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Rodriguez LE, Weber JM, Barge LM. Evaluating Pigments as a Biosignature: Abiotic/Prebiotic Synthesis of Pigments and Pigment Mimics in Planetary Environments. ASTROBIOLOGY 2024. [PMID: 38768415 DOI: 10.1089/ast.2023.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Pigments serve a multitude of functions in biology including light harvesting for photosynthesis, radiation protection, membrane support, and defense. The ubiquity of pigments-especially within extremophiles found in high-radiation, high-salinity, and dry environments-and their detectability via mission-ready techniques have elevated these molecules as promising targets in the search for evidence of life elsewhere. Moreover, the detection of pigments has been proposed as a "smoking gun" for extraterrestrial life as it has been suggested that these molecules cannot be generated abiotically. However, while pigments may hold promise as a biosignature, current understanding of their possible prebiotic origins remains understudied and uncertain. Better understanding of the abiotic synthesis of pigments is critical for evaluating the biogenicity of any pigment detected during missions, including by the Mars Perseverance rover or from returned samples. Compounding this uncertainty is the broad definition of pigment as it includes any compound capable of absorbing visible light and by itself does not specify a particular chemical motif. While not experimentally verified, there are promising prebiotic routes for generating pigments including hemes, chlorophylls, and carotenoids. Herein, we review the biochemistry of pigments, the inherent assumptions made when searching for these molecules in the field, their abiotic synthesis in industry and prebiotic reactions, prebiotically relevant molecules that can mimic their spectral signatures, and implications/recommendations for future work.
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Affiliation(s)
- Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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2
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Stavenga DG. Butterfly blues and greens caused by subtractive colour mixing of carotenoids and bile pigments. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:371-380. [PMID: 37436440 PMCID: PMC11106126 DOI: 10.1007/s00359-023-01656-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/13/2023]
Abstract
Butterflies often have conspicuously patterned wings, due to pigmentary and/or structurally wing scales that cover the wing membrane. The wing membrane of several butterfly species is also pigmentary coloured, notably by the bile pigments pterobilin, pharcobilin and sarpedobilin. The absorption spectra of the bilins have bands in the ultraviolet and red wavelength range, resulting in blue-cyan colours. Here, a survey of papilionoid and nymphalid butterflies reveals that several species with wings containing bile pigments combine them with carotenoids and other short-wavelength absorbing pigments, e.g., papiliochrome II, ommochromes and flavonoids, which creates green-coloured patterns. Various uncharacterized, long-wavelength absorbing wing pigments were encountered, particularly in heliconiines. The wings thus exhibit quite variable reflectance spectra, extending the enormous pigmentary and structural colouration richness of butterflies.
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Affiliation(s)
- Doekele G Stavenga
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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3
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Fujii S, Tamiaki H. Self-aggregation of zinc bacteriochlorophyll-d analogs with an acylhydrazone moiety as the 13-keto-carbonyl alternative. Photochem Photobiol 2024. [PMID: 38581225 DOI: 10.1111/php.13949] [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: 01/25/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Zinc methyl 3-hydroxymethyl-pyropheophorbides-a possessing an acylhydrazinylidene group at the 131-position were prepared by chemically modifying chlorophyll-a, which were models of bacteriochlorophyll-d as one of the light-harvesting pigments in photosynthetic green bacteria. Similar to the self-aggregation of natural bacteriochlorophyll-d in the antenna systems called chlorosomes, some of the synthetic models self-aggregated in an aqueous Triton X-100 solution to give red-shifted and broadened visible absorption bands. The newly appeared oligomeric bands were ascribable to the exciton coupling of the chlorin π-systems along the molecular y-axis, leading to intense circular dichroism bands in the red-shifted Qy and Soret regions. The self-aggregation in the aqueous micelle was dependent on the steric size of the terminal substituent at the 13-acylhydrazone moiety. An increase in the length of the oligomethylene chain as the terminal moved the red-shifted Qy maxima to shorter wavelengths, and branched alkyl and benzyl substitutes afforded no more self-aggregates to leave monomeric species in the hydrophobic environment inside the micelle. These results indicated that the acyl groups on the 13-hydrazone as the alternative of the natural 13-ketone regulated the chlorosome-like self-aggregation.
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Affiliation(s)
- Satoru Fujii
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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4
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Dong CS, Liu L. Fluorination of a conserved tyrosine in POR offers new clues for proton transfer. FEBS J 2024; 291:1400-1403. [PMID: 38297957 DOI: 10.1111/febs.17074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/02/2024]
Abstract
Reduction of the 17,18-double bond in the D-ring during chlorophyll biosynthesis is catalyzed by the rare, naturally occurring photoenzyme protochlorophyllide oxidoreductase (POR). A conserved tyrosine residue has been suggested to donate a proton to C18 of the substrate in the past decades. Taylor and colleagues scrutinized the model with a powerful tool that utilized a modified genetic code to introduce fluorinated tyrosine analogues into POR. The presented results show that the suggested catalytically critical tyrosine is unlikely to participate in the reaction chemistry but is required for substrate binding, and instead, a cysteine residue preceding the lid helix is proposed to have the role of proton donor.
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Affiliation(s)
| | - Lin Liu
- School of Life Sciences, Anhui University, China
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5
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Zdubek A, Maliszewska I. On the Possibility of Using 5-Aminolevulinic Acid in the Light-Induced Destruction of Microorganisms. Int J Mol Sci 2024; 25:3590. [PMID: 38612403 PMCID: PMC11011456 DOI: 10.3390/ijms25073590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Antimicrobial photodynamic inactivation (aPDI) is a method that specifically kills target cells by combining a photosensitizer and irradiation with light at the appropriate wavelength. The natural amino acid, 5-aminolevulinic acid (5-ALA), is the precursor of endogenous porphyrins in the heme biosynthesis pathway. This review summarizes the recent progress in understanding the biosynthetic pathways and regulatory mechanisms of 5-ALA synthesis in biological hosts. The effectiveness of 5-ALA-aPDI in destroying various groups of pathogens (viruses, fungi, yeasts, parasites) was presented, but greater attention was focused on the antibacterial activity of this technique. Finally, the clinical applications of 5-ALA in therapies using 5-ALA and visible light (treatment of ulcers and disinfection of dental canals) were described.
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Affiliation(s)
| | - Irena Maliszewska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland;
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6
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Yasui M, Tamiaki H. Supramolecular chirality in self-assembly of zinc protobacteriochlorophyll-d analogs possessing enantiomeric esterifying groups. Photochem Photobiol Sci 2024; 23:421-434. [PMID: 38265754 DOI: 10.1007/s43630-023-00528-9] [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: 10/31/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
Zinc 3-hydroxymethyl-pyroprotopheophorbides-a esterified with a chiral secondary alcohol at the 17-propionate residue were prepared as bacteriochlorophyll-d analogs. The synthetic zinc 31-hydroxy-131-oxo-porphyrins self-aggregated in an aqueous Triton X-100 micellar solution to give red-shifted and broadened Soret and Qy absorption bands in comparison with their monomeric bands. The intense, exciton-coupled circular dichroism spectra of their self-aggregates were dependent on the chirality of the esterifying groups. The observation indicated that the self-aggregates based on the J-type stacking of the porphyrin cores were sensitive to the peripheral 17-propionate residues. The supramolecular structures of the present J-aggregates as models of bacteriochlorophyll aggregates in natural chlorosomes were remotely regulated by the esterifying groups.
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Affiliation(s)
- Mizuki Yasui
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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Tsuji JM, Shaw NA, Nagashima S, Venkiteswaran JJ, Schiff SL, Watanabe T, Fukui M, Hanada S, Tank M, Neufeld JD. Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre. Nature 2024; 627:915-922. [PMID: 38480893 PMCID: PMC10972752 DOI: 10.1038/s41586-024-07180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/08/2024] [Indexed: 04/01/2024]
Abstract
Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified1,2. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes3 and bacteriochlorophylls4 related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.
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Affiliation(s)
- J M Tsuji
- University of Waterloo, Waterloo, Ontario, Canada.
