Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Catalytic and hydrodynamic properties of styrene monooxygenases from Rhocodoccus opacus 1CP are modulated by cofactor binding.
Riedel, A. ; Heine, T. ; Westphal, A.H. ; Conrad, C. ; Rathsack, P. ; Berkel, W.J.H. van; Tischler, D. - \ 2015
AMB Express 5 (2015). - ISSN 2191-0855 - 11 p.
recombinant escherichia-coli - pseudomonas-fluorescens st - functional-analysis - crystal-structure - catabolism genes - strain vlb120 - putida ca-3 - degradation - mechanism - oxide
Styrene monooxygenases (SMOs) are flavoenzymes catalyzing the epoxidation of styrene into styrene oxide. SMOs are composed of a monooxygenase (StyA) and a reductase (StyB). The latter delivers reduced FAD to StyA on the expense of NADH. We identified Rhodococcus opacus 1CP as the first microorganism to possess three different StyA isoforms occurring in two systems StyA1/StyA2B and StyA/StyB, respectively. The hydrodynamic properties of StyA isozymes were found to be modulated by the binding of the (reduced) FAD cofactor. StyA1 and SyA2B mainly occur as dimers in their active forms while StyA is a monomer. StyA1 showed the highest epoxidation activity and excellent enantioselectivity in aromatic sulfoxidation. The hydrodynamic and biocatalytic properties of SMOs from strain 1CP are of relevance for investigation of possible industrial applications.
Migration of diadromous and landlocked smelt populations studies by otolith geochemistry
Phung, A.T. ; Tulp, I.Y.M. ; Baeyens, W. ; Elskens, M. ; Leermakers, M. ; Gao, Y. - \ 2015
Fisheries Research 167 (2015). - ISSN 0165-7836 - p. 123 - 131.
eel anguilla-anguilla - laser-ablation icpms - crystal-structure - lake ijsselmeer - fish otoliths - japanese eels - habitat use - water - ratios - strontium
Laser ablation inductively coupled mass spectrometry (LA-ICPMS) was used to determine Sr and Ba profiles along the growth axis of otholiths of European smelt caught in the Wadden Sea, the IJsselmeer and the Markermeer and to investigate the migration behaviour of the fish between the freshwater lakes and the marine environment. The use of Sr and Ba otolith profiles and their dissolved concentrations in the three aquatic systems provided a robust method for habitat classification and migration behaviour of the 111 individual smelts. No evidence was found of the migration of individuals from the Wadden Sea to the Ijsselmeer due to no marine Sr/Ba signal in the Ijsselmeer smelt. The Ba and Sr concentrations in the otoliths of Wadden Sea smelt suggest a mixture of two populations: juveniles that were born in the Wadden Sea and species that were born in Lakes IJsselmeer or Markermeer and migrated to the Wadden Sea. In the IJsselmeer different types of otolith profiles were observed depending on the migration history of the individuals in that lake: some individuals have probably not moved a lot, others may have used tributaries (e.g. the river IJssel) as spawning grounds or migrated from Markermeer to Ijsselmeer.
Two Distinct DNA Binding Modes Guide Dual Roles of a CRISPR-Cas Protein
Blosser, T.R. ; Loeff, L. ; Westra, E.R. ; Vlot, M. ; Künne, T.A. ; Sobota, M. ; Dekker, C. ; Brouns, S.J.J. ; Joo, C. - \ 2015
Molecular Cell 58 (2015)1. - ISSN 1097-2765 - p. 60 - 70.
bacterial immune-system - in-vitro reconstitution - memory b-cells - surveillance complex - crystal-structure - streptococcus-thermophilus - adaptive immunity - escherichia-coli - seed sequence - rna
Small RNA-guided protein complexes play an essential role in CRISPR-mediated immunity in prokaryotes. While these complexes initiate interference by flagging cognate invader DNA for destruction, recent evidence has implicated their involvement in new CRISPR memory formation, called priming, against mutated invader sequences. The mechanism by which the target recognition complex mediates these disparate responses-interference and priming-remains poorly understood. Using single-molecule FRET, we visualize how bona fide and mutated targets are differentially probed by E. coli Cascade. We observe that the recognition of bona fide targets is an ordered process that is tightly controlled for high fidelity. Mutated targets are recognized with low fidelity, which is featured by short-lived and PAM- and seed-independent binding by any segment of the crRNA. These dual roles of Cascade in immunity with distinct fidelities underpin CRISPR-Cas robustness, allowing for efficient degradation of bona fide targets and priming of mutated DNA targets
H2O2 Production in Species of the Lactobacillus acidophilus Group: a Central Role for a Novel NADH-Dependent Flavin Reductase
Hertzberger, R. ; Arents, J. ; Dekker, H.L. ; Pridmore, R.D. ; Gysler, C. ; Kleerebezem, M. ; Mattos, M.J.T. de - \ 2014
Applied and Environmental Microbiology 80 (2014)7. - ISSN 0099-2240 - p. 2229 - 2239.
