteine residues, called ‘redox switches’ are susceptible to such reversible modifications. In line with the most recent reports, it was emphasized that sulfane sulfur-containing compounds (mainly hydrogen persulfides and polysulfides) are real and better mediators of S-sulfhydration-based signalling than H2S. We also overviewed proteins participating in the formation and transport of RSS and in mitochondrial H2S oxidation. In addition, we reviewed many reports about proteins unrelated to sulfur metabolism which are modified by S-sulfhydration that influences their catalytic activity. We also addressed the problem of the regulatory function of S-sulfhydration reaction in the activation of KATP channels (vasorelaxant) and transcription factors (e.g. NFκB) as well as in the mechanism of therapeutic action of garlic-derived sulfur compounds. Some aspects of comparison between RNS and RSS are also discussed in this review.
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78
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Wang Y, Kim SH, Feng L. Highly luminescent N, S- Co-doped carbon dots and their direct use as mercury(II) sensor. Anal Chim Acta 2015; 890:134-42. [DOI: 10.1016/j.aca.2015.07.051] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/01/2015] [Accepted: 07/03/2015] [Indexed: 01/24/2023]
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Shen J, Keithly ME, Armstrong RN, Higgins KA, Edmonds KA, Giedroc DP. Staphylococcus aureus CstB Is a Novel Multidomain Persulfide Dioxygenase-Sulfurtransferase Involved in Hydrogen Sulfide Detoxification. Biochemistry 2015; 54:4542-54. [PMID: 26177047 DOI: 10.1021/acs.biochem.5b00584] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen sulfide (H2S) is both a lethal gas and an emerging gasotransmitter in humans, suggesting that the cellular H2S level must be tightly regulated. CstB is encoded by the cst operon of the major human pathogen Staphylococcus aureus and is under the transcriptional control of the persulfide sensor CstR and H2S. Here, we show that CstB is a multifunctional Fe(II)-containing persulfide dioxygenase (PDO), analogous to the vertebrate protein ETHE1 (ethylmalonic encephalopathy protein 1). Chromosomal deletion of ethe1 is fatal in vertebrates. In the presence of molecular oxygen (O2), hETHE1 oxidizes glutathione persulfide (GSSH) to generate sulfite and reduced glutathione. In contrast, CstB oxidizes major cellular low molecular weight (LMW) persulfide substrates from S. aureus, coenzyme A persulfide (CoASSH) and bacillithiol persulfide (BSSH), directly to generate thiosulfate (TS) and reduced thiols, thereby avoiding the cellular toxicity of sulfite. Both Cys201 in the N-terminal PDO domain (CstB(PDO)) and Cys408 in the C-terminal rhodanese domain (CstB(Rhod)) strongly enhance the TS generating activity of CstB. CstB also possesses persulfide transferase (PT; reverse rhodanese) activity, which generates TS when provided with LMW persulfides and sulfite, as well as conventional thiosulfate transferase (TST; rhodanese) activity; both of these activities require Cys408. CstB protects S. aureus against H2S toxicity, with the C201S and C408S cstB genes being unable to rescue a NaHS-induced ΔcstB growth phenotype. Induction of the cst operon by NaHS reveals that functional CstB impacts cellular TS concentrations. These data collectively suggest that CstB may have evolved to facilitate the clearance of LMW persulfides that occur upon elevation of the level of cellular H2S and hence may have an impact on bacterial viability under H2S misregulation, in concert with the other enzymes encoded by the cst operon.
