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Publications (10 of 25) Show all publications
Chaudhari, A. S., Chatterjee, A., Domingos, C. A. O., Andrikopoulos, P. C., Liu, Y., Andersson, I., . . . Fuertes, G. (2023). Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222. Protein Science, 32(4), Article ID e4590.
Open this publication in new window or tab >>Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222
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2023 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 32, no 4, article id e4590Article in journal (Refereed) Published
Abstract [en]

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at 45 positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
flavoproteins, FTIR spectroscopy, genetic code expansion, kinetics, photosensory receptors, protein structural dynamics, signal transduction, site-specific vibrational probes, time-resolved methods, UV, vis spectroscopy
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-500016 (URN)10.1002/pro.4590 (DOI)000950351200001 ()36764820 (PubMedID)
Funder
Akademie Ved Ceske Republiky, RVO86652036European Regional Development Fund (ERDF), CZ.02.1.01/0.0/0.0/15_003/0000447European Regional Development Fund (ERDF), CZ.02.1.01/0.0/0.0/18_046/0015974
Available from: 2023-04-19 Created: 2023-04-19 Last updated: 2023-05-23Bibliographically approved
Zhou, Y., Gunn, L., Birch, R., Andersson, I. & Whitney, S. M. (2023). Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth. NATURE PLANTS, 9, 978-986
Open this publication in new window or tab >>Grafting Rhodobacter sphaeroides with red algae Rubisco to accelerate catalysis and plant growth
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2023 (English)In: NATURE PLANTS, E-ISSN 2055-0278, Vol. 9, p. 978-986Article in journal (Refereed) Published
Abstract [en]

Improving the carboxylation properties of Rubisco has primarily arisen from unforeseen amino acid substitutions remote from the catalytic site. The unpredictability has frustrated rational design efforts to enhance plant Rubisco towards the prized growth-enhancing carboxylation properties of red algae Griffithsia monilis GmRubisco. To address this, we determined the crystal structure of GmRubisco to 1.7 angstrom. Three structurally divergent domains were identified relative to the red-type bacterial Rhodobacter sphaeroides RsRubisco that, unlike GmRubisco, are expressed in Escherichia coli and plants. Kinetic comparison of 11 RsRubisco chimaeras revealed that incorporating C329A and A332V substitutions from GmRubisco Loop 6 (corresponding to plant residues 328 and 331) into RsRubisco increased the carboxylation rate (kcatc) by 60%, the carboxylation efficiency in air by 22% and the CO2/O-2 specificity (Sc/o) by 7%. Plastome transformation of this RsRubisco Loop 6 mutant into tobacco enhanced photosynthesis and growth up to twofold over tobacco producing wild-type RsRubisco. Our findings demonstrate the utility of RsRubisco for the identification and in planta testing of amino acid grafts from algal Rubisco that can enhance the enzyme's carboxylase potential.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-508453 (URN)10.1038/s41477-023-01436-7 (DOI)001008762600018 ()37291398 (PubMedID)
Funder
Swedish Research Council Formas, 2017-00963
Available from: 2023-08-02 Created: 2023-08-02 Last updated: 2023-08-02Bibliographically approved
Bielecki, J., Hantke, M. F., Daurer, B. J., Reddy, H. K. N., Hasse, D., Larsson, D. S. D., . . . Maia, F. R. N. (2019). Electrospray sample injection for single-particle imaging with x-ray lasers. Science Advances, 5(5), Article ID eaav8801.
Open this publication in new window or tab >>Electrospray sample injection for single-particle imaging with x-ray lasers
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-387970 (URN)10.1126/sciadv.aav8801 (DOI)000470125000080 ()31058226 (PubMedID)
Available from: 2019-05-03 Created: 2019-06-27 Last updated: 2023-10-31Bibliographically approved
Hasse, D., Hülsemann, J., Carlsson, G., Valegård, K. & Andersson, I. (2019). Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus. Acta Crystallographica Section D: Structural Biology , 75, 1107-1118
Open this publication in new window or tab >>Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus
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2019 (English)In: Acta Crystallographica Section D: Structural Biology , E-ISSN 2059-7983, Vol. 75, p. 1107-1118Article in journal (Refereed) Published
Abstract [en]

The core of beta-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. beta-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid alpha-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form alpha-aminoadipate semialdehyde) to alpha-aminoadipic acid, is catalysed by the NAD(+)-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD(+), the product alpha-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD(+) binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results.