hydrogen-peroxide production - alkyl hydroperoxide reductase - activated-receptor-gamma - lactic-acid bacteria - escherichia-coli - streptococcus-pneumoniae - amphibacillus-xylanus - pseudomonas-putida - johnsonii ncc-533 - crystal-structure
Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H2O2, inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H2O2 production (e.g., pyruvate oxidase, NADH oxidase, and lactate oxidase) did not affect this. Here we describe the purification of a novel NADH-dependent flavin reductase encoded by two highly similar genes (LJ_0548 and LJ_0549) that are conserved in lactobacilli belonging to the Lactobacillus acidophilus group. The genes are predicted to encode two 20-kDa proteins containing flavin mononucleotide (FMN) reductase conserved domains. Reductase activity requires FMN, flavin adenine dinucleotide (FAD), or riboflavin and is specific for NADH and not NADPH. The K-m for FMN is 30 +/- 8 mu M, in accordance with its proposed in vivo role in H2O2 production. Deletion of the encoding genes in L. johnsonii led to a 40-fold reduction of hydrogen peroxide formation. H2O2 production in this mutant could only be restored by in trans complementation of both genes. Our work identifies a novel, conserved NADH-dependent flavin reductase that is prominently involved in H2O2 production in L. johnsonii.
IdsA is the major geranylgeranyl pyrophosphate synthase involved in carotenogenesis in Corynebacterium glutamicum
Heider, S.A.E. ; Peters-Wendisch, P. ; Beekwilder, M.J. ; Wendisch, V.F. - \ 2014
FEBS Journal 281 (2014)21. - ISSN 1742-464X - p. 4906 - 4920.
farnesyl-diphosphate synthase - site-directed mutagenesis - chain-length determination - cytochrome-bo operon - escherichia-coli - crystal-structure - mycobacterium-tuberculosis - isoprenoid biosynthesis - conserved aspartate - micrococcus-luteus
Corynebacterium glutamicum, a yellow-pigmented soil bacterium that synthesizes the rare cyclic C50 carotenoid decaprenoxanthin and its glucosides, has been engineered for the production of various carotenoids. CrtE was assumed to be the major geranylgeranyl pyrophosphate (GGPP) synthase in carotenogenesis; however, deletion of crtE did not abrogate carotenoid synthesis. In silico analysis of the repertoire of prenyltransferases encoded by the C. glutamicum genome revealed two candidate GGPPS genes (idsA and ispB). The absence of pigmentation of an idsA deletion mutant and complementation experiments with a double deletion mutant lacking both idsA and crtE showed that IdsA is the major GGPPS of C. glutamicum and that crtE overexpression compensated for the lack of IdsA, whereas plasmid-borne overexpression of ispB did not. Purified His-tagged CrtE was active as a homodimer, whereas the active form of IdsA was homotetrameric. Both enzymes catalyzed prenyl transfer with isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate, geranyl pyrophosphate and farnesylphosphate (FPP) as substrates. IdsA showed the highest catalytic efficiency with dimethylallyl pyrophosphate and IPP, whereas the catalytic efficiency of CrtE was highest with geranyl pyrophosphate and IPP. Finally, application of prenyltransferase overexpression revealed that combined overexpression of idsA and the IPP isomerase gene idi in the absence of crtE led to the highest decaprenoxanthin titer reported to date.