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Affiliation(s)
| | - Mary E Keithly
- §Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard N Armstrong
- §Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States.,∥Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6304, United States
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80
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Luebke JL, Giedroc DP. Cysteine sulfur chemistry in transcriptional regulators at the host-bacterial pathogen interface. Biochemistry 2015; 54:3235-49. [PMID: 25946648 DOI: 10.1021/acs.biochem.5b00085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hosts employ myriad weapons to combat invading microorganisms as an integral feature of the host-bacterial pathogen interface. This interface is dominated by highly reactive small molecules that collectively induce oxidative stress. Successful pathogens employ transcriptional regulatory proteins that sense these small molecules directly or indirectly via a change in the ratio of reduced to oxidized low-molecular weight (LMW) thiols that collectively comprise the redox buffer in the cytoplasm. These transcriptional regulators employ either a prosthetic group or reactive cysteine residue(s) to effect changes in the transcription of genes that encode detoxification and repair systems that is driven by regulator conformational switching between high-affinity and low-affinity DNA-binding states. Cysteine harbors a highly polarizable sulfur atom that readily undergoes changes in oxidation state in response to oxidative stress to produce a range of regulatory post-translational modifications (PTMs), including sulfenylation (S-hydroxylation), mixed disulfide bond formation with LMW thiols (S-thiolation), di- and trisulfide bond formation, S-nitrosation, and S-alkylation. Here we discuss several examples of structurally characterized cysteine thiol-specific transcriptional regulators that sense changes in cellular redox balance, focusing on the nature of the cysteine PTM itself and the interplay of small molecule oxidative stressors in mediating a specific transcriptional response.
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Affiliation(s)
- Justin L Luebke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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81
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Rycovska-Blume A, Lü W, Andrade S, Fendler K, Einsle O. Structural and Functional Studies of NirC from Salmonella typhimurium. Methods Enzymol 2015; 556:475-97. [PMID: 25857796 DOI: 10.1016/bs.mie.2014.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
NirC is a pentameric transport system for monovalent anions that is expressed in the context of assimilatory nitrite reductase NirBD in a wide variety of enterobacterial species. A NirC pentamer contains individual pores in each protomer that mediate the passage of at least the nitrite [Formula: see text] and nitrate [Formula: see text] anions. As a member of the formate/nitrite transporter family of membrane transport proteins, NirC shares a range of structural and functional features with the formate channel FocA and the hydrosulfide channel AsrD (HSC). NirC from the enteropathogen Salmonella typhimurium has been studied by X-ray crystallography, proton uptake assays, and different electrophysiological techniques, and the picture that has emerged shows a fast and versatile transport system for nitrite that doubles as a defense system during the enteric life of the bacterium. Structural and functional assays are described, which shed light on the transport mechanism of this important molecular machine.
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Affiliation(s)
- Adriana Rycovska-Blume
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Wei Lü
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
| | - Susana Andrade
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
| | - Klaus Fendler
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg im Breisgau, Germany
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82
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Identity of a Plasmodium lactate/H(+) symporter structurally unrelated to human transporters. Nat Commun 2015; 6:6284. [PMID: 25669138 DOI: 10.1038/ncomms7284] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/12/2015] [Indexed: 11/09/2022] Open
Abstract
Maintenance of a high glycolytic flow rate is critical for the rapid growth and virulence of malarial parasites. The parasites release two moles of lactic acid per mole of glucose as the anaerobic end product. However, the molecular identity of the Plasmodium lactate transporter is unknown. Here we show that a member of the microbial formate-nitrite transporter family, PfFNT, acts as a lactate/proton symporter in Plasmodium falciparum. Besides L-lactate, PfFNT transports physiologically relevant D-lactate, as well as pyruvate, acetate and formate, and is inhibited by the antiplasmodial compounds phloretin, furosemide and cinnamate derivatives, but not by p-chloromercuribenzene sulfonate (pCMBS). Our data on PfFNT monocarboxylate transport are consistent with those obtained with living parasites. Moreover, PfFNT is the only transporter of the plasmodial glycolytic pathway for which structure information is available from crystals of homologous proteins, rendering it amenable to further evaluation as a novel antimalarial drug target.
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83
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KIMURA H. Hydrogen sulfide and polysulfides as signaling molecules. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:131-59. [PMID: 25864468 PMCID: PMC4568289 DOI: 10.2183/pjab.91.131] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Hydrogen sulfide (H2S) is a familiar toxic gas that smells of rotten eggs. After the identification of endogenous H2S in the mammalian brain two decades ago, studies of this molecule uncovered physiological roles in processes such as neuromodulation, vascular tone regulation, cytoprotection against oxidative stress, angiogenesis, anti-inflammation, and oxygen sensing. Enzymes that produce H2S, such as cystathionine β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase have been studied intensively and well characterized. Polysulfides, which have a higher number of inner sulfur atoms than that in H2S, were recently identified as potential signaling molecules that can activate ion channels, transcription factors, and tumor suppressors with greater potency than that of H2S. This article focuses on our contribution to the discovery of these molecules and their metabolic pathways and mechanisms of action.