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan.
| | - N A Shaw
- University of Waterloo, Waterloo, Ontario, Canada
| | - S Nagashima
- Tokyo Metropolitan University, Tokyo, Japan
- Kanagawa University, Yokohama, Japan
| | - J J Venkiteswaran
- University of Waterloo, Waterloo, Ontario, Canada
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - S L Schiff
- University of Waterloo, Waterloo, Ontario, Canada
| | - T Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - M Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - S Hanada
- Tokyo Metropolitan University, Tokyo, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Tank
- Tokyo Metropolitan University, Tokyo, Japan
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - J D Neufeld
- University of Waterloo, Waterloo, Ontario, Canada.
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8
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Yokoyama R. How to make green and purple from gold. PLANT PHYSIOLOGY 2024; 194:1268-1270. [PMID: 38069683 PMCID: PMC10904317 DOI: 10.1093/plphys/kiad653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 03/02/2024]
Affiliation(s)
- Ryo Yokoyama
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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9
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Gisriel CJ. Recent structural discoveries of photosystems I and II acclimated to absorb far-red light. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149032. [PMID: 38401604 DOI: 10.1016/j.bbabio.2024.149032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 02/26/2024]
Abstract
Photosystems I and II are the photooxidoreductases central to oxygenic photosynthesis and canonically absorb visible light (400-700 nm). Recent investigations have revealed that certain cyanobacteria can acclimate to environments enriched in far-red light (700-800 nm), yet can still perform oxygenic photosynthesis in a process called far-red light photoacclimation, or FaRLiP. During this process, the photosystem subunits and pigment compositions are altered. Here, the current structural understanding of the photosystems expressed during FaRLiP is described. The design principles may be useful for guiding efforts to engineer shade tolerance in organisms that typically cannot utilize far-red light.
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10
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Gisriel CJ, Shen G, Brudvig GW, Bryant DA. Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335. J Biol Chem 2024; 300:105590. [PMID: 38141759 PMCID: PMC10810746 DOI: 10.1016/j.jbc.2023.105590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 12/25/2023] Open
Abstract
Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.
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Affiliation(s)
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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11
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Skotnicová P, Srivastava A, Aggarwal D, Talbot J, Karlínová I, Moos M, Mareš J, Bučinská L, Koník P, Šimek P, Tichý M, Sobotka R. A thylakoid biogenesis BtpA protein is required for the initial step of tetrapyrrole biosynthesis in cyanobacteria. THE NEW PHYTOLOGIST 2024; 241:1236-1249. [PMID: 37986097 DOI: 10.1111/nph.19397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/21/2023] [Indexed: 11/22/2023]
Abstract
Biogenesis of the photosynthetic apparatus requires complicated molecular machinery, individual components of which are either poorly characterized or unknown. The BtpA protein has been described as a factor required for the stability of photosystem I (PSI) in cyanobacteria; however, how the BtpA stabilized PSI remains unexplained. To clarify the role of BtpA, we constructed and characterized the btpA-null mutant (ΔbtpA) in the cyanobacterium Synechocystis sp. PCC 6803. The mutant contained only c. 1% of chlorophyll and nearly no thylakoid membranes. However, this strain, growing only in the presence of glucose, was genetically unstable and readily generated suppressor mutations that restore the photoautotrophy. Two suppressor mutations were mapped into the hemA gene encoding glutamyl-tRNA reductase (GluTR) - the first enzyme of tetrapyrrole biosynthesis. Indeed, the GluTR was not detectable in the ΔbtpA mutant and the suppressor mutations restored biosynthesis of tetrapyrroles and photoautotrophy by increased GluTR expression or by improved GluTR stability/processivity. We further demonstrated that GluTR associates with a large BtpA oligomer and that BtpA is required for the stability of GluTR. Our results show that the BtpA protein is involved in the biogenesis of photosystems at the level of regulation of tetrapyrrole biosynthesis.
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Affiliation(s)
- Petra Skotnicová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Amit Srivastava
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Department of Biological and Environmental Science, Nanoscience Centre, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Divya Aggarwal
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Jana Talbot
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, Tas., 7005, Australia
| | - Iva Karlínová
- Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Martin Moos
- Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Jan Mareš
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Lenka Bučinská
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
| | - Peter Koník
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Petr Šimek
- Biology Centre of the Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Martin Tichý
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň, 379 01, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
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12
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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13
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Weaver BR, Perkins LJ, Fernandez Candelaria FO, Burstyn JN, Buller AR. Molecular Determinants of Efficient Cobalt-Substituted Hemoprotein Production in E. coli. ACS Synth Biol 2023; 12:3669-3679. [PMID: 37963151 DOI: 10.1021/acssynbio.3c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Exchanging the native iron of heme for other metals yields artificial metalloproteins with new properties for spectroscopic studies and biocatalysis. Recently, we reported a method for the biosynthesis and incorporation of a non-natural metallocofactor, cobalt protoporphyrin IX (CoPPIX), into hemoproteins using the common laboratory strain Escherichia coli BL21(DE3). This discovery inspired us to explore the determinants of metal specificity for metallocofactor biosynthesis in E. coli. Herein, we report detailed kinetic analysis of the ferrochelatase responsible for metal insertion, EcHemH (E. coli ferrochelatase). This enzyme exhibits a small, less than 2-fold preference for Fe2+ over the non-native Co2+ substrate in vitro. To test how mutations impact EcHemH, we used a surrogate metal specificity screen to identify variants with altered metal insertion preferences. This engineering process led to a variant with an ∼30-fold shift in specificity toward Co2+. When assayed in vivo, however, the impact of this mutation is small compared to the effects of alteration of the external metal concentrations. These data suggest that incorporation of cobalt into PPIX is enabled by the native promiscuity of EcHemH coupled with BL21's impaired ability to maintain transition-metal homeostasis. With this knowledge, we generated a method for CoPPIX production in rich media, which yields cobalt-substituted hemoproteins with >95% cofactor purity and yields comparable to standard expression protocols for the analogous native hemoproteins.
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Affiliation(s)
- Brian R Weaver
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J Perkins
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | | | - Judith N Burstyn
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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14
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Colorado Gómez MA, Melo-Bolívar JF, Ruíz Pardo RY, Rodriguez JA, Villamil LM. Unveiling the Probiotic Potential of the Anaerobic Bacterium Cetobacterium sp. nov. C33 for Enhancing Nile Tilapia ( Oreochromis niloticus) Cultures. Microorganisms 2023; 11:2922. [PMID: 38138066 PMCID: PMC10745334 DOI: 10.3390/microorganisms11122922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium.
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Affiliation(s)
- Mario Andrés Colorado Gómez
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
- Fundación Clínica Shaio, Bogotá 110121, Colombia
| | - Javier Fernando Melo-Bolívar
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Ruth Yolanda Ruíz Pardo
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Jorge Alberto Rodriguez
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
| | - Luisa Marcela Villamil
- Doctorado en Biociencias, Facultad de Ingeniería, Universidad de La Sabana, Chía 250001, Colombia; (M.A.C.G.); (J.F.M.-B.); (R.Y.R.P.); (J.A.R.)
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15
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Traxler C, Gaines TA, Küpper A, Luemmen P, Dayan FE. The nexus between reactive oxygen species and the mechanism of action of herbicides. J Biol Chem 2023; 299:105267. [PMID: 37734554 PMCID: PMC10591016 DOI: 10.1016/j.jbc.2023.105267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Herbicides are small molecules that act by inhibiting specific molecular target sites within primary plant metabolic pathways resulting in catastrophic and lethal consequences. The stress induced by herbicides generates reactive oxygen species (ROS), but little is known about the nexus between each herbicide mode of action (MoA) and their respective ability to induce ROS formation. Indeed, some herbicides cause dramatic surges in ROS levels as part of their primary MoA, whereas other herbicides may generate some ROS as a secondary effect of the stress they imposed on plants. In this review, we discuss the types of ROS and their respective reactivity and describe their involvement for each known MoA based on the new Herbicide Resistance Action Committee classification.
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Affiliation(s)
- Catherine Traxler
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Anita Küpper
- Plant Biotechnology Division, Bayer CropScience, Chesterfield, Missouri, USA
| | - Peter Luemmen
- Research & Development Division, Bayer AG, Industriepark Höchst, Frankfurt am Main, Germany
| | - Franck E Dayan
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA.