Biobased furandicarboxylic acids (FDCAs): effects of isomeric substitution on polyester synthesis and properties
Thiyagarajan, S. ; Vogelzang, W. ; Knoop, J.R.I. ; Frissen, A.E. ; Haveren, J. van; Es, D.S. van - \ 2014
Green Chemistry 16 (2014)4. - ISSN 1463-9262 - p. 1957 - 1966.
diethylene glycol formation - crystal-structure - polyethylene terephthalate - renewable resources - bishydroxyethyl terephthalate - poly(ethylene terephthalate) - 2,5-furandicarboxylic acid - 3,4-furandicarboxylic acid - poly(ethylene-terephthalate) - kinetics
In this study we present the application of different isomers of furandicarboxylic acid, or FDCA, obtained from agro-residues, in polyester synthesis. New polyesters based on 2,4-FDCA and 3,4-FDCA isomers with (linear) diols were thoroughly characterised and compared with their as-synthesised 2,5-FDCA analogues. All polymers were obtained by melt polycondensation of linear diols with FDCA dimethyl esters and exhibit molecular weights in the range Mw = 34000–65000 and polydispersities close to 2.0. Thermogravimetric analysis (TGA) of the new polyesters shows that they have comparable or even higher thermal stability compared to the 2,5-FDCA polyesters. Interestingly, the glass-transition temperatures (Tg) of 2,4-FDCA derived polyesters are similar to those of the 2,5-FDCA isomers. Both differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) analyses showed that 2,4-PEF is amorphous, while 2,5-PEF and 3,4-PEF are semi-crystalline materials.
RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus
Staals, R.H.J. ; Zhu, Y. ; Taylor, D.W. ; Kornfeld, J.E. ; Sharma, K. ; Barendregt, A. ; Koehorst, J.J. ; Vlot, M. ; Neupane, N. ; Varossieau, K. ; Sakamoto, K. ; Suzuki, T. ; Schaap, P.J. ; Urlaub, H. ; Heck, A.J.R. ; Nogales, E. ; Doudna, J.A. ; Shinkai, A. ; Oost, J. van der - \ 2014
Molecular Cell 56 (2014)4. - ISSN 1097-2765 - p. 518 - 530.
guided surveillance complex - bacterial immune-system - adaptive immunity - mass-spectrometry - crystal-structure - escherichia-coli - haloferax-volcanii - antiviral defense - seed sequence - protein
CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1–Csm5) with an uneven stoichiometry and a single crRNA of variable size (35–53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence.
IL-10 encoded by viruses: a remarkable example of independent acquisition of a cellular gene by viruses and its subsequent evolution in the viral genome
Ouyang, P. ; Rakus, K. ; Beurden, S.J. van; Westphal, A.H. ; Davison, A.J. ; Gatherer, D. ; Vanderplasschen, A.F. - \ 2014
Journal of General Virology 95 (2014)2. - ISSN 0022-1317 - p. 245 - 262.
epstein-barr-virus - inhibits cytokine synthesis - collagen-induced arthritis - human dendritic cells - tumor-necrosis-factor - human b-lymphocytes - hla-class-i - human cytomegalovirus - crystal-structure - orf virus
Many viruses have evolved strategies to deregulate the host immune system. These strategies include mechanisms to subvert or recruit the host cytokine network. IL-10 is a pleiotropic cytokine that has both immunostimulatory and immunosuppressive properties. However, its key features relate mainly to its capacity to exert potent immunosuppressive effects. Several viruses have been shown to upregulate the expression of cellular IL-10 (cIL-10) with, in some cases, enhancement of infection by suppression of immune functions. Other viruses encode functional orthologues of cIL-10, called viral IL-10s (vIL-10s). The present review is devoted to these virokines. To date, vIL-10 orthologues have been reported for 12 members of the family Herpesviridae, two members of the family Alloherpesviridae and seven members of the family Poxviridae. Study of vIL-10s demonstrated several interesting aspects on the origin and the evolution of these viral genes, e.g. the existence of multiple (potentially up to nine) independent gene acquisition events at different times during evolution, viral gene acquisition resulting from recombination with cellular genomic DNA or cDNA derived from cellular mRNA and the evolution of cellular sequence in the viral genome to restrict the biological activities of the viral orthologues to those beneficial for the virus life cycle. Here, various aspects of the vIL-10s described to date are reviewed, including their genetic organization, protein structure, origin, evolution, biological properties and potential in applied research.