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Affiliation(s)
- Hideo KIMURA
- Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, Tokyo, Japan
- Correspondence should be addressed: H. Kimura, Department of Molecular Pharmacology, National Institute of Neuroscience, NCNP, 4-1-1 Ogawahigashi, Kodaira, Tokyo 187-8502, Japan (e-mail: )
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84
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Luebke JL, Shen J, Bruce KE, Kehl-Fie TE, Peng H, Skaar EP, Giedroc DP. The CsoR-like sulfurtransferase repressor (CstR) is a persulfide sensor in Staphylococcus aureus. Mol Microbiol 2014; 94:1343-60. [PMID: 25318663 DOI: 10.1111/mmi.12835] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2014] [Indexed: 12/20/2022]
Abstract
How cells regulate the bioavailability of utilizable sulfur while mitigating the effects of hydrogen sulfide toxicity is poorly understood. CstR [Copper-sensing operon repressor (CsoR)-like sulfurtransferase repressor] represses the expression of the cst operon encoding a putative sulfide oxidation system in Staphylococcus aureus. Here, we show that the cst operon is strongly and transiently induced by cellular sulfide stress in an acute phase and specific response and that cst-encoded genes are necessary to mitigate the effects of sulfide toxicity. Growth defects are most pronounced when S. aureus is cultured in chemically defined media with thiosulfate (TS) as a sole sulfur source, but are also apparent when cystine is used or in rich media. Under TS growth conditions, cells fail to grow as a result of either unregulated expression of the cst operon in a ΔcstR strain or transformation with a non-inducible C31A/C60A CstR that blocks cst induction. This suggests that the cst operon contributes to cellular sulfide homeostasis. Tandem high-resolution mass spectrometry reveals derivatization of CstR by both inorganic tetrasulfide and an organic persulfide, glutathione persulfide, to yield a mixture of Cys31-Cys60' interprotomer cross-links, including di-, tri- and tetrasulfide bonds, which allosterically inhibit cst operator DNA binding by CstR.
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Affiliation(s)
- Justin L Luebke
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
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85
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Rennenberg H, Herschbach C. A detailed view on sulphur metabolism at the cellular and whole-plant level illustrates challenges in metabolite flux analyses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5711-24. [PMID: 25124317 DOI: 10.1093/jxb/eru315] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding the dynamics of physiological process in the systems biology era requires approaches at the genome, transcriptome, proteome, and metabolome levels. In this context, metabolite flux experiments have been used in mapping metabolite pathways and analysing metabolic control. In the present review, sulphur metabolism was taken to illustrate current challenges of metabolic flux analyses. At the cellular level, restrictions in metabolite flux analyses originate from incomplete knowledge of the compartmentation network of metabolic pathways. Transport of metabolites through membranes is usually not considered in flux experiments but may be involved in controlling the whole pathway. Hence, steady-state and snapshot readings need to be expanded to time-course studies in combination with compartment-specific metabolite analyses. Because of species-specific differences, differences between tissues, and stress-related responses, the quantitative significance of different sulphur sinks has to be elucidated; this requires the development of methods for whole-sulphur metabolome approaches. Different cell types can contribute to metabolite fluxes to different extents at the tissue and organ level. Cell type-specific analyses are needed to characterize these contributions. Based on such approaches, metabolite flux analyses can be expanded to the whole-plant level by considering long-distance transport and, thus, the interaction of roots and the shoot in metabolite fluxes. However, whole-plant studies need detailed empirical and mathematical modelling that have to be validated by experimental analyses.