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16
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Shvarev D, Scholz AI, Moeller A. Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis. mBio 2023; 14:e0189323. [PMID: 37737632 PMCID: PMC10653834 DOI: 10.1128/mbio.01893-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
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Affiliation(s)
- Dmitry Shvarev
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Alischa Ira Scholz
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Arne Moeller
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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17
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Buckley S, Hardy K, Hallgren F, Kubiak-Martens L, Miliauskienė Ž, Sheridan A, Sobkowiak-Tabaka I, Subirà ME. Human consumption of seaweed and freshwater aquatic plants in ancient Europe. Nat Commun 2023; 14:6192. [PMID: 37848451 PMCID: PMC10582258 DOI: 10.1038/s41467-023-41671-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
During the Mesolithic in Europe, there is widespread evidence for an increase in exploitation of aquatic resources. In contrast, the subsequent Neolithic is characterised by the spread of farming, land ownership, and full sedentism, which lead to the perception of marine resources subsequently representing marginal or famine food or being abandoned altogether even at the furthermost coastal limits of Europe. Here, we examine biomarkers extracted from human dental calculus, using sequential thermal desorption- and pyrolysis-GCMS, to report direct evidence for widespread consumption of seaweed and submerged aquatic and freshwater plants across Europe. Notably, evidence of consumption of these resources extends through the Neolithic transition to farming and into the Early Middle Ages, suggesting that these resources, now rarely eaten in Europe, only became marginal much more recently. Understanding ancient foodstuffs is crucial to reconstructing the past, while a better knowledge of local, forgotten resources is likewise important today.
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Affiliation(s)
- Stephen Buckley
- Department of Archaeology, University of York, Kings Manor, Exhibition Square, York, YO1 7EP, UK.
| | - Karen Hardy
- Department of Archaeology, University of Glasgow, Molema Building, Lilybank Gardens, Glasgow, G12 8RZ, UK.
| | - Fredrik Hallgren
- The Cultural Heritage Foundation, Stiftelsen Kulturmiljövård, Pilgatan 8D, 721 30, Västerås, Sweden
| | | | - Žydrūnė Miliauskienė
- Department of Anatomy, Histology and Anthropology, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Alison Sheridan
- Department of Scottish History and Archaeology, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF, UK
| | - Iwona Sobkowiak-Tabaka
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61-614, Poznań, Poland
| | - Maria Eulalia Subirà
- GREAB, Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia. Facultat de Biociències. Universitat Autònoma de Barcelona, Barcelona, Spain
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18
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Jiang Y, Cao T, Yang Y, Zhang H, Zhang J, Li X. A chlorophyll c synthase widely co-opted by phytoplankton. Science 2023; 382:92-98. [PMID: 37797009 DOI: 10.1126/science.adg7921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.
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Affiliation(s)
- Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jingyu Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
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19
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Hisahara Y, Nakano T, Tamiaki H. Self-aggregation behavior of dimeric chlorophyll-a derivatives linked with ethynylene and m-phenylene moieties. Photochem Photobiol Sci 2023; 22:2329-2339. [PMID: 37464173 DOI: 10.1007/s43630-023-00454-w] [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: 05/10/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023]
Abstract
Chlorophyll(Chl)-a derivatives inserting an ethynylene-m-phenylene group between a zinc chlorin ring and a hydroxymethyl group, in which various substituents were introduced on the benzene spacer, were prepared as model compounds for the light-harvesting antennae (chlorosomes) of photosynthetic green bacteria. These compounds were synthesized from a C3-ethynylated Chl-a derivative via sequential Sonogashira cross-coupling reaction, and the effects of the substituents on the phenylene linker on their self-aggregation behaviors were investigated by electronic absorption, circular dichroism, and infrared absorption spectroscopic measurements. These studies exhibited that some compounds gave the disordered self-assemblies including several species; however, the zinc complex of the dimeric Chl-a derivative primarily allowed a single J-aggregate species in an aqueous Triton X-100 micellar solution. Additional control experiments revealed that its self-assembly was constructed through the hydrogen and coordination bonding involving the hydroxymethyl group on benzene ring, keto-carbonyl group at C13-position, and central zinc atom, and this is consistent with a conventional chlorosomal manner.
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Affiliation(s)
- Yuma Hisahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Takeo Nakano
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
- Department of Chemistry, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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20
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Gisriel CJ, Elias E, Shen G, Soulier NT, Brudvig GW, Croce R, Bryant DA. Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01048-4. [PMID: 37773575 DOI: 10.1007/s11120-023-01048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/05/2023] [Indexed: 10/01/2023]
Abstract
Allophycocyanins are phycobiliproteins that absorb red light and transfer the energy to the reaction centers of oxygenic photosynthesis in cyanobacteria and red algae. Recently, it was shown that some allophycocyanins absorb far-red light and that one subset of these allophycocyanins, comprising subunits from the ApcD4 and ApcB3 subfamilies (FRL-AP), form helical nanotubes. The lowest energy absorbance maximum of the oligomeric ApcD4-ApcB3 complexes occurs at 709 nm, which is unlike allophycocyanin (AP; ApcA-ApcB) and allophycocyanin B (AP-B; ApcD-ApcB) trimers that absorb maximally at ~ 650 nm and ~ 670 nm, respectively. The molecular bases of the different spectra of AP variants are presently unclear. To address this, we structurally compared FRL-AP with AP and AP-B, performed spectroscopic analyses on FRL-AP, and leveraged computational approaches. We show that among AP variants, the α-subunit constrains pyrrole ring A of its phycocyanobilin chromophore to different extents, and the coplanarity of ring A with rings B and C sets a baseline for the absorbance maximum of the chromophore. Upon oligomerization, the α-chromophores of all AP variants exhibit a red shift of the absorbance maximum of ~ 25 to 30 nm and band narrowing. We exclude excitonic coupling in FRL-AP as the basis for this red shift and extend the results to discuss AP and AP-B. Instead, we attribute these spectral changes to a conformational alteration of pyrrole ring D, which becomes more coplanar with rings B and C upon oligomerization. This study expands the molecular understanding of light-harvesting attributes of phycobiliproteins and will aid in designing phycobiliproteins for biotechnological applications.
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Affiliation(s)
| | - Eduard Elias
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, 1081 HV, Amsterdam, Netherlands
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nathan T Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, 1081 HV, Amsterdam, Netherlands.
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
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21
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Gisriel CJ, Flesher DA, Long Z, Liu J, Wang J, Bryant DA, Batista VS, Brudvig GW. A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center. PHOTOSYNTHESIS RESEARCH 2023:10.1007/s11120-023-01047-5. [PMID: 37749456 DOI: 10.1007/s11120-023-01047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023]
Abstract
Chlorophylls and bacteriochlorophylls are the primary pigments used by photosynthetic organisms for light harvesting, energy transfer, and electron transfer. Many molecular structures of (bacterio)chlorophyll-containing protein complexes are available, some of which contain mixtures of different (bacterio)chlorophyll types. Differentiating these, which sometimes are structurally similar, is challenging but is required for leveraging structural data to gain functional insight. The reaction center complex from Chloroacidobacterium thermophilum has a hybrid (bacterio)chlorophyll antenna system containing both chlorophyll a and bacteriochlorophyll a molecules. The recent availability of its cryogenic electron microscopy (cryo-EM) structure provides an opportunity for a quantitative analysis of their identities and chemical environments. Here, we describe a theoretical basis for differentiating chlorophyll a and bacteriochlorophyll a in a cryo-EM map, and apply the approach to the experimental cryo-EM maps of the (bacterio)chlorophyll sites of the chloroacidobacterial reaction center. The comparison reveals that at ~ 2.2-Å resolution, chlorophyll a and bacteriochlorophyll a are easily distinguishable, but the orientation of the bacteriochlorophyll a acetyl moiety is not; however, the latter can confidently be assigned by identifying a hydrogen bond donor from the protein environment. This study reveals the opportunities and challenges in assigning (bacterio)chlorophyll types in structural biology, the accuracy of which is vital for downstream investigations.
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Affiliation(s)
| | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zhuoran Long
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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22
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Nguyen KU, Zhang Y, Liu Q, Zhang R, Jin X, Taniguchi M, Miller ES, Lindsey JS. Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review. Molecules 2023; 28:6132. [PMID: 37630384 PMCID: PMC10459692 DOI: 10.3390/molecules28166132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.