The evolutionary journey of Argonaute proteins
Swarts, D.C. ; Makarova, K. ; Wang, Y. ; Nakanishi, K. ; Ketting, R.F. ; Koonin, E.V. ; Patel, D.J. ; Oost, J. van der - \ 2014
Nature Structural and Molecular Biology 21 (2014)9. - ISSN 1545-9985 - p. 743 - 753.
eukaryote trypanosoma-brucei - germline gene-expression - seed-target recognition - piwi-interacting rnas - dicer-like proteins - crystal-structure - paz domain - structural basis - slicer activity - guide rna
Argonaute proteins are conserved throughout all domains of life. Recently characterized prokaryotic Argonaute proteins (pAgos) participate in host defense by DNA interference, whereas eukaryotic Argonaute proteins (eAgos) control a wide range of processes by RNA interference. Here we review molecular mechanisms of guide and target binding by Argonaute proteins, and describe how the conformational changes induced by target binding lead to target cleavage. On the basis of structural comparisons and phylogenetic analyses of pAgos and eAgos, we reconstruct the evolutionary journey of the Argonaute proteins through the three domains of life and discuss how different structural features of pAgos and eAgos relate to their distinct physiological roles.
Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3
Gong, B. ; Shin, M. ; Sun, J. ; Jung, C.H. ; Bolt, E.L. ; Oost, J. van der; Kim, J.S. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)46. - ISSN 0027-8424 - p. 16359 - 16364.
bacterial immune-system - in-vitro reconstitution - escherichia-coli - antiviral defense - adaptive immunity - crystal-structure - structural basis - rna - complex - cascade
Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.
Unravelling the structural and mechanistic basis of CRISPR-Cas systems
Oost, J. van der; Westra, E.R. ; Jackson, R.N. ; Wiedenheft, B. - \ 2014
Nature Reviews Microbiology 12 (2014)7. - ISSN 1740-1526 - p. 479 - 492.
short palindromic repeats - bacterial immune-system - rna silencing complex - processes pre-crrna - human gut virome - crystal-structure - escherichia-coli - streptococcus-thermophilus - thermus-thermophilus - interference complex
Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR–Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.
Mutational analysis of the Ve1 immune receptor that mediates Verticillium resistance in tomato
Zhang, Z. ; Song, Y. ; Liu, Chun-Ming ; Thomma, B.P.H.J. - \ 2014
PLoS ONE 9 (2014)6. - ISSN 1932-6203 - 8 p.
leucine-rich repeat - brassinosteroid perception - crystal-structure - structural basis - plant defense - arabidopsis - proteins - recognition - specificity - disease
Pathogenic Verticillium species are economically important plant pathogens that cause vascular wilt diseases in hundreds of plant species. The Ve1 gene of tomato confers resistance against race 1 strains of Verticillium dahliae and V. albo-atrum. Ve1 encodes an extracellular leucine-rich repeat (eLRR) receptor-like protein (RLP) that serves as a cell surface receptor for recognition of the recently identified secreted Verticillium effector Ave1. To investigate recognition of Ave1 by Ve1, alanine scanning was performed on the solvent exposed ß-strand/ß-turn residues across the eLRR domain of Ve1. In addition, alanine scanning was also employed to functionally characterize motifs that putatively mediate protein-protein interactions and endocytosis in the transmembrane domain and the cytoplasmic tail of the Ve1 protein. Functionality of the mutant proteins was assessed by screening for the occurrence of a hypersensitive response upon co-expression with Ave1 upon Agrobacterium tumefaciens-mediated transient expression (agroinfiltration). In order to confirm the agroinfiltration results, constructs encoding Ve1 mutants were transformed into Arabidopsis and the transgenes were challenged with race 1 Verticillium. Our analyses identified several regions of the Ve1 protein that are required for functionality.
Disturbed excitation energy transfer in Arabidopsis thaliana mutants lacking minor antenna complexes of photosystem II
Dall'Osto, L. ; Ünlü, C. ; Cazzaniga, S. ; Amerongen, H. van - \ 2014
Biochimica et Biophysica Acta. B, Bioenergetics 1837 (2014)12. - ISSN 0005-2728 - p. 1981 - 1988.
light-harvesting-complex - primary charge separation - chlamydomonas-reinhardtii - thylakoid membrane - electron-transport - crystal-structure - green plants - redox state - wild-type - proteins
Minor light-harvesting complexes (Lhcs) CP24, CP26 and CP29 occupy a position in photosystem II (PSII) of plants between the major light-harvesting complexes LHCII and the PSII core subunits. Lack of minor Lhcs in vivo causes impairment of PSII organization, and negatively affects electron transport rates and photoprotection capacity. Here we used picosecond-fluorescence spectroscopy to study excitation-energy transfer (EET) in thylakoid membranes isolated from Arabidopsis thaliana wild-type plants and knockout lines depleted of either two (koCP26/24 and koCP29/24) or all minor Lhcs (NoM). In the absence of all minor Lhcs, the functional connection of LHCII to the PSII cores appears to be seriously impairedwhereas the “disconnected” LHCII is substantially quenched. For both double knock-out mutants, excitation trapping in PSII is faster than in NoM thylakoids but slower than in WT thylakoids. In NoM thylakoids, the loss of all minor Lhcs is accompanied by an over-accumulation of LHCII, suggesting a compensating response to the reduced trapping efficiency in limiting light,which leads to a photosynthetic phenotype resembling that of low-light-acclimated plants. Finally, fluorescence kinetics and biochemical results show that the missing minor complexes are not replaced by other Lhcs, implying that they are unique among the antenna subunits and crucial for the functioning and macroorganization of PSII.