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Affiliation(s)
- Heinz Rennenberg
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany Centre for Biosystems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Cornelia Herschbach
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany
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86
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Intracellular metabolite levels shape sulfur isotope fractionation during microbial sulfate respiration. Proc Natl Acad Sci U S A 2014; 111:18116-25. [PMID: 25362045 DOI: 10.1073/pnas.1407502111] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a quantitative model for sulfur isotope fractionation accompanying bacterial and archaeal dissimilatory sulfate respiration. By incorporating independently available biochemical data, the model can reproduce a large number of recent experimental fractionation measurements with only three free parameters: (i) the sulfur isotope selectivity of sulfate uptake into the cytoplasm, (ii) the ratio of reduced to oxidized electron carriers supporting the respiration pathway, and (iii) the ratio of in vitro to in vivo levels of respiratory enzyme activity. Fractionation is influenced by all steps in the dissimilatory pathway, which means that environmental sulfate and sulfide levels control sulfur isotope fractionation through the proximate influence of intracellular metabolites. Although sulfur isotope fractionation is a phenotypic trait that appears to be strain specific, we show that it converges on near-thermodynamic behavior, even at micromolar sulfate levels, as long as intracellular sulfate reduction rates are low enough (<<1 fmol H2S⋅cell(-1)⋅d(-1)).
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87
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García-Solares SM, Ordaz A, Monroy-Hermosillo O, Jan-Roblero J, Guerrero-Barajas C. High sulfate reduction efficiency in a UASB using an alternative source of sulfidogenic sludge derived from hydrothermal vent sediments. Appl Biochem Biotechnol 2014; 174:2919-40. [PMID: 25234397 DOI: 10.1007/s12010-014-1237-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/10/2014] [Indexed: 10/24/2022]
Abstract
Sulfidogenesis in reactors is mostly achieved through adaptation of predominantly methanogenic granular sludge to sulfidogenesis. In this work, an upflow anaerobic sludge blanket (UASB) reactor operated under sulfate-reducing conditions was inoculated with hydrothermal vent sediments to carry out sulfate reduction using volatile fatty acids (VFAs) as substrate and chemical oxygen demand (COD)/SO4 (-2) ratios between 0.49 and 0.64. After a short period of adaptation, a robust non-granular sludge was capable of achieving high sulfate reduction efficiencies while avoiding competence with methanogens and toxicity to the microorganisms due to high sulfide concentration. The highest sulfide concentration (2,552 mg/L) was obtained with acetate/butyrate, and sulfate reduction efficiencies were up to 98 %. A mixture of acetate/butyrate, which produced a higher yielding of HS(-), was preferred over acetate/propionate/butyrate since the consumption of COD was minimized during the process. Sludge was analyzed, and some of the microorganisms identified in the sludge belong to the genera Desulfobacterium, Marinobacter, and Clostridium. The tolerance of the sludge to sulfide may be attributed to the syntrophy among these microorganisms, some of which have been reported to tolerate high concentrations of sulfide. To the best of our knowledge, this is the first report on the analysis of the direct utilization of hydrothermal vent sediments as an alternate source of sludge for sulfate reduction under high sulfide concentrations.
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Affiliation(s)
- Selene Montserrat García-Solares
- Departamento de Bioprocesos, Laboratorio de Biotecnología Ambiental, Unidad Profesional Interdisciplinaria de Biotecnología (UPIBI), Instituto Politécnico Nacional, Mexico City, 07340, Mexico
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88
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Rambow J, Wu B, Rönfeldt D, Beitz E. Aquaporins with anion/monocarboxylate permeability: mechanisms, relevance for pathogen-host interactions. Front Pharmacol 2014; 5:199. [PMID: 25225485 PMCID: PMC4150397 DOI: 10.3389/fphar.2014.00199] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/12/2014] [Indexed: 11/22/2022] Open
Abstract
Classically, aquaporins are divided based on pore selectivity into water specific, orthodox aquaporins and solute-facilitating aquaglyceroporins, which conduct, e.g., glycerol and urea. However, more aquaporin-passing substrates have been identified over the years, such as the gasses ammonia and carbon dioxide or the water-related hydrogen peroxide. It became apparent that not all aquaporins clearly fit into one of only two subfamilies. Furthermore, certain aquaporins from both major subfamilies have been reported to conduct inorganic anions, such as chloride, or monoacids/monocarboxylates, such as lactic acid/lactate. Here, we summarize the findings on aquaporin anion transport, analyze the pore layout of such aquaporins in comparison to prototypical non-selective anion channels, monocarboxylate transporters, and formate–nitrite transporters. Finally, we discuss in which scenarios anion conducting aquaporins may be of physiological relevance.