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Affiliation(s)
- Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Qihui Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Xiaohe Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA;
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
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23
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Chen GE, Hunter CN. Engineering Chlorophyll, Bacteriochlorophyll, and Carotenoid Biosynthetic Pathways in Escherichia coli. ACS Synth Biol 2023; 12:2236-2244. [PMID: 37531642 PMCID: PMC10443036 DOI: 10.1021/acssynbio.3c00237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Indexed: 08/04/2023]
Abstract
The biosynthesis of chlorophylls (Chls) and bacteriochlorophylls (BChls) represents a key aspect of photosynthesis research. Our previous work assembled the complete pathway for the synthesis of Chl a in Escherichia coli; here we engineer the more complex BChl a pathway in the same heterotrophic host. Coexpression of 18 genes enabled E. coli to produce BChl a, verifying that we have identified the minimum set of genes for the BChl a biosynthesis pathway. The protochlorophyllide reduction step was mediated by the bchNBL genes, and this same module was used to modify the Chl a pathway previously constructed in E. coli, eliminating the need for the light-dependent protochlorophyllide reductase. Furthermore, we demonstrate the feasibility of synthesizing more than one family of photosynthetic pigments in one host by engineering E. coli strains that accumulate the carotenoids neurosporene and β-carotene in addition to BChl a.
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Affiliation(s)
- Guangyu E. Chen
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - C. Neil Hunter
- School
of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
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24
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Mateos G, Martínez-Bonilla A, Martínez JM, Amils R. Vitamin B 12 Auxotrophy in Isolates from the Deep Subsurface of the Iberian Pyrite Belt. Genes (Basel) 2023; 14:1339. [PMID: 37510244 PMCID: PMC10378866 DOI: 10.3390/genes14071339] [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: 05/24/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Vitamin B12 is an enzymatic cofactor that is essential for both eukaryotes and prokaryotes. The development of life in extreme environments depends on cofactors such as vitamin B12 as well. The genomes of twelve microorganisms isolated from the deep subsurface of the Iberian Pyrite Belt have been analyzed in search of enzymatic activities that require vitamin B12 or are involved in its synthesis and import. Results have revealed that vitamin B12 is needed by these microorganisms for several essential enzymes such as ribonucleotide reductase, methionine synthase and epoxyqueosine reductase. Isolate Desulfosporosinus sp. DEEP is the only analyzed genome that holds a set core of proteins that could lead to the production of vitamin B12. The rest are dependent on obtaining it from the subsurface oligotrophic environment in which they grow. Sought proteins involved in the import of vitamin B12 are not widespread in the sample. The dependence found in the genomes of these microorganisms is supported by the production of vitamin B12 by microorganisms such as Desulfosporosinus sp. DEEP, showing that the operation of deep subsurface biogeochemical cycles is dependent on cofactors such as vitamin B12.
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Affiliation(s)
- Guillermo Mateos
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Adrián Martínez-Bonilla
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José M Martínez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
- Centro de Astrobiología (CAB-INTA), 28850 Torrejón de Ardoz, Spain
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25
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Veseli I, Chen YT, Schechter MS, Vanni C, Fogarty EC, Watson AR, Jabri B, Blekhman R, Willis AD, Yu MK, Fernàndez-Guerra A, Füssel J, Eren AM. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540289. [PMID: 37293035 PMCID: PMC10245760 DOI: 10.1101/2023.05.10.540289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.
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Affiliation(s)
- Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Yiqun T. Chen
- Data Science Institute and Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Matthew S. Schechter
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Chiara Vanni
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Emily C. Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Andrea R. Watson
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ran Blekhman
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Amy D. Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Michael K. Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60605, USA
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Marine ‘Omics Bridging Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany
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26
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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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27
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Chiral-phase HPLC separation of (divinyl-)protochlorophyllide-a enantiomers as key precursors in chlorophyll biosynthesis from their 13 2-stereoisomeric prime forms. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148960. [PMID: 36822491 DOI: 10.1016/j.bbabio.2023.148960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Protochlorophyllide(PChlide)-a and its 8-vinylated analog, divinyl(DV)-PChlide-a, are common and essential intermediates in the biosynthesis of all naturally occurring chlorophyll (Chl) pigments. These porphyrinoid-type pigments have a single optically active (asymmetric) carbon atom at the 132-position, so their stereoisomers are (132R)- and (132S)-enantiomers. The former and latter are called (DV-)PChlide-a and (DV-)PChlide-a', respectively. In this study, chiral-phase HPLC separation of enantiomeric (DV-)PChlides-a/a' was demonstrated. The (132R)-enantiomeric PChlide-a was eluted more slowly than the corresponding (132S)-enantiomeric PChlide-a' under the present HPLC conditions. On the other hand, the elution order of (132R)-DV-PChlide-a and (132S)-DV-PChlide-a' was reverse to that of PChlides-a/a'. After the separation of each enantiomer by the chiral-phase HPLC, the stereoisomeric configuration at the 132-position was characterized by means of circular dichroism spectroscopy. The present chiral-phase HPLC method enables us to evaluate optical purities of (DV-)PChlide-a species. For example, PChlide-a and/or DV-PChlide-a extracted from the spent medium and harvested cells of cultured purple photosynthetic bacterial mutants, the former of which has been often used as the source of (DV-)PChlide-a substrates for enzymatic reactions, were revealed to be mostly racemized, giving enantiomeric mixtures of (DV-)PChlides-a/a'.
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28
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Hirose M, Tsukatani Y, Harada J, Tamiaki H. In vitro reversible dehydration in C3-substituents of zinc chlorophyll analogs by BchF and BchV enzymes: Stereoselectivity and substrate specificity in the dehydration. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148959. [PMID: 36822492 DOI: 10.1016/j.bbabio.2023.148959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
In the biosynthetic pathway of bacteriochlorophyll(BChl)-a/b/c/d/e molecules, BchF and BchV enzymes catalyze the hydration of a C3-vinyl to C3-1-hydroxyethyl group. In this study, the in vitro reactions catalyzed by BchF and BchV partially afforded a C31-epimeric mixture of the hydrated products (secondary alcohols), with the primary recovery of the C3-vinylated substrate. The stereoselectivity and substrate specificity for the in vitro reverse enzymatic dehydration were examined using zinc chlorophyll analogs as model substrates by BchF and BchV, which were obtained from extracts of Escherichia coli overexpressing the respective genes from Chlorobaculum tepidum and used without further purification. Both BchF and BchV preferred dehydration of the (31R)-epimers over the (31S)-epimers. The (31R)-epimer was directly dehydrated by BchF and BchV to give the C3-vinylated product. By contrast, two reaction pathways for BchF and BchV dehydrations of the (31S)-epimer were proposed: (1) the (31S)-epimer would be directly dehydrated to C3-vinyl group. (2) the (31S)-epimer would be epimerized to the (31R)-epimer, and the resulting epimer was dehydrated. The results indicated that both BchF and BchV did function as a hydratase/dehydratase and could play a role in the C31-epimerization. An increase in the alkyl size at the C8-position gradually suppressed the BchF and BchV-catalyzed dehydration in vitro, while the C121- and C20-methylation only slightly affected the reaction. Using the BchF dehydration, a large amount of 3-vinyl-bacteriochlorophyllide-a was successfully prepared, with the retention of the chemically labile, central magnesium atom.