Genetically engineered silk-collagen-like copolymer for biomedical applications: Production, characterization and evaluation of cellular response
Wlodarczyk-Biegun, M.K. ; Werten, M.W.T. ; Wolf, F.A. de; Beucken, J.J.J.P. van den; Leeuwenburgh, S.C.G. ; Kamperman, M.M.G. ; Cohen Stuart, M.A. - \ 2014
Acta Biomaterialia 10 (2014)8. - ISSN 1742-7061 - p. 3620 - 3629.
crystal-structure - protein - scaffolds - biomaterials - polymer - polypeptides - hydrogels - elastin - gels - morphology
Genetically engineered protein polymers (GEPP) are a class of multifunctional materials with precisely controlled molecular structure and property profile. Representing a promising alternative for currently used materials in biomedical applications, GEPP offer multiple benefits over natural and chemically synthesized polymers. However, producing them in sufficient quantities for preclinical research remains challenging. Here, we present results from an in vitro cellular response study of a recombinant protein polymer that is soluble at low pH but self-organizes into supramolecular fibers and physical hydrogels at neutral pH. It has a triblock structure denoted as C2SH48C2, which consists of hydrophilic collagen-inspired and histidine-rich silk-inspired blocks. The protein was successfully produced by the yeast Pichia pastoris in laboratory-scale bioreactors, and it was purified by selective precipitation. This efficient and inexpensive production method provided material of sufficient quantities, purity and sterility for cell culture study. Rheology and erosion studies showed that it forms hydrogels exhibiting long-term stability, self-healing behavior and tunable mechanical properties. Primary rat bone marrow cells cultured in direct contact with these hydrogels remained fully viable; however, proliferation and mineralization were relatively low compared to collagen hydrogel controls, probably because of the absence of cell-adhesive motifs. As biofunctional factors can be readily incorporated to improve material performance, our approach provides a promising route towards biomedical applications.
Light harvesting in a fluctuating antenna
Chmeliov, J. ; Trinkunas, G. ; Amerongen, H. van; Valkunas, L. - \ 2014
Journal of the American Chemical Society 136 (2014)25. - ISSN 0002-7863 - p. 8963 - 8972.
excitation-energy transfer - photosystem-ii supercomplexes - thylakoid membrane - charge separation - crystal-structure - photosynthetic systems - photoprotective mode - lhcii complex - fluorescence - annihilation
One of the major players in oxygenic photosynthesis, photosystem II (PSII), exhibits complex multiexponential fluorescence decay kinetics that for decades has been ascribed to reversible charge separation taking place in the reaction center (RC). However, in this description the protein dynamics is not taken into consideration. The intrinsic dynamic disorder of the light-harvesting proteins along with their fluctuating dislocations within the antenna inevitably result in varying connectivity between pigment–protein complexes and therefore can also lead to nonexponential excitation decay kinetics. On the basis of this presumption, we propose a simple conceptual model describing excitation diffusion in a continuous medium and accounting for possible variations of the excitation transfer rates. Recently observed fluorescence kinetics of PSII of different sizes are perfectly reproduced with only two adjustable parameters instead of the many decay times and amplitudes required in standard analysis procedures; no charge recombination in the RC is required. The model is also able to provide valuable information about the structural and functional organization of the photosynthetic antenna and in a straightforward way solves various contradictions currently existing in the literature.
