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Oyamada Y, Ogawa S, Fujishiro T. Nickel-chelatase activity of SirB variants mimicking the His arrangement in the naturally occurring nickel-chelatase CfbA. FEBS Open Bio 2024. [PMID: 38923868 DOI: 10.1002/2211-5463.13849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Metal-tetrapyrrole cofactors are involved in multiple cellular functions, and chelatases are key enzymes for the biosynthesis of these cofactors. CfbA is an ancestral, homodimeric-type class II chelatase which is able to use not only Ni2+ as a physiological metal substrate, but also Co2+ as a nonphysiological substrate with higher activity than for Ni2+. The Ni/Co-chelatase function found in CfbA is also observed in SirB, a descendant, monomeric-type class II chelatase. This is despite the distinct active site structure of CfbA and SirB; specifically, CfbA shows a unique four His residue arrangement, unlike other monomeric class II chelatases such as SirB. Herein, we studied the Ni-chelatase activity of SirB variants R134H, L200H, and R134H/L200H, the latter of which mimics the His alignment of CfbA. Our results showed that the SirB R134H variant exhibited the highest Ni-chelatase activity among the SirB enzymes, which in turn suggests that the position of His134 could be more important for the Ni-chelatase activity than that of His200. The SirB R134H/L200H variant showed lower activity than R134H, despite the four His residues found in SirB R134H/L200H. CD spectroscopy showed secondary structure denaturation and a slight difficulty in Ni-binding of SirB R134H/L200H, which may be related to its lower activity. Finally, a docking simulation suggested that the His134 of the SirB R134H variant could function as a base catalyst for the Ni-chelatase reaction in a class II chelatase architecture.
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Affiliation(s)
- Yuuma Oyamada
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shoko Ogawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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2
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Jensen GC, Janis MK, Nguyen HN, David OW, Zastrow ML. Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life. ACS Sens 2024; 9:1622-1643. [PMID: 38587931 PMCID: PMC11073808 DOI: 10.1021/acssensors.3c02695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.
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Affiliation(s)
- Gary C Jensen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Makena K Janis
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Hazel N Nguyen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Ogonna W David
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Melissa L Zastrow
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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3
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Young TR, Deery E, Foster AW, Martini MA, Osman D, Warren MJ, Robinson NJ. Two Distinct Thermodynamic Gradients for Cellular Metalation of Vitamin B 12. JACS AU 2023; 3:1472-1483. [PMID: 37234125 PMCID: PMC10206600 DOI: 10.1021/jacsau.3c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The acquisition of CoII by the corrin component of vitamin B12 follows one of two distinct pathways, referred to as early or late CoII insertion. The late insertion pathway exploits a CoII metallochaperone (CobW) from the COG0523 family of G3E GTPases, while the early insertion pathway does not. This provides an opportunity to contrast the thermodynamics of metalation in a metallochaperone-requiring and a metallochaperone-independent pathway. In the metallochaperone-independent route, sirohydrochlorin (SHC) associates with the CbiK chelatase to form CoII-SHC. CoII-buffered enzymatic assays indicate that SHC binding enhances the thermodynamic gradient for CoII transfer from the cytosol to CbiK. In the metallochaperone-dependent pathway, hydrogenobyrinic acid a,c-diamide (HBAD) associates with the CobNST chelatase to form CoII-HBAD. Here, CoII-buffered enzymatic assays indicate that CoII transfer from the cytosol to HBAD-CobNST must somehow traverse a highly unfavorable thermodynamic gradient for CoII binding. Notably, there is a favorable gradient for CoII transfer from the cytosol to the MgIIGTP-CobW metallochaperone, but further transfer of CoII from the GTP-bound metallochaperone to the HBAD-CobNST chelatase complex is thermodynamically unfavorable. However, after nucleotide hydrolysis, CoII transfer from the chaperone to the chelatase complex is calculated to become favorable. These data reveal that the CobW metallochaperone can overcome an unfavorable thermodynamic gradient for CoII transfer from the cytosol to the chelatase by coupling this process to GTP hydrolysis.