Place, publisher, year, edition, pages
INT UNION CRYSTALLOGRAPHY, 2019
Keywords
beta-lactam biosynthesis pathway, alpha-aminoadipic acid, beta-lactam antibiotics, picolinic acid, Streptomyces clavuligerus, aldehyde dehydrogenase fold, enzyme mechanism
National Category
Structural Biology Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-400425 (URN)10.1107/S2059798319014852 (DOI)000501134600007 ()31793904 (PubMedID)
Available from: 2019-12-20 Created: 2019-12-20 Last updated: 2022-01-29Bibliographically approved
Valegård, K., Andralojc, P. J., Haslam, R. P., Pearce, F. G., Eriksen, G. K., Madgwickn, P. J., . . . Andersson, I. (2018). Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications. Journal of Biological Chemistry, 293(34), 13033-13043
Open this publication in new window or tab >>Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications
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2018 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 293, no 34, p. 13033-13043Article in journal (Refereed) Published
Abstract [en]

The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO2-fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL, and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The V-max and K-m for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (S-c/o) at 15, 25, and 35 degrees C were determined. The S-c/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO(2 )relative to O-2. Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short beta A-beta B loop and a C-terminal extension that forms a beta-hairpin structure (beta E-beta F loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, beta-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO2 fixation in arctic diatom Rubiscos.

National Category
Botany
Identifiers
urn:nbn:se:uu:diva-364046 (URN)10.1074/jbc.RA118.003518 (DOI)000442730200006 ()29925588 (PubMedID)
Funder
Swedish Research Council Formas
Available from: 2018-12-10 Created: 2018-12-10 Last updated: 2023-10-31Bibliographically approved
Valegård, K., Hasse, D., Andersson, I. & Gunn, L. H. (2018). Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bis­phosphate. Acta Crystallographica Section D: Structural Biology , 74(1), 1-9
Open this publication in new window or tab >>Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bis­phosphate
2018 (English)In: Acta Crystallographica Section D: Structural Biology , E-ISSN 2059-7983, Vol. 74, no 1, p. 1-9Article in journal (Refereed) Published
Abstract [en]

The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L8S8 hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.

Keywords
ribulose-1, 5-bisphosphate, carboxylase/oxygenase, Rubisco, 2-carboxy­arabinitol-1, 5-bisphosphate, carbon fixation, Arabidopsis thaliana, rbcS multigene family, isoforms, merohedral twinning
National Category
Structural Biology
Research subject
Biology; Biology with specialization in Structural Biology
Identifiers
urn:nbn:se:uu:diva-341464 (URN)10.1107/S2059798317017132 (DOI)000423422400001 ()29372894 (PubMedID)
Funder
Swedish Research Council, 2015-05007
Available from: 2018-02-09 Created: 2018-02-09 Last updated: 2020-11-11Bibliographically approved
Carlsson, G. H., Hasse, D., Cardinale, F., Prandi, C. & Andersson, I. (2018). The elusive ligand complexes of the DWARF14 strigolactone receptor. Journal of Experimental Botany, 69(9), 2345-2354
Open this publication in new window or tab >>The elusive ligand complexes of the DWARF14 strigolactone receptor
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2018 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 69, no 9, p. 2345-2354Article in journal (Refereed) Published
Abstract [en]

Strigolactones, a group of terpenoid lactones, control many aspects of plant growth and development, but the active forms of these plant hormones and their mode of action at the molecular level are still unknown. The strigolactone protein receptor is unusual because it has been shown to cleave the hormone and supposedly forms a covalent bond with the cleaved hormone fragment. This interaction is suggested to induce a conformational change in the receptor that primes it for subsequent interaction with partners in the signalling pathway. Substantial efforts have been invested into describing the interaction of synthetic strigolactone analogues with the receptor, resulting in a number of crystal structures. This investigation combines a re-evaluation of models in the Protein Data Bank with a search for new conditions that may permit the capture of a receptor-ligand complex. While weak difference density is frequently observed in the binding cavity, possibly due to a low-occupancy compound, the models often contain features not supported by the X-ray data. Thus, at this stage, we do not believe that any detailed deductions about the nature, conformation, or binding mode of the ligand can be made with any confidence.