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Affiliation(s)
- Mitsuaki Hirose
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yusuke Tsukatani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka 830-0011, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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29
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Zhang C, Ma C, Zhu L, Yao M. Simultaneous determination of protoporphyrin IX and magnesium protoporphyrin IX in Arabidopsis thaliana and Camellia sinensis using UPLC-MS/MS. PLANT METHODS 2023; 19:34. [PMID: 36998023 PMCID: PMC10061815 DOI: 10.1186/s13007-023-01008-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUNDS Insertion of Mg2+ into protoporphyrin IX (PPIX) to produce magnesium-protoporphyrin IX (Mg-PPIX) was the first step toward chlorophyll biosynthesis, which not only imparts plants green pigmentation but underpins photosynthesis. Plants that blocked the conversion of PPIX to Mg-PPIX displayed yellowish or albino-lethal phenotypes. However, the lack of systematic study of the detection method and the metabolic difference between species have caused the research on chloroplast retrograde signaling controversial for a long time. RESULTS An advanced and sensitive UPLC-MS/MS strategy for determining PPIX and Mg-PPIX was established in two metabolic different plants, Arabidopsis thaliana (Columbia-0) and Camellia sinensis var. sinensis. Two metabolites could be extracted by 80% acetone (v/v) and 20% 0.1 M NH4OH (v/v) without hexane washing. Since the Mg-PPIX could be substantially de-metalized into PPIX in acidic conditions, analysis was carried out by UPLC-MS/MS with 0.1% ammonia (v/v) and 0.1% ammonium acetonitrile (v/v) as mobile phases using negative ion multiple reaction monitoring modes. Interestingly, it could be easier to monitor these two compounds in dehydrated samples rather than in fresh samples. Validation was performed in spiked samples and mean recoveries ranged from 70.5 to 916%, and the intra-day and inter-day variations were less than 7.5 and 10.9%, respectively. The limit of detection was 0.01 mg·kg- 1 and the limit of quantification was 0.05 mg·kg- 1. The contents of PPIX (1.67 ± 0.12 mg·kg- 1) and Mg-PPIX (3.37 ± 0.10 mg·kg- 1) in tea were significantly higher than in Arabidopsis (PPIX: 0.05 ± 0.02 mg·kg- 1; Mg-PPIX: 0.08 ± 0.01 mg·kg- 1) and they were only detected in the leaf. CONCLUSIONS Our study establishes a universal and reliable method for determining PPIX and Mg-PPIX in two plants using UPLC-MS/MS. This procedure will facilitate studying chlorophyll metabolism and natural chlorophyll production.
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Affiliation(s)
- Chenyu Zhang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Chunlei Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Li Zhu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
| | - Mingzhe Yao
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
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30
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Ghosh M, Misra R, Bhattacharya S, Majhi K, Jung KH, Sheves M. Retinal-Carotenoid Interactions in a Sodium-Ion-Pumping Rhodopsin: Implications on Oligomerization and Thermal Stability. J Phys Chem B 2023; 127:2128-2137. [PMID: 36857147 PMCID: PMC10026069 DOI: 10.1021/acs.jpcb.2c07502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Microbial rhodopsin (also called retinal protein)-carotenoid conjugates represent a unique class of light-harvesting (LH) complexes, but their specific interactions and LH properties are not completely elucidated as only few rhodopsins are known to bind carotenoids. Here, we report a natural sodium-ion (Na+)-pumping Nonlabens (Donghaeana) dokdonensis rhodopsin (DDR2) binding with a carotenoid salinixanthin (Sal) to form a thermally stable rhodopsin-carotenoid complex. Different spectroscopic studies were employed to monitor the retinal-carotenoid interaction as well as the thermal stability of the protein, while size-exclusion chromatography (SEC) and homology modeling are performed to understand the protein oligomerization process. In analogy with that of another Na+-pumping protein Krokinobacter eikastus rhodopsin 2 (KR2), we propose that DDR2 (studied concentration range: 2 × 10-6 to 4 × 10-5 M) remains mainly as a pentamer at room temperature and neutral pH, while heating above 55 °C partially converted it into a thermally less stable oligomeric form of the protein. This process is affected by both the pH and concentration. At high concentrations (4 × 10-5 to 2 × 10-4 M), the protein adopts a pentamer form reflected in the excitonic circular dichroism (CD) spectrum. In the presence of Sal, the thermal stability of DDR2 is increased significantly, and the pigment is stable even at 85 °C. The results presented could have implications in designing stable rhodopsin-carotenoid antenna complexes.
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Affiliation(s)
- Mihir Ghosh
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ramprasad Misra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sudeshna Bhattacharya
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Koushik Majhi
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, South Korea
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Freire MÁ. The origins of photosynthetic systems: Clues from the phosphorus and sulphur chemical scenarios. Biosystems 2023; 226:104873. [PMID: 36906114 DOI: 10.1016/j.biosystems.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Photosynthesis is the predominant biochemical process of carbon dioxide assimilation in the biosphere. To reduce carbon dioxide into organic compounds, photosynthetic organisms have one or two distinct photochemical reaction centre complexes with which they capture solar energy and generate ATP and reducing power. The core polypeptides of the photosynthetic reaction centres show low homologies but share overlapping structural folds, overall architecture, similar functional properties and highly conserved positions in protein sequences suggesting a common ancestry. However, the other biochemical components of photosynthetic apparatus appear to be a mosaic resulting from different evolutionary trajectories. The current proposal focusses on the nature and biosynthetic pathways of some organic redox cofactors that participate in the photosynthetic systems: quinones, chlorophyll and heme rings and their attached isoprenoid side chains, as well as on the coupled proton motive forces and associated carbon fixation pathways. This perspective highlights clues about the involvement of the phosphorus and sulphur chemistries that would have shaped the different types of photosynthetic systems.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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32
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Dey D, Tanaka R, Ito H. Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach. J Mol Evol 2023; 91:225-235. [PMID: 36869271 DOI: 10.1007/s00239-023-10100-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023]
Abstract
Chlorophyllide a oxygenase (CAO) is responsible for converting chlorophyll a to chlorophyll b in a two-step oxygenation reaction. CAO belongs to the family of Rieske-mononuclear iron oxygenases. Although the structure and reaction mechanism of other Rieske monooxygenases have been described, a member of plant Rieske non-heme iron-dependent monooxygenase has not been structurally characterized. The enzymes in this family usually form a trimeric structure and electrons are transferred between the non-heme iron site and the Rieske center of the adjoining subunits. CAO is supposed to form a similar structural arrangement. However, in Mamiellales such as Micromonas and Ostreococcus, CAO is encoded by two genes where non-heme iron site and Rieske cluster localize on the distinct polypeptides. It is not clear if they can form a similar structural organization to achieve the enzymatic activity. In this study, the tertiary structures of CAO from the model plant Arabidopsis thaliana and the Prasinophyte Micromonas pusilla were predicted by deep learning-based methods, followed by energy minimization and subsequent stereochemical quality assessment of the predicted models. Furthermore, the chlorophyll a binding cavity and the interaction of ferredoxin, which is the electron donor, on the surface of Micromonas CAO were predicted. The electron transfer pathway was predicted in Micromonas CAO and the overall structure of the CAO active site was conserved even though it forms a heterodimeric complex. The structures presented in this study will serve as a basis for understanding the reaction mechanism and regulation of the plant monooxygenase family to which CAO belongs.
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Affiliation(s)
- Debayan Dey
- Graduate School of Life Science, Hokkaido University, N10 W8, Sapporo, 060-0810, Japan
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Ryouichi Tanaka
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan
| | - Hisashi Ito
- Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan.
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33
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Meslé MM, Gray CR, Dlakić M, DuBois JL. Bacteroides thetaiotaomicron, a Model Gastrointestinal Tract Species, Prefers Heme as an Iron Source, Yields Protoporphyrin IX as a Product, and Acts as a Heme Reservoir. Microbiol Spectr 2023; 11:e0481522. [PMID: 36862015 PMCID: PMC10100974 DOI: 10.1128/spectrum.04815-22] [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: 12/07/2022] [Accepted: 02/03/2023] [Indexed: 03/03/2023] Open
Abstract
Members of the phylum Bacteroidetes are abundant in healthy gastrointestinal (GI) tract flora. Bacteroides thetaiotaomicron is a commensal heme auxotroph and representative of this group. Bacteroidetes are sensitive to host dietary iron restriction but proliferate in heme-rich environments that are also associated with colon cancer. We hypothesized that B. thetaiotaomicron may act as a host reservoir for iron and/or heme. In this study, we defined growth-promoting quantities of iron for B. thetaiotaomicron. B. thetaiotaomicron preferentially consumed and hyperaccumulated iron in the form of heme when presented both heme and nonheme iron sources in excess of its growth needs, leading to an estimated 3.6 to 8.4 mg iron in a model GI tract microbiome consisting solely of B. thetaiotaomicron. Protoporphyrin IX was identified as an organic coproduct of heme metabolism, consistent with anaerobic removal of iron from the heme leaving the intact tetrapyrrole as the observed product. Notably, no predicted or discernible pathway for protoporphyrin IX generation exists in B. thetaiotaomicron. Heme metabolism in congeners of B. thetaiotaomicron has previously been associated with the 6-gene hmu operon, based on genetic studies. A bioinformatics survey demonstrated that the intact operon is widespread in but confined to members of the Bacteroidetes phylum and ubiquitous in healthy human GI tract flora. Anaerobic heme metabolism by commensal Bacteroidetes via hmu is likely a major contributor to human host metabolism of the heme from dietary red meat and a driver for the selective growth of these species in the GI tract consortium. IMPORTANCE Research on bacterial iron metabolism has historically focused on the host-pathogen relationship, where the host suppresses pathogen growth by cutting off access to iron. Less is known about how host iron is shared with bacterial species that live commensally in the anaerobic human GI tract, typified by members of phylum Bacteroidetes. While many facultative pathogens avidly produce and consume heme iron, most GI tract anaerobes are heme auxotrophs whose metabolic preferences we aimed to describe. Understanding iron metabolism by model microbiome species like Bacteroides thetaiotaomicron is essential for modeling the ecology of the GI tract, which serves the long-term biomedical goals of manipulating the microbiome to facilitate host metabolism of iron and remediate dysbiosis and associated pathologies (e.g., inflammation and cancer).