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Affiliation(s)
- Tessa R. Young
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Evelyne Deery
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
| | - Andrew W. Foster
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Maria Alessandra Martini
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Inorganic Spectroscopy, Max Planck Institute
for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Deenah Osman
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Martin J. Warren
- School
of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K.
- Quadram
Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, U.K.
| | - Nigel J. Robinson
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
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4
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5
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Soleja N, Irfan, Mohsin M. Ratiometric imaging of flux dynamics of cobalt with an optical sensor. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Fujishiro T, Shimada Y, Nakamura R, Ooi M. Structure of sirohydrochlorin ferrochelatase SirB: the last of the structures of the class II chelatase family. Dalton Trans 2019; 48:6083-6090. [PMID: 30778451 DOI: 10.1039/c8dt04727h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structure of Bacillus subtilis SirB, which catalyses the insertion of Fe2+ into the substrate sirohydrochlorin (SHC) in siroheme biosynthesis, is reported herein as the last of the structures of class II chelatases. The structure of SirB with Co2+ showed that the active site of SirB is located at the N-terminal domain with metal-binding amino acid residues His10, Glu43, and His76, which was also predicted for CbiX, but is distinct from the C-terminal active sites of CbiK and HemH. The biosynthetic model reactions using SirB, Co2+ and uroporphyrin I or protoporphyrin IX as a SHC analogue revealed that SirB showed chelatase activity for uroporphyrin I, but not for protoporphyrin IX. Simulations of tetrapyrroles docking to SirB provided an insight into its tetrapyrrole substrate recognition: SHC and uroporphyrin I were suitably bound beside the Co2+ ion-binding site at the active site cavity; protoporphyrin IX was also docked to the active site but its orientation was different from those of the other two tetrapyrroles. Summarizing the present data, it was proposed that the key structural features for substrate recognition of SirB could be the hydrophobic area at the active site as well as the substituents of the tetrapyrroles.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
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7
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Videira MAM, Lobo SAL, Sousa FL, Saraiva LM. Identification of the sirohaem biosynthesis pathway in Staphylococcus aureus. FEBS J 2019; 287:1537-1553. [PMID: 31605669 DOI: 10.1111/febs.15091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 10/09/2019] [Indexed: 11/27/2022]
Abstract
Sirohaem is a modified tetrapyrrole and a key prosthetic group of several enzymes involved in nitrogen and sulfur metabolisms. This work shows that Staphylococcus aureus produces sirohaem through a pathway formed by three independent enzymes. Of the two putative sirohaem synthases encoded in the S. aureus genome and annotated as cysG, one is herein shown to be a uroporphyrinogen III methyltransferase that converts uroporphyrinogen III to precorrin-2, and was renamed as UroM. The second cysG gene encodes a precorrin-2 dehydrogenase that converts precorrin-2 to sirohydrochlorin, and was designated as P2D. The last step was found to be performed by the gene nirR that, in fact, codes for a protein with sirohydrochlorin ferrochelatase activity, labelled as ShfC. Additionally, site-directed mutagenesis studies of S. aureus ShfC revealed that residues H22 and H87, which are predicted by homology modelling to be located at the active site, control the ferrochelatase activity. Within bacteria, sirohaem synthesis may occur via one, two or three enzymes, and we propose to name the correspondent pathways as Types 1, 2 and 3, respectively. A phylogenetic analysis revealed that Type 1 is the most used pathway in Gammaproteobacteria and Streptomycetales, Type 2 predominates in Fibrobacteres and Vibrionales, and Type 3 predominates in Firmicutes of the Bacillales order. Altogether, we concluded that the current distribution of sirohaem pathways within bacteria, which changes at the genus or species level and within taxa, seems to be the result of evolutionary multiple fusion/fission events.