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Affiliation(s)
- Janis Rambow
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel Kiel, Germany
| | - Binghua Wu
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel Kiel, Germany
| | - Deike Rönfeldt
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel Kiel, Germany
| | - Eric Beitz
- Department of Pharmaceutical and Medicinal Chemistry, Christian-Albrechts-University of Kiel Kiel, Germany
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89
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Doberenz C, Zorn M, Falke D, Nannemann D, Hunger D, Beyer L, Ihling CH, Meiler J, Sinz A, Sawers RG. Pyruvate formate-lyase interacts directly with the formate channel FocA to regulate formate translocation. J Mol Biol 2014; 426:2827-39. [PMID: 24887098 DOI: 10.1016/j.jmb.2014.05.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 11/26/2022]
Abstract
The FNT (formate-nitrite transporters) form a superfamily of pentameric membrane channels that translocate monovalent anions across biological membranes. FocA (formate channel A) translocates formate bidirectionally but the mechanism underlying how translocation of formate is controlled and what governs substrate specificity remains unclear. Here we demonstrate that the normally soluble dimeric enzyme pyruvate formate-lyase (PflB), which is responsible for intracellular formate generation in enterobacteria and other microbes, interacts specifically with FocA. Association of PflB with the cytoplasmic membrane was shown to be FocA dependent and purified, Strep-tagged FocA specifically retrieved PflB from Escherichia coli crude extracts. Using a bacterial two-hybrid system, it could be shown that the N-terminus of FocA and the central domain of PflB were involved in the interaction. This finding was confirmed by chemical cross-linking experiments. Using constraints imposed by the amino acid residues identified in the cross-linking study, we provide for the first time a model for the FocA-PflB complex. The model suggests that the N-terminus of FocA is important for interaction with PflB. An in vivo assay developed to monitor changes in formate levels in the cytoplasm revealed the importance of the interaction with PflB for optimal translocation of formate by FocA. This system represents a paradigm for the control of activity of FNT channel proteins.
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Affiliation(s)
- Claudia Doberenz
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Michael Zorn
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Dörte Falke
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - David Nannemann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA
| | - Doreen Hunger
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Lydia Beyer
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA
| | - Andrea Sinz
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.
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90
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Hartle MD, Sommer SK, Dietrich SR, Pluth MD. Chemically reversible reactions of hydrogen sulfide with metal phthalocyanines. Inorg Chem 2014; 53:7800-2. [PMID: 24785654 PMCID: PMC4123935 DOI: 10.1021/ic500664c] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Hydrogen sulfide (H2S)
is an important signaling molecule that exerts action on various bioinorganic
targets. Despite this importance, few studies have investigated the
differential reactivity of the physiologically relevant H2S and HS– protonation states with metal complexes.
Here we report the distinct reactivity of H2S and HS– with zinc(II) and cobalt(II) phthalocyanine (Pc) complexes
and highlight the chemical reversibility and cyclability of each metal.
ZnPc reacts with HS–, but not H2S, to
generate [ZnPc-SH]−, which can be converted back
to ZnPc by protonation. CoPc reacts with HS–, but
not H2S, to form [CoIPc]−,
which can be reoxidized to CoPc by air. Taken together, these results
demonstrate the chemically reversible reaction of HS– with metal phthalocyanine complexes and highlight the importance
of H2S protonation state in understanding the reactivity
profile of H2S with biologically relevant metal scaffolds. The protonation state of H2S influences
its reactivity with different metal phthalocyanine (Pc) complexes.
Both ZnPc and CoPc react with H2S in a chemically reversible
manner, with redox-inactive ZnPc binding HS− and
redox-active CoPc undergoing reduction. The [ZnPc-SH]− product can be reverted to ZnPc by protonation, and [CoIPc]− can be redoxidized to CoPc with air.