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Affiliation(s)
- Margaux M. Meslé
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Chase R. Gray
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Mensur Dlakić
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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34
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Zhang J, Li Q, Wang Q, Zhao J, Zhu Y, Su T, Qi Q, Wang Q. Heme biosensor-guided in vivo pathway optimization and directed evolution for efficient biosynthesis of heme. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:33. [PMID: 36859288 PMCID: PMC9979517 DOI: 10.1186/s13068-023-02285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/18/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND Heme has attracted much attention because of its wide applications in medicine and food. The products of genes hemBCDEFY convert 5-aminolevulinic acid to protoporphyrin IX (PPIX; the immediate precursor of heme); protoporphyrin ferrochelatase (FECH) inserts Fe2+ into PPIX to generate heme. Biosynthesis of heme is limited by the need for optimized expression levels of multiple genes, complex regulatory mechanisms, and low enzymatic activity; these problems need to be overcome in metabolic engineering to improve heme synthesis. RESULTS We report a heme biosensor-guided screening strategy using the heme-responsive protein HrtR to regulate tcR expression in Escherichia coli, providing a quantifiable link between the intracellular heme concentration and cell survival in selective conditions (i.e., the presence of tetracycline). This system was used for rapid enrichment screening of heme-producing strains from a library with random ribosome binding site (RBS) variants and from a FECH mutant library. Through up to four rounds of iterative evolution, strains with optimal RBS intensities for the combination of hemBCDEFY were screened; we obtained a PPIX titer of 160.8 mg/L, the highest yield yet reported in shaken-flask fermentation. A high-activity FECH variant was obtained from the saturation mutagenesis library. Fed-batch fermentation of strain SH20C, harboring the optimized hemBCDEFY and the FECH mutant, produced 127.6 mg/L of heme. CONCLUSION We sequentially improved the multigene biosynthesis pathway of PPIX and performed in vivo directed evolution of FECH, based on a heme biosensor, which demonstrated the effectiveness of the heme biosensor-based pathway optimization strategy and broadens our understanding of the mechanism of heme synthesis.
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Affiliation(s)
- Jian Zhang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingbin Li
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qi Wang
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Jingyu Zhao
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yuan Zhu
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Tianyuan Su
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Qingsheng Qi
- grid.27255.370000 0004 1761 1174National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 People’s Republic of China ,grid.9227.e0000000119573309CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 People’s Republic of China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, People's Republic of China.
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Ushimaru R, Lyu J, Abe I. Diverse enzymatic chemistry for propionate side chain cleavages in tetrapyrrole biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad016. [PMID: 37422437 PMCID: PMC10548856 DOI: 10.1093/jimb/kuad016] [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: 05/03/2023] [Accepted: 07/07/2023] [Indexed: 07/10/2023]
Abstract
Tetrapyrroles represent a unique class of natural products that possess diverse chemical architectures and exhibit a broad range of biological functions. Accordingly, they attract keen attention from the natural product community. Many metal-chelating tetrapyrroles serve as enzyme cofactors essential for life, while certain organisms produce metal-free porphyrin metabolites with biological activities potentially beneficial for the producing organisms and for human use. The unique properties of tetrapyrrole natural products derive from their extensively modified and highly conjugated macrocyclic core structures. Most of these various tetrapyrrole natural products biosynthetically originate from a branching point precursor, uroporphyrinogen III, which contains propionate and acetate side chains on its macrocycle. Over the past few decades, many modification enzymes with unique catalytic activities, and the diverse enzymatic chemistries employed to cleave the propionate side chains from the macrocycles, have been identified. In this review, we highlight the tetrapyrrole biosynthetic enzymes required for the propionate side chain removal processes and discuss their various chemical mechanisms. ONE-SENTENCE SUMMARY This mini-review describes various enzymes involved in the propionate side chain cleavages during the biosynthesis of tetrapyrrole cofactors and secondary metabolites.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jiaqi Lyu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Oyagi K, Ogasawara S, Tamiaki H. Linker-length dependent intra/intermolecular coordination of synthetic zinc chlorophyll-a derivatives bearing a pyridine terminal in the C132-substituent. Tetrahedron 2023. [DOI: 10.1016/j.tet.2023.133334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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McCorvie TJ, Ferreira D, Yue WW, Froese DS. The complex machinery of human cobalamin metabolism. J Inherit Metab Dis 2023; 46:406-420. [PMID: 36680553 DOI: 10.1002/jimd.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Vitamin B12 (cobalamin, Cbl) is required as a cofactor by two human enzymes, 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) and methylmalonyl-CoA mutase (MMUT). Within the body, a vast array of transporters, enzymes and chaperones are required for the generation and delivery of these cofactor forms. How they perform these functions is dictated by the structure and interactions of the proteins involved, the molecular bases of which are only now being elucidated. In this review, we highlight recent insights into human Cbl metabolism and address open questions in the field by employing a protein structure and interactome based perspective. We discuss how three very similar proteins-haptocorrin, intrinsic factor and transcobalamin-exploit slight structural differences and unique ligand receptor interactions to effect selective Cbl absorption and internalisation. We describe recent advances in the understanding of how endocytosed Cbl is transported across the lysosomal membrane and the implications of the recently solved ABCD4 structure. We detail how MMACHC and MMADHC cooperate to modify and target cytosolic Cbl to the client enzymes MTR and MMUT using ingenious modifications to an ancient nitroreductase fold, and how MTR and MMUT link with their accessory enzymes to sustainably harness the supernucleophilic potential of Cbl. Finally, we provide an outlook on how future studies may combine structural and interactome based approaches and incorporate knowledge of post-translational modifications to bring further insights.
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Affiliation(s)
- Thomas J McCorvie
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Douglas Ferreira
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wyatt W Yue
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, Switzerland
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Liu XL. Collision-induced dissociation as "mass spectrometric filter" for rapid screening of tetrapyrrole derivatives and their chelated metal species in complex biological and environmental samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9413. [PMID: 36222097 DOI: 10.1002/rcm.9413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
RATIONALE Cyclic tetrapyrroles, such as chlorophylls and their diagenetic derivatives, are structurally diverse and often chelated with certain metal species in the natural environment. A high throughput analytical method enabling quick tetrapyrrole screening in complex samples will promote the study of tetrapyrrole biogeochemistry and probably discoveries of new tetrapyrroles. METHODS Total lipid extracts of biological and environmental samples were injected onto a C18 column to separate compounds with a reverse-phase gradient. Collision-induced dissociation (CID) was performed at different energy levels, from 40 to 200 eV, on a quadrupole time-of-flight mass spectrometry (QTOF-MS) to identify cyclic tetrapyrroles in complex matrices. RESULTS Under 200 eV CID cyclic tetrapyrroles exhibit a unique fragmentation behavior, the production of fragments larger than 300 Da. Utilizing such feature as a filter to extract product ions in the range of 300-500 Da, various cyclic tetrapyrrole derivatives are readily recognized in all tested biological and environmental samples. The 200 eV CID setup also dissociates chelated to porphyrin metals, including Cu, Fe, Mn, Ni, and V, as single-charged ions for direct MS detection. CONCLUSIONS The 200 eV CID setup provides an efficient approach for the identification of cyclic tetrapyrroles, such as chlorophylls and fossil metalloporphyrins, in complex environmental samples. The direct detection of chelated to porphyrin metal ions with QTOF-MS shows the potential for compound-specific metal isotope analysis.