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Affiliation(s)
- Marco A M Videira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana A L Lobo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Filipa L Sousa
- Department of Ecogenomics and Systems Biology, University of Vienna, Austria
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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8
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Osman D, Martini MA, Foster AW, Chen J, Scott AJP, Morton RJ, Steed JW, Lurie-Luke E, Huggins TG, Lawrence AD, Deery E, Warren MJ, Chivers PT, Robinson NJ. Bacterial sensors define intracellular free energies for correct enzyme metalation. Nat Chem Biol 2019; 15:241-249. [PMID: 30692683 PMCID: PMC6420079 DOI: 10.1038/s41589-018-0211-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/04/2018] [Indexed: 01/06/2023]
Abstract
There is a challenge for metalloenzymes to acquire their correct metals because some inorganic elements form more stable complexes with proteins than do others. These preferences can be overcome provided some metals are more available than others. However, while the total amount of cellular metal can be readily measured, the available levels of each metal have been more difficult to define. Metal-sensing transcriptional regulators are tuned to the intracellular availabilities of their cognate ions. Here we have determined the standard free energy for metal complex formation to which each sensor, in a set of bacterial metal sensors, is attuned: The less competitive the metal, the less favorable the free energy and hence greater availability to which the cognate allosteric mechanism is tuned. Comparing these free energies with values derived from the metal affinities of a metalloprotein reveals the mechanism of correct metalation exemplified here by a cobalt-chelatase for vitamin B12.
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Affiliation(s)
- Deenah Osman
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | | | - Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Junjun Chen
- Procter and Gamble, Mason Business Center, Cincinnati, OH, USA
| | | | - Richard J Morton
- Department of Mathematics, Physics and Electrical Engineering, Northumbria University, Newcastle-upon-Tyne, UK
| | | | | | | | | | - Evelyne Deery
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Peter T Chivers
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
| | - Nigel J Robinson
- Department of Biosciences, Durham University, Durham, UK. .,Department of Chemistry, Durham University, Durham, UK.
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9
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Dey S, Wayland BB, Zdilla MJ. Solution and Solid State Properties for Low-Spin Cobalt(II) Dibenzotetramethyltetraaza[14]annulene [(tmtaa)Co II] and the Monopyridine Complex. Inorg Chem 2019; 58:1224-1233. [PMID: 30618250 DOI: 10.1021/acs.inorgchem.8b02644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The single-crystal X-ray structure of solvent-free (tmtaa)CoII reveals three different π-π intermacrocyclic interactions between tmtaa units (tmtaa = dibenzotetramethyltetraaza[14]annulene). Pairs of inequivalent (tmtaa)CoII units in the unit cell link into a one-dimensional π-π stacked array in the solid state. Magnetic susceptibility (χ) studies from 300 to 2 K reveal the effects of intermolecular interactions between (tmtaa)CoII units in the solid state. The effective magnetic moment per CoII center is constant at 2.83 μB from 300 to 100 K and begins to significantly decrease at lower temperatures. The magnetic data are fit to a singlet ( S = 0) ground state with a triplet ( S = 1) excited state that is 13 cm-1 higher in energy (-2 J = 13 cm-1). Toluene solutions of (tmtaa)CoII have 1H nuclear magnetic resonance (NMR) paramagnetic shifts, a solution-phase magnetic moment μeff (295 K) of 2.1 μB, and toluene glass electron paramagnetic resonance spectra that are most consistent with a low-spin ( S = 1/2) CoII with the unpaired electron located in the d yz orbital. Pyridine interacts with (tmtaa)CoII to form a five-coordinate monopyridine complex in which the unpaired electron is in the d z2 orbital. The five-coordinate complex has been structurally characterized by single-crystal X-ray diffraction, and the equilibrium constant for pyridine binding at 295 K has been evaluated by both electronic and 1H NMR spectra. Density functional theory computation using the UB3LYP hybrid functional places the unpaired electron for (tmtaa)CoII in the d yz orbital and that for the monopyridine complex in the d z2 orbital, consistent with spectroscopic observations.