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Affiliation(s)
- Matthew D Hartle
- Department of Chemistry and Biochemistry, Materials Science Institute, University of Oregon , Eugene, Oregon 97403-1253, United States
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91
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Panwar P, Lemieux MJ. Expression and Purification of
Haemophilus influenzae
Rhomboid Intramembrane Protease GlpG for Structural Studies. ACTA ACUST UNITED AC 2014; 76:29.9.1-29.9.25. [DOI: 10.1002/0471140864.ps2909s76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pankaj Panwar
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta Canada
| | - M. Joanne Lemieux
- Department of Biochemistry, Membrane Protein Disease Research Group, Faculty of Medicine and Dentistry, University of Alberta Edmonton Alberta Canada
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92
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Abstract
SIGNIFICANCE Hydrogen sulfide (H2S) has been recognized as a physiological mediator with a variety of functions. It regulates synaptic transmission, vascular tone, inflammation, transcription, and angiogenesis; protects cells from oxidative stress and ischemia-reperfusion injury; and promotes healing of ulcers. RECENT ADVANCES In addition to cystathionine β-synthase and cystathionine γ-lyase, 3-mercaptopyruvate sulfurtransferase along with cysteine aminotransferase was recently demonstrated to produce H2S. Even in bacteria, H2S produced by these enzymes functions as a defense against antibiotics, suggesting that the cytoprotective effect of H2S is a universal defense mechanism in organisms from bacteria to mammals. CRITICAL ISSUES The functional form of H2S-undissociated H2S gas, dissociated HS ion, or some other form of sulfur-has not been identified. FUTURE DIRECTIONS The regulation of H2S production by three enzymes may lead to the identification of the physiological signals that are required to release H2S. The identification of the physiological functions of other forms of sulfur may also help understand the biological significance of H2S.
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Affiliation(s)
- Hideo Kimura
- NCNP, National Institute of Neuroscience , Kodaira, Japan
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93
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Bruni R, Kloss B. High-throughput cloning and expression of integral membrane proteins in Escherichia coli. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2013; 74:29.6.1-29.6.34. [PMID: 24510647 PMCID: PMC3920300 DOI: 10.1002/0471140864.ps2906s74] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recently, several structural genomics centers have been established and a remarkable number of three-dimensional structures of soluble proteins have been solved. For membrane proteins, the number of structures solved has been significantly trailing those for their soluble counterparts, not least because over-expression and purification of membrane proteins is a much more arduous process. By using high-throughput technologies, a large number of membrane protein targets can be screened simultaneously and a greater number of expression and purification conditions can be employed, leading to a higher probability of successfully determining the structure of membrane proteins. This unit describes the cloning, expression, and screening of membrane proteins using high-throughput methodologies developed in the laboratory. Basic Protocol 1 describes cloning of inserts into expression vectors by ligation-independent cloning. Basic Protocol 2 describes the expression and purification of the target proteins on a miniscale. Lastly, for the targets that do express on the miniscale, Basic Protocols 3 and 4 outline the methods employed for the expression and purification of targets on a midi-scale, as well as a procedure for detergent screening and identification of detergent(s) in which the target protein is stable.
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Affiliation(s)
- Renato Bruni
- New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center (NYSBC), New York
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center (NYSBC), New York
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94
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Jennings ML. Transport of H2S and HS(-) across the human red blood cell membrane: rapid H2S diffusion and AE1-mediated Cl(-)/HS(-) exchange. Am J Physiol Cell Physiol 2013; 305:C941-50. [PMID: 23864610 PMCID: PMC4042536 DOI: 10.1152/ajpcell.00178.2013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rates of H2S and HS(-) transport across the human erythrocyte membrane were estimated by measuring rates of dissipation of pH gradients in media containing 250 μM H2S/HS(-). Net acid efflux is caused by H2S/HS(-) acting analogously to CO2/HCO3(-) in the Jacobs-Stewart cycle. The steps are as follows: 1) H2S efflux through the lipid bilayer and/or a gas channel, 2) extracellular H2S deprotonation, 3) HS(-) influx in exchange for Cl(-), catalyzed by the anion exchange protein AE1, and 4) intracellular HS(-) protonation. Net acid transport by the Cl(-)/HS(-)/H2S cycle is more efficient than by the Cl(-)/HCO3(-)/CO2 cycle because of the rapid H2S-HS(-) interconversion in cells and medium. The rates of acid transport were analyzed by solving the mass flow equations for the cycle to produce estimates of the HS(-) and H2S transport rates. The data indicate that HS(-) is a very good substrate for AE1; the Cl(-)/HS(-) exchange rate is about one-third as rapid as Cl(-)/HCO3(-) exchange. The H2S permeability coefficient must also be high (>10(-2) cm/s, half time <0.003 s) to account for the pH equilibration data. The results imply that H2S and HS(-) enter erythrocytes very rapidly in the microcirculation of H2S-producing tissues, thereby acting as a sink for H2S and lowering the local extracellular concentration, and the fact that HS(-) is a substrate for a Cl(-)/HCO3(-) exchanger indicates that some effects of exogenous H2S/HS(-) may not result from a regulatory role of H2S but, rather, from net acid flux by H2S and HS(-) transport in a Jacobs-Stewart cycle.