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Affiliation(s)
- Xiao-Lei Liu
- School of Geosciences, University of Oklahoma, Norman, Oklahoma, USA
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40
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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Ciuti S, Toninato J, Barbon A, Zarrabi N, Poddutoori PK, van der Est A, Di Valentin M. Solvent dependent triplet state delocalization in a co-facial porphyrin heterodimer. Phys Chem Chem Phys 2022; 24:30051-30061. [PMID: 36472461 DOI: 10.1039/d2cp04291f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The excited triplet state of a cofacial aluminum(III) porphyrin-phosphorus(V) porphyrin heterodimer is investigated using transient EPR spectroscopy and quantum chemical calculations. In the dimer, the two porphyrins are bound covalently to each other via a μ-oxo bond between the Al and P centres, which results in strong electronic interaction between the porphyrin rings. The spin polarized transient EPR spectrum of the dimer is narrower than the spectra of the constituent monomers and the magnitude of the zero-field splitting parameter D is solvent dependent, decreasing as the polarity of the solvent increases. The quantum chemical calculations show that the spin density of the triplet state is delocalized over both porphyrins, while magnetophotoselection measurements reveal that, in contrast to the value of D, the relative orientation of the ZFS axes and the excitation transition dipole moments are not solvent dependent. Together the results indicate that triplet state wavefunction is delocalized over both porphyrins and has a modest degree of charge-transfer character that increases with increasing solvent polarity. The sign of the spin polarization pattern of the dimer triplet state is opposite to that of the monomers. The positive sign of D predicted for the monomers and dimer by the quantum chemical calculations implies that the different signs of the spin polarization patterns is a result of a difference in the spin selectivity of the intersystem crossing.
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Affiliation(s)
- Susanna Ciuti
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Jacopo Toninato
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Antonio Barbon
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Niloofar Zarrabi
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, 1038 University Drive, Duluth, Minnesota 55812, USA.
| | - Prashanth K Poddutoori
- Department of Chemistry & Biochemistry, University of Minnesota Duluth, 1038 University Drive, Duluth, Minnesota 55812, USA.
| | - Art van der Est
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada.
| | - Marilena Di Valentin
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, 35131 Padova, Italy.
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Mathur Y, Hazra AB. Methylations in vitamin B 12 biosynthesis and catalysis. Curr Opin Struct Biol 2022; 77:102490. [PMID: 36371846 DOI: 10.1016/j.sbi.2022.102490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2022]
Abstract
Vitamin B12 is an essential biomolecule that assists in the catalysis of methyl transfer and radical-based reactions in cellular metabolism. The structure of B12 is characterized by a tetrapyrrolic corrin ring with a central cobalt ion coordinated with an upper ligand, and a lower ligand anchored via a nucleotide loop. Multiple methyl groups decorate B12, and their presence (or absence) have structural and functional consequences. In this minireview, we focus on the methyl groups that distinguish vitamin B12 from other tetrapyrrolic biomolecules and from its own naturally occurring analogues called cobamides. We draw information from recent advances in the field to understand the origins of these methyl groups and the enzymes that incorporate them, and discuss their biological significance.
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Affiliation(s)
- Yamini Mathur
- Department of Biology, Indian Institute of Science Education and Research, Pune, India. https://twitter.com/yaminipmathur
| | - Amrita B Hazra
- Department of Biology, Indian Institute of Science Education and Research, Pune, India; Department of Chemistry, Indian Institute of Science Education and Research, Pune, India.
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Sinha N, Eirich J, Finkemeier I, Grimm B. Glutamate 1-semialdehyde aminotransferase is connected to GluTR by GluTR-binding protein and contributes to the rate-limiting step of 5-aminolevulinic acid synthesis. THE PLANT CELL 2022; 34:4623-4640. [PMID: 35972388 PMCID: PMC9614494 DOI: 10.1093/plcell/koac237] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/28/2022] [Indexed: 06/01/2023]
Abstract
Tetrapyrroles play fundamental roles in crucial processes including photosynthesis, respiration, and catalysis. In plants, 5-aminolevulinic acid (ALA) is the common precursor of tetrapyrroles. ALA is synthesized from activated glutamate by the enzymes glutamyl-tRNA reductase (GluTR) and glutamate-1-semialdehyde aminotransferase (GSAAT). ALA synthesis is recognized as the rate-limiting step in this pathway. We aimed to explore the contribution of GSAAT to the control of ALA synthesis and the formation of a protein complex with GluTR. In Arabidopsis thaliana, two genes encode GSAAT isoforms: GSA1 and GSA2. A comparison of two GSA knockout mutants with the wild-type revealed the correlation of reduced GSAAT activity and ALA-synthesizing capacity in leaves with lower chlorophyll content. Growth and green pigmentation were more severely impaired in gsa2 than in gsa1, indicating the predominant role of GSAAT2 in ALA synthesis. Interestingly, GluTR accumulated to higher levels in gsa2 than in the wild-type and was mainly associated with the plastid membrane. We propose that the GSAAT content modulates the amount of soluble GluTR available for ALA synthesis. Several different biochemical approaches revealed the GSAAT-GluTR interaction through the assistance of GluTR-binding protein (GBP). A modeled structure of the tripartite protein complex indicated that GBP mediates the stable association of GluTR and GSAAT for adequate ALA synthesis.
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Affiliation(s)
- Neha Sinha
- Institute of Biology/Plant Physiology, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Jürgen Eirich
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
| | - Iris Finkemeier
- Institute for Plant Biology and Biotechnology, Plant Physiology, Westfälische Wilhelms-Universität, 48149 Muenster, Germany
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Liu J, Knapp M, Jo M, Dill Z, Bridwell-Rabb J. Rieske Oxygenase Catalyzed C-H Bond Functionalization Reactions in Chlorophyll b Biosynthesis. ACS CENTRAL SCIENCE 2022; 8:1393-1403. [PMID: 36313167 PMCID: PMC9615114 DOI: 10.1021/acscentsci.2c00058] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Rieske oxygenases perform precise C-H bond functionalization reactions in anabolic and catabolic pathways. These reactions are typically characterized as monooxygenation or dioxygenation reactions, but other divergent reactions are also catalyzed by Rieske oxygenases. Chlorophyll(ide) a oxygenase (CAO), for example is proposed to catalyze two monooxygenation reactions to transform a methyl-group into the formyl-group of Chlorophyll b. This formyl group, like the formyl groups found in other chlorophyll pigments, tunes the absorption spectra of chlorophyllb and supports the ability of several photosynthetic organisms to adapt to environmental light. Despite the importance of this reaction, CAO has never been studied in vitro with purified protein, leaving many open questions regarding whether CAO can facilitate both oxygenation reactions using just the Rieske oxygenase machinery. In this study, we demonstrated that four CAO homologues in partnership with a non-native reductase convert a Chlorophyll a precursor, chlorophyllidea, into chlorophyllideb in vitro. Analysis of this reaction confirmed the existence of the proposed intermediate, highlighted the stereospecificity of the reaction, and revealed the potential of CAO as a tool for synthesizing custom-tuned natural and unnatural chlorophyll pigments. This work thus adds to our fundamental understanding of chlorophyll biosynthesis and Rieske oxygenase chemistry.
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Comprehensive Empirical Model of Substitution—Influence on Hydrogen Bonding in Aromatic Schiff Bases. Int J Mol Sci 2022; 23:ijms232012439. [DOI: 10.3390/ijms232012439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, over 500 structures of tri-ring aromatic Schiff bases with different substitution patterns were investigated to develop a unified description of the substituent effect on the intramolecular hydrogen bridge. Both proximal and distal effects were examined using Density Functional Theory (DFT) in the gas phase and with solvent reaction field (Polarizable Continuum Model (PCM) and water as the solvent). In order to investigate and characterize the non-covalent interactions, a topological analysis was performed using the Quantum Theory of Atoms In Molecules (QTAIM) theory and Non-Covalent Interactions (NCI) index. The obtained results were summarized as the generalized, empirical model of the composite substituent effect, assessed using an additional group of simple ring-based Schiff bases. The composite substituent effect has been divided into separate increments describing the different interactions of the hydrogen bridge and the substituent: the classical substituent effect, involving resonance and induction mediated through the ring, steric increment based on substituent proximity to the bridge elements, and distal increment, derived from substitution on the distal ring.