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Affiliation(s)
- Soumyajit Dey
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Bradford B Wayland
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Michael J Zdilla
- Department of Chemistry , Temple University , 1901 Northy 13th Street , Philadelphia , Pennsylvania 19122 , United States
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10
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Tavares NK, Escalante-Semerena JC. A snapshot of evolution in action: emergence of new heme transport function derived from a coenzyme B 12 biosynthetic enzyme. Environ Microbiol 2016; 19:8-10. [PMID: 27588714 DOI: 10.1111/1462-2920.13517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/02/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Norbert K Tavares
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
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11
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Lobo SAL, Videira MAM, Pacheco I, Wass MN, Warren MJ, Teixeira M, Matias PM, Romão CV, Saraiva LM. Desulfovibrio vulgaris CbiK P cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues. Environ Microbiol 2016; 19:106-118. [PMID: 27486032 DOI: 10.1111/1462-2920.13479] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/27/2016] [Indexed: 11/26/2022]
Abstract
The sulfate-reducing bacteria of the Desulfovibrio genus make three distinct modified tetrapyrroles, haem, sirohaem and adenosylcobamide, where sirohydrochlorin acts as the last common biosynthetic intermediate along the branched tetrapyrrole pathway. Intriguingly, D. vulgaris encodes two sirohydrochlorin chelatases, CbiKP and CbiKC , that insert cobalt/iron into the tetrapyrrole macrocycle but are thought to be distinctly located in the periplasm and cytoplasm respectively. Fusing GFP onto the C-terminus of CbiKP confirmed that the protein is transported to the periplasm. The structure-function relationship of CbiKP was studied by constructing eleven site-directed mutants and determining their chelatase activities, oligomeric status and haem binding abilities. Residues His154 and His216 were identified as essential for metal-chelation of sirohydrochlorin. The tetrameric form of the protein is stabilized by Arg54 and Glu76, which form hydrogen bonds between two subunits. His96 is responsible for the binding of two haem groups within the main central cavity of the tetramer. Unexpectedly, CbiKP is shown to bind two additional haem groups through interaction with His103. Thus, although still retaining cobaltochelatase activity, the presence of His96 and His103 in CbiKP , which are absent from all other known bacterial cobaltochelatases, has evolved CbiKP a new function as a haem binding protein permitting it to act as a potential haem chaperone or transporter.
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Affiliation(s)
- Susana A L Lobo
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Marco A M Videira
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Isabel Pacheco
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Mark N Wass
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Giles Lane, Canterbury, Kent, CT2 7NJ, UK
| | - Miguel Teixeira
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal.,iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal
| | - Célia V Romão
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
| | - Lígia M Saraiva
- Instituto de Tecnologia Química e Biológica NOVA, Avenida da República (EAN), Oeiras, 2780-157, Portugal
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12
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Bali S, Palmer DJ, Schroeder S, Ferguson SJ, Warren MJ. Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d 1. Cell Mol Life Sci 2014; 71:2837-63. [PMID: 24515122 PMCID: PMC11113276 DOI: 10.1007/s00018-014-1563-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/19/2013] [Accepted: 01/10/2014] [Indexed: 02/05/2023]
Abstract
Hemes (a, b, c, and o) and heme d 1 belong to the group of modified tetrapyrroles, which also includes chlorophylls, cobalamins, coenzyme F430, and siroheme. These compounds are found throughout all domains of life and are involved in a variety of essential biological processes ranging from photosynthesis to methanogenesis. The biosynthesis of heme b has been well studied in many organisms, but in sulfate-reducing bacteria and archaea, the pathway has remained a mystery, as many of the enzymes involved in these characterized steps are absent. The heme pathway in most organisms proceeds from the cyclic precursor of all modified tetrapyrroles uroporphyrinogen III, to coproporphyrinogen III, which is followed by oxidation of the ring and finally iron insertion. Sulfate-reducing bacteria and some archaea lack the genetic information necessary to convert uroporphyrinogen III to heme along the "classical" route and instead use an "alternative" pathway. Biosynthesis of the isobacteriochlorin heme d 1, a cofactor of the dissimilatory nitrite reductase cytochrome cd 1, has also been a subject of much research, although the biosynthetic pathway and its intermediates have evaded discovery for quite some time. This review focuses on the recent advances in the understanding of these two pathways and their surprisingly close relationship via the unlikely intermediate siroheme, which is also a cofactor of sulfite and nitrite reductases in many organisms. The evolutionary questions raised by this discovery will also be discussed along with the potential regulation required by organisms with overlapping tetrapyrrole biosynthesis pathways.