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Affiliation(s)
- Michael L Jennings
- Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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95
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del Mar Fernández-Arjona M, Bañares-España E, García-Sánchez MJ, Hernández-López M, López-Rodas V, Costas E, Flores-Moya A. Disentangling mechanisms involved in the adaptation of photosynthetic microorganisms to the extreme sulphureous water from Los Baños de Vilo (S Spain). MICROBIAL ECOLOGY 2013; 66:742-751. [PMID: 23880793 DOI: 10.1007/s00248-013-0268-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 07/09/2013] [Indexed: 06/02/2023]
Abstract
Los Baños de Vilo (S Spain) is a natural spa characterized by extreme sulphureous waters; however, populations of chlorophyceans inhabit in the spa. The adaptation mechanisms allowing resistance by photosynthetic microorganisms to the extreme sulphureous waters were studied by using a modified Luria-Delbrück fluctuation analysis. For this purpose, the adaptation of the chlorophycean Dictyosphaerium chlorelloides and the cyanobacterium Microcystis aeruginosa (both isolated from non-sulphureous water) were analysed in order to distinguish between physiological adaptation (acclimation) and genetic adaptation by the selection of rare spontaneous mutations. Acclimation to the extreme water was achieved by D. chlorelloides; however, M. aeruginosa cells proliferated as a consequence of selection of favoured mutants (i.e. genetic adaptation). The resistant cells of M. aeruginosa appeared with a frequency of 7.1 × 10(-7) per cell per generation, and the frequency of the resistant allele, under non-selective conditions, was estimated to be 1.1 × 10(-6) per cells as a consequence of the balance mutation-selection. It could be hypothesized that the populations of eukaryotic algae living in the Los Baños de Vilo could be the descendants of chlorophyceans that arrived fortuitously at the spa in the past. On the other hand, cyanobacteria could quickly adapt by the selection of favoured mutants. The single mutation that allows resistance to sulphureous water from Baños de Vilo in M. aeruginosa represents a phenotypic burden impairing growth rate and photosynthetic performance. The resistant-variant cells of M. aeruginosa showed a lower acclimated growth rate and a decreased maximum quantum yield and photosynthetic efficiency, in comparison to the wild-type cells.
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Affiliation(s)
- María del Mar Fernández-Arjona
- Departamento de Biología Vegetal, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071, Málaga, Spain
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96
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Meininger DJ, Caranto JD, Arman HD, Tonzetich ZJ. Studies of iron(III) porphyrinates containing silanethiolate ligands. Inorg Chem 2013; 52:12468-76. [PMID: 24138018 DOI: 10.1021/ic401467k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The chemistry of several iron(III) porphyrinates containing silanethiolate ligands is described. The complexes are prepared by protonolysis reactions of silanethiols with the iron(III) precursors, [Fe(OMe)(TPP)] and [Fe(OH)(H2O)(TMP)] (TPP = dianion of meso-tetraphenylporphine; TMP = dianion of meso-tetramesitylporphine). Each of the compounds has been fully characterized in solution and the solid state. The stability of the silanethiolate complexes versus other iron(III) porphyrinate complexes containing sulfur-based ligands allows for an examination of their reactivity with several biologically relevant small molecules including H2S, NO, and 1-methylimidazole. Electrochemically, the silanethiolate complexes display a quasi-reversible one-electron oxidation event at potentials higher than that observed for an analogous arenethiolate complex. The behavior of these complexes versus other sulfur-ligated iron(III) porphyrinates is discussed.