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46
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Dey D, Nishijima M, Tanaka R, Kurisu G, Tanaka H, Ito H. Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae. Protein Sci 2022; 31:e4430. [PMID: 36173179 PMCID: PMC9514216 DOI: 10.1002/pro.4430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022]
Abstract
Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.
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Affiliation(s)
- Debayan Dey
- Graduate School of Life ScienceHokkaido UniversitySapporoJapan
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | | | - Ryouichi Tanaka
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
| | - Genji Kurisu
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hideaki Tanaka
- Institute for Protein ResearchOsaka UniversitySuitaJapan
| | - Hisashi Ito
- Institute of Low Temperature ScienceHokkaido UniversitySapporoJapan
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Hirose M, Tsukatani Y, Harada J, Tamiaki H. Characterization of regioisomeric diterpenoid tails in bacteriochlorophylls produced by geranylgeranyl reductase from Halorhodospira halochloris and Blastochloris viridis. PHOTOSYNTHESIS RESEARCH 2022; 154:1-12. [PMID: 35852706 DOI: 10.1007/s11120-022-00938-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Geranylgeranyl reductase (GGR) encoded by the bchP gene catalyzes the reductions of three unsaturated C = C double bonds (C6 = C7, C10 = C11, and C14 = C15) in a geranylgeranyl (GG) group of the esterifying moiety in 17-propionate residue of bacteriochlorophyll (BChl) molecules. It was recently reported that GGR in Halorhodospira halochloris potentially catalyzes two hydrogenations, yielding BChl with a tetrahydrogeranylgeranyl (THGG) tail. Furthermore, its engineered GGR, in which N-terminal insertion peptides characteristic for H. halochloris were deleted, performed single hydrogenation, producing BChl with a dihydrogeranylgeranyl (DHGG) tail. In some of these enzymatic reactions, it remained unclear in which order the C = C double bond in a GG group was first reduced. In this study, we demonstrated that the (variant) GGR from H. halochloris catalyzed an initial reduction of the C6 = C7 double bond to yield a 6,7-DHGG tail. The intact GGR of H. halochloris catalyzed the further hydrogenation of the C14 = C15 double bonds to give a 6,7,14,15-THGG group, whereas deleting the characteristic peptide region from the GGR suppressed the C14 = C15 reduction. We also verified that in a model bacterium, Blastochloris viridis producing standard BChl-b, the reduction of a GG to phytyl group occurred via 10,11-DHGG and 6,7,10,11-THGG. The high-performance liquid chromatographic elution profiles of BChls-a/b employed in this study are essential for identifying the regioisomeric diterpenoid tails in the BChls of phototrophic bacteria distributed in nature and elucidating GGR enzymatic reactions.
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Affiliation(s)
- Mitsuaki Hirose
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Yusuke Tsukatani
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, 237-0061, Japan
| | - Jiro Harada
- Department of Medical Biochemistry, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Hitoshi Tamiaki
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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48
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Abstract
Heme (protoheme IX) is an essential cofactor for a large variety of proteins whose functions vary from one electron reactions to binding gases. While not ubiquitous, heme is found in the great majority of known life forms. Unlike most cofactors that are acquired from dietary sources, the vast majority of organisms that utilize heme possess a complete pathway to synthesize the compound. Indeed, dietary heme is most frequently utilized as an iron source and not as a source of heme. In Nature there are now known to exist three pathways to synthesize heme. These are the siroheme dependent (SHD) pathway which is the most ancient, but least common of the three; the coproporphyrin dependent (CPD) pathway which with one known exception is found only in gram positive bacteria; and the protoporphyrin dependent (PPD) pathway which is found in gram negative bacteria and all eukaryotes. All three pathways share a core set of enzymes to convert the first committed intermediate, 5-aminolevulinate (ALA) into uroporphyrinogen III. In the current review all three pathways are reviewed as well as the two known pathways to synthesize ALA. In addition, interesting features of some heme biosynthesis enzymes are discussed as are the regulation and disorders of heme biosynthesis.
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Affiliation(s)
- Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Department of Microbiology, University of Georgia, Athens, GA 30602-1111, USA
| | - Amy E Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-1111, USA
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, USA
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49
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Wang P, Ji S, Grimm B. Post-translational regulation of metabolic checkpoints in plant tetrapyrrole biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4624-4636. [PMID: 35536687 PMCID: PMC9992760 DOI: 10.1093/jxb/erac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/06/2022] [Indexed: 06/02/2023]
Abstract
Tetrapyrrole biosynthesis produces metabolites that are essential for critical reactions in photosynthetic organisms, including chlorophylls, heme, siroheme, phytochromobilins, and their derivatives. Due to the paramount importance of tetrapyrroles, a better understanding of the complex regulation of tetrapyrrole biosynthesis promises to improve plant productivity in the context of global climate change. Tetrapyrrole biosynthesis is known to be controlled at multiple levels-transcriptional, translational and post-translational. This review addresses recent advances in our knowledge of the post-translational regulation of tetrapyrrole biosynthesis and summarizes the regulatory functions of the various auxiliary factors involved. Intriguingly, the post-translational network features three prominent metabolic checkpoints, located at the steps of (i) 5-aminolevulinic acid synthesis (the rate-limiting step in the pathway), (ii) the branchpoint between chlorophyll and heme synthesis, and (iii) the light-dependent enzyme protochlorophyllide oxidoreductase. The regulation of protein stability, enzymatic activity, and the spatial organization of the committed enzymes in these three steps ensures the appropriate flow of metabolites through the tetrapyrrole biosynthesis pathway during photoperiodic growth. In addition, we offer perspectives on currently open questions for future research on tetrapyrrole biosynthesis.
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Affiliation(s)
- Peng Wang
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13 (Haus 12), 10115 Berlin, Germany
| | - Shuiling Ji
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstraße 13 (Haus 12), 10115 Berlin, Germany
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50
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Foster AW, Clough SE, Aki Z, Young TR, Clarke AR, Robinson NJ. Metalation calculators for E. coli strain JM109 (DE3): Aerobic, anaerobic and hydrogen peroxide exposed cells cultured in LB media. Metallomics 2022; 14:6657815. [PMID: 35933161 PMCID: PMC9434800 DOI: 10.1093/mtomcs/mfac058] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/24/2022] [Indexed: 11/14/2022]
Abstract
Three web-based calculators, and three analogous spreadsheets, have been generated that predict in vivo metal occupancies of proteins based on known metal affinities. The calculations exploit estimates of the availabilities of the labile buffered pools of different metals inside a cell. Here, metal availabilities have been estimated for a strain of E. coli that is commonly used in molecular biology and biochemistry research, for example in the production of recombinant proteins. Metal availabilities have been examined for cells grown in LB medium aerobically, anaerobically and in response to H2O2 by monitoring the abundance of a selected set of metal-responsive transcripts by qPCR. The selected genes are regulated by DNA-binding metal sensors that have been thermodynamically characterised in related bacterial cells enabling gene expression to be read-out as a function of intracellular metal availabilities expressed as free energies for forming metal complexes. The calculators compare these values with the free energies for forming complexes with the protein of interest, derived from metal affinities, to estimate how effectively the protein can compete with exchangeable binding sites in the intracellular milieu. The calculators then inter-compete the different metals, limiting total occupancy of the site to a maximum stoichiometry of 1, to output percentage occupancies with each metal. In addition to making these new and conditional calculators available, an original purpose of this article was to provide a tutorial which discusses constraints of this approach and presents ways in which such calculators might be exploited in basic and applied research, and in next-generation manufacturing.
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Affiliation(s)
- Andrew W Foster
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Sophie E Clough
- Department of Biosciences, Durham University, Durham, UK.,Department of Chemistry, Durham University, Durham, UK
| | - Zeynep Aki
- Advanced Research Computing, Durham University, Durham, UK
| | - Tessa R Young
- 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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