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Affiliation(s)
- Shilpa Bali
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - David J. Palmer
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
| | - Susanne Schroeder
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
| | - Stuart J. Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Martin J. Warren
- School of Biosciences, University of Kent, Kent, Canterbury, CT2 7NZ UK
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13
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Chen L, Zhu Y, Song Z, Wang J, Zhang W. An orphan response regulator Sll0649 involved in cadmium tolerance and metal homeostasis in photosynthetic Synechocystis sp. PCC 6803. J Proteomics 2014; 103:87-102. [DOI: 10.1016/j.jprot.2014.03.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/07/2014] [Accepted: 03/23/2014] [Indexed: 10/25/2022]
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Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl Environ Microbiol 2014; 80:2133-41. [PMID: 24463969 DOI: 10.1128/aem.03477-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Corrinoids are essential cofactors of reductive dehalogenases in Dehalococcoides mccartyi, an important bacterium in bioremediation, yet sequenced D. mccartyi strains do not possess the complete pathway for de novo corrinoid biosynthesis. Pelosinus sp. and Desulfovibrio sp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growing D. mccartyi strain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)- and lactate-amended medium in cocultures with Desulfovibrio vulgaris Hildenborough (DvH) or Pelosinus fermentans R7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.
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15
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Ferrer M, Ruiz A, Lanza F, Haange SB, Oberbach A, Till H, Bargiela R, Campoy C, Segura MT, Richter M, von Bergen M, Seifert J, Suarez A. Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ Microbiol 2012; 15:211-26. [PMID: 22891823 DOI: 10.1111/j.1462-2920.2012.02845.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent research has disclosed a tight connection between obesity, metabolic gut microbial activities and host health. Obtaining a complete understanding of this relationship remains a major goal. Here, we conducted a comparative metagenomic and metaproteomic investigation of gut microbial communities in faecal samples taken from an obese and a lean adolescent. By analysing the diversity of 16S rDNA amplicons (10% operational phylogenetic units being common), 22 Mbp of consensus metagenome sequences (~70% common) and the expression profiles of 613 distinct proteins (82% common), we found that in the obese gut, the total microbiota was more abundant on the phylum Firmicutes (94.6%) as compared with Bacteroidetes (3.2%), although the metabolically active microbiota clearly behaves in a more homogeneous manner with both contributing equally. The lean gut showed a remarkable shift towards Bacteroidetes (18.9% total 16S rDNA), which become the most active fraction (81% proteins). Although the two gut communities maintained largely similar gene repertoires and functional profiles, improved pili- and flagella-mediated host colonization and improved capacity for both complementary aerobic and anaerobic de novo B(12) synthesis, 1,2-propanediol catabolism (most likely participating in de novo B(12) synthesis) and butyrate production were observed in the obese gut, whereas bacteria from lean gut seem to be more engaged in vitamin B(6) synthesis. Furthermore, this study provides functional evidence that variable combinations of species from different phyla could 'presumptively' fulfil overlapping and/or complementary functional roles required by the host, a scenario where minor bacterial taxa seem to be significant active contributors.
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Lobo SAL, Warren MJ, Saraiva LM. Sulfate-reducing bacteria reveal a new branch of tetrapyrrole metabolism. Adv Microb Physiol 2012; 61:267-95. [PMID: 23046956 DOI: 10.1016/b978-0-12-394423-8.00007-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sulfate-reducing microorganisms are a diverse group of bacteria and archaea that occupy important environmental niches and have potential for significant biotechnological impact. Desulfovibrio, the most studied genus among the sulfate-reducing microorganisms, contains proteins with a wide variety of tetrapyrrole-derived cofactors, including some unique derivatives such as uroporphyrin I and coproporphyrin III. Herein, we review tetrapyrrole metabolism in Desulfovibrio spp., including the production of sirohaem and cobalamin, and compare and contrast the biochemical properties of the enzymes involved in these biosynthetic pathways. Furthermore, we describe a novel pathway used by Desulfovibrio to synthesize haem b, which provides a previously unrecognized link between haem, sirohaem, and haem d(1). Finally, the organization and regulation of genes involved in the tetrapyrrole biosynthetic pathway is discussed.