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Affiliation(s)
- Daniel J Meininger
- Department of Chemistry, University of Texas at San Antonio (UTSA) , San Antonio, Texas 78249, United States
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97
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Tinajero-Trejo M, Jesse HE, Poole RK. Gasotransmitters, poisons, and antimicrobials: it's a gas, gas, gas! F1000PRIME REPORTS 2013; 5:28. [PMID: 23967379 PMCID: PMC3732073 DOI: 10.12703/p5-28] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We review recent examples of the burgeoning literature on three gases that have major impacts in biology and microbiology. NO, CO and H2S are now co-classified as endogenous gasotransmitters with profound effects on mammalian physiology and, potentially, major implications in therapeutic applications. All are well known to be toxic yet, at tiny concentrations in human and cell biology, play key signalling and regulatory functions. All may also be endogenously generated in microbes. NO and H2S share the property of being biochemically detoxified, yet are beneficial in resisting the bactericidal properties of antibiotics. The mechanism underlying this protection is currently under debate. CO, in contrast, is not readily removed; mounting evidence shows that CO, and especially organic donor compounds that release the gas in biological environments, are themselves effective, novel antimicrobial agents.
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98
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Waight AB, Czyzewski BK, Wang DN. Ion selectivity and gating mechanisms of FNT channels. Curr Opin Struct Biol 2013; 23:499-506. [PMID: 23773802 DOI: 10.1016/j.sbi.2013.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 05/04/2013] [Accepted: 05/21/2013] [Indexed: 01/01/2023]
Abstract
The phospholipid bilayer has evolved to be a protective and selective barrier by which the cell maintains high concentrations of life sustaining organic and inorganic material. As gatekeepers responsible for an immense amount of bidirectional chemical traffic between the cytoplasm and extracellular milieu, ion channels have been studied in detail since their postulated existence nearly three-quarters of a century ago. Over the past fifteen years, we have begun to understand how selective permeability can be achieved for both cationic and anionic ions. Our mechanistic knowledge has expanded recently with studies of a large family of anion channels, the Formate Nitrite Transport (FNT) family. This family has proven amenable to structural studies at a resolution high enough to reveal intimate details of ion selectivity and gating. With five representative members having yielded a total of 15 crystal structures, this family represents one of the richest sources of structural information for anion channels.
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Affiliation(s)
- Andrew B Waight
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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99
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Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJM, Jetten MSM, Keltjens JT. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev 2013; 37:428-61. [PMID: 23210799 DOI: 10.1111/1574-6976.12014] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/25/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.
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Affiliation(s)
- Boran Kartal
- Department of Microbiology, Faculty of Science, Institute of Wetland and Water Research, Radboud University of Nijmegen, Nijmegen, The Netherlands
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100
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Coordination of FocA and pyruvate formate-lyase synthesis in Escherichia coli demonstrates preferential translocation of formate over other mixed-acid fermentation products. J Bacteriol 2013; 195:1428-35. [PMID: 23335413 DOI: 10.1128/jb.02166-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterobacteria such as Escherichia coli generate formate, lactate, acetate, and succinate as major acidic fermentation products. Accumulation of these products in the cytoplasm would lead to uncoupling of the membrane potential, and therefore they must be either metabolized rapidly or exported from the cell. E. coli has three membrane-localized formate dehydrogenases (FDHs) that oxidize formate. Two of these have their respective active sites facing the periplasm, and the other is in the cytoplasm. The bidirectional FocA channel translocates formate across the membrane delivering substrate to these FDHs. FocA synthesis is tightly coupled to synthesis of pyruvate formate-lyase (PflB), which generates formate. In this study, we analyze the consequences on the fermentation product spectrum of altering FocA levels, uncoupling FocA from PflB synthesis or blocking formate metabolism. Changing the focA translation initiation codon from GUG to AUG resulted in a 20-fold increase in FocA during fermentation and an ∼3-fold increase in PflB. Nevertheless, the fermentation product spectrum throughout the growth phase remained similar to that of the wild type. Formate, acetate, and succinate were exported, but only formate was reimported by these cells. Lactate accumulated in the growth medium only in mutants lacking FocA, despite retaining active PflB, or when formate could not be metabolized intracellularly. Together, these results indicate that FocA has a strong preference for formate as a substrate in vivo and not other acidic fermentation products. The tight coupling between FocA and PflB synthesis ensures adequate substrate delivery to the appropriate FDH.
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