Keywords
Crystal structure, DWARF14, ligand binding, Oryza sativa, strigolactone, strigolactone receptor
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-354969 (URN)10.1093/jxb/ery036 (DOI)000430727000014 ()29394369 (PubMedID)
Available from: 2018-06-25 Created: 2018-06-25 Last updated: 2018-06-25Bibliographically approved
Gunn, L., Valegard, K. & Andersson, I. (2017). A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphatecarboxylase/oxygenase (Rubisco) acts as a small subunit mimic. Journal of Biological Chemistry, 292(16), 6838-6850, Article ID jbc.M116.767145.
Open this publication in new window or tab >>A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphatecarboxylase/oxygenase (Rubisco) acts as a small subunit mimic
2017 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 292, no 16, p. 6838-6850, article id jbc.M116.767145Article in journal (Refereed) Published
Abstract [en]

The catalytic inefficiencies of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) often limit plant productivity. Strategies to engineer more efficient plant Rubiscos have been hampered by evolutionary constraints, prompting interest in Rubisco isoforms from non-photosynthetic organisms. The methanogenic archaeon Methanococcoides burtonii contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) byproduct of purine/pyrimidine metabolism. The crystal structure of M. burtonii Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L2)5 and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric L8S8 enzymes. MbR contains a unique 29-amino-acid insertion near the C-terminus, which folds as a separate domain in the structure. This domain, which is visualized for the first time in this study, is located in a similar position to SSus in L8S8 enzymes between LSus of adjacent L2 dimers, where negatively charged residues co-ordinate around a Mg2+ ion in a fashion that suggests this domain may be important for the assembly process. The Rubisco assembly domain is thus an inbuilt SSu mimic that concentrates L2 dimers. MbR assembly is ligand-stimulated and we show that only 6-carbon molecules with a particular stereochemistry at the C3 carbon can induce oligomerization. Based on MbR structure, subunit arrangement, sequence, phylogenetic distribution and function, MbR and a subset of Rubiscos from the Methanosarcinales order are proposed to belong to a new Rubisco sub-group, named form IIIB.

Keywords
ribulose‐1, 5‐bisphosphate carboxylase/oxygenase (Rubisco), carbon fixation, X‐ray crystallography, structure‐function, oligomerization, archaea, metal ion‐protein interaction, protein evolution
National Category
Structural Biology Biochemistry and Molecular Biology Evolutionary Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:uu:diva-314323 (URN)10.1074/jbc.M116.767145 (DOI)000399813400033 ()
Available from: 2017-02-01 Created: 2017-02-01 Last updated: 2017-09-18Bibliographically approved
Larsson, A. M., Hasse, D., Valegård, K. & Andersson, I. (2017). Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore. Journal of Experimental Botany, 68(14), 3857-3867
Open this publication in new window or tab >>Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore
2017 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 14, p. 3857-3867Article in journal (Refereed) Published
Abstract [en]

Cyanobacterial CO2 fixation is promoted by encapsulating and co-localizing the CO2-fixing enzymes within a protein shell, the carboxysome. A key feature of the carboxysome is its ability to control selectively the flux of metabolites in and out of the shell. The beta-carboxysome shell protein CcmP has been shown to form a double layer of pseudohexamers with a relatively large central pore (similar to 13 angstrom diameter), which may allow passage of larger metabolites such as the substrate for CO2 fixation, ribulose 1,5-bisphosphate, through the shell. Here we describe two crystal structures, at 1.45 angstrom and 1.65 angstrom resolution, of CcmP from Synechococcus elongatus PCC7942 (SeCcmP). The central pore of CcmP is open or closed at its ends, depending on the conformation of two conserved residues, Glu69 and Arg70. The presence of glycerol resulted in a pore that is open at one end and closed at the opposite end. When glycerol was omitted, both ends of the barrel became closed. A binding pocket at the interior of the barrel featured residual density with distinct differences in size and shape depending on the conformation, open or closed, of the central pore of SeCcmP, suggestive of a metabolite-driven mechanism for the gating of the pore.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS, 2017
Keywords
BMC domain, carboxysome, beta-cyanobacteria, gated transport, microcompartment, shell protein
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-335687 (URN)10.1093/jxb/erx070 (DOI)000410239600014 ()28369612 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

Title in WoS: Crystal structures of beta-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore

Available from: 2017-12-19 Created: 2017-12-19 Last updated: 2017-12-19Bibliographically approved
Daurer, B. J., Okamoto, K., Bielecki, J., Maia, F. R. N., Mühlig, K., Seibert, M. M., . . . Larsson, D. S. D. (2017). Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ, 4, 251-262
Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
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2017 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-323439 (URN)10.1107/S2052252517003591 (DOI)000400460500008 ()28512572 (PubMedID)
Projects
eSSENCE
Available from: 2017-04-07 Created: 2017-11-14 Last updated: 2023-10-30Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-2729-0787

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