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Affiliation(s)
- Susana A L Lobo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República EAN, Oeiras, Portugal
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Abstract
Dissimilatory sulfate and sulfur reduction evolved billions of years ago and while the bacteria and archaea that use this unique metabolism employ a variety of electron donors, H(2) is most commonly used as the energy source. These prokaryotes use multiheme c-type proteins to shuttle electrons from electron donors, and electron transport complexes presumed to contain b-type hemoproteins contribute to proton charging of the membrane. Numerous sulfate and sulfur reducers use an alternate pathway for heme synthesis and, frequently, uniquely specific axial ligands are used to secure c-type heme to the protein. This review presents some of the types and functional activities of hemoproteins involved in these two dissimilatory reduction pathways.
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Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization. Proc Natl Acad Sci U S A 2010; 108:97-102. [PMID: 21173279 DOI: 10.1073/pnas.1014298108] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class II chelatases associated with heme, siroheme, and cobalamin biosynthesis are structurally related enzymes that insert a specific metal ion (Fe(2+) or Co(2+)) into the center of a modified tetrapyrrole (protoporphyrin or sirohydrochlorin). The structures of two related class II enzymes, CbiX(S) from Archaeoglobus fulgidus and CbiK from Salmonella enterica, that are responsible for the insertion of cobalt along the cobalamin biosynthesis pathway are presented in complex with their metallated product. A further structure of a CbiK from Desulfovibrio vulgaris Hildenborough reveals how cobalt is bound at the active site. The crystal structures show that the binding of sirohydrochlorin is distinctly different to porphyrin binding in the protoporphyrin ferrochelatases and provide a molecular overview of the mechanism of chelation. The structures also give insights into the evolution of chelatase form and function. Finally, the structure of a periplasmic form of Desulfovibrio vulgaris Hildenborough CbiK reveals a novel tetrameric arrangement of its subunits that are stabilized by the presence of a heme b cofactor. Whereas retaining colbaltochelatase activity, this protein has acquired a central cavity with the potential to chaperone or transport metals across the periplasmic space, thereby evolving a new use for an ancient protein subunit.
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Functional characterization of the early steps of tetrapyrrole biosynthesis and modification in Desulfovibrio vulgaris Hildenborough. Biochem J 2009; 420:317-25. [DOI: 10.1042/bj20090151] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The biosynthesis of the tetrapyrrole framework has been investigated in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough by characterization of the enzymes required for the transformation of aminolaevulinic acid into sirohydrochlorin. PBG (porphobilinogen) synthase (HemB) was found to be a zinc-dependent enzyme that exists in its native state as a homohexamer. PBG deaminase (HemC) was shown to contain the dipyrromethane cofactor. Uroporphyrinogen III synthase is found fused with a uroporphyrinogen III methyltransferase (HemD-CobA). Both activities could be demonstrated in this amalgamated protein and the individual enzyme activities were separated by dissecting the relevant gene to allow the production of two distinct proteins. A gene annotated in the genome as a bifunctional precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase was in fact shown to act only as a dehydrogenase and is simply capable of synthesizing sirohydrochlorin rather than sirohaem. Genome analysis also reveals a lack of any uroporphyrinogen III decarboxylase, an enzyme necessary for the classical route to haem synthesis. However, the genome does encode some predicted haem d1 biosynthetic enzymes even though the bacterium does not contain the cd1 nitrite reductase. We suggest that sirohydrochlorin acts as a substrate for haem synthesis using a novel pathway that involves homologues of the d1 biogenesis system. This explains why the uroporphyrinogen III synthase is found fused with the methyltransferase, bypassing the need for uroporphyrinogen III decarboxylase activity.
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