Natural strategies for photosynthetic light harvesting
Croce, R. ; Amerongen, H. van - \ 2014
Nature Chemical Biology 10 (2014). - ISSN 1552-4450 - p. 492 - 501.
photosystem-ii antenna - excitation-energy transfer - chlamydomonas-reinhardtii - oxygenic photosynthesis - chlorophyll-d - acaryochloris-marina - angstrom resolution - carotenoid protein - state transitions - crystal-structure
Photosynthetic organisms are crucial for life on Earth as they provide food and oxygen and are at the basis of most energy resources. They have a large variety of light-harvesting strategies that allow them to live nearly everywhere where sunlight can penetrate. They have adapted their pigmentation to the spectral composition of light in their habitat, they acclimate to slowly varying light intensities and they rapidly respond to fast changes in light quality and quantity. This is particularly important for oxygen-producing organisms because an overdose of light in combination with oxygen can be lethal. Rapid progress is being made in understanding how different organisms maximize light harvesting and minimize deleterious effects. Here we summarize the latest findings and explain the main design principles used in nature. The available knowledge can be used for optimizing light harvesting in both natural and artificial photosynthesis to improve light-driven production processes.
Kinetic and structural analysis of two transferase domains inPasteurella multocida hyaluronan synthase
Kooy, F.K. ; Beeftink, H.H. ; Eppink, M.H.M. ; Tramper, J. ; Eggink, G. ; Boeriu, C.G. - \ 2014
Journal of Molecular Catalysis. B, Enzymatic 102 (2014). - ISSN 1381-1177 - p. 138 - 145.
blood-group-b - enzymological characterization - conformational-changes - n-acetylglucosamine - crystal-structure - group-a - glycosyltransferase - polypeptide - mechanism - substrate
Pasteurella multocida hyaluronan synthase (PmHAS) encompasses two transferase domains that elongatea growing hyaluronan (HA) oligosaccharide chain by addition of either GlcNAc or GlcUA residues froma corresponding UDP-sugar. Initial velocity studies of single-step elongations were conducted for bothdomains by independently varying the concentrations of the HA oligosaccharide and the UDP-sugar.Two-substrate models were discriminated by their goodness-of-fit parameters and by dead-end inhi-bition studies. A mechanistic shift from a steady-state ordered bi-bi to rapid equilibrium ordered bi-bimechanism was observed at the NAc-site between the HA6and HA8elongation. This shift was invokedby a minor reduction in turnover number kcat. Both NAc- and UA-transferase domains follow a sequentialkinetic mechanism, most likely an ordered one in which the UDP-sugar donor binds first, followed bythe HA oligosaccharide. After transfer of the sugar moiety, both products are released, first the elongatedHA oligosaccharide and then the UDP sugar. This mechanism was visualized with a structural model ofPmHAS that presented two flexible loops, one in each transferase domain; these loops form a bridgeabove the active site.
Molecular Characterization of an NADPH-Dependent Acetoin Reductase/2,3-Butanediol Dehydrogenase from Clostridium beijerinckii NCIMB 8052
Raedts, J.G.J. ; Siemerink, M.A.J. ; Levisson, M. ; Oost, J. van der; Kengen, S.W.M. - \ 2014
Applied and Environmental Microbiology 80 (2014)6. - ISSN 0099-2240 - p. 2011 - 2020.
l-threonine dehydrogenase - protein-structure prediction - crystal-structure - alcohol dehydrogenases - (2r,3r)-2,3-butanediol dehydrogenase - thermoanaerobacter-brockii - escherichia-coli - meso-2,3-butanediol dehydrogenase - sulfolobus-solfataricus - butanol fer
Acetoin reductase is an important enzyme for the fermentative production of 2,3-butanediol, a chemical compound with a very broad industrial use. Here, we report on the discovery and characterization of an acetoin reductase from Clostridium beijerinckii NCIMB 8052. An in silico screen of the C. beijerinckii genome revealed eight potential acetoin reductases. One of them (CBEI_1464) showed substantial acetoin reductase activity after expression in Escherichia coli. The purified enzyme (C. beijerinckii acetoin reductase [Cb-ACR]) was found to exist predominantly as a homodimer. In addition to acetoin (or 2,3-butanediol), other secondary alcohols and corresponding ketones were converted as well, provided that another electronegative group was attached to the adjacent C-3 carbon. Optimal activity was at pH 6.5 (reduction) and 9.5 (oxidation) and around 68°C. Cb-ACR accepts both NADH and NADPH as electron donors; however, unlike closely related enzymes, NADPH is preferred (Km, 32 µM). Cb-ACR was compared to characterized close homologs, all belonging to the "threonine dehydrogenase and related Zn-dependent dehydrogenases" (COG1063). Metal analysis confirmed the presence of 2 Zn(2+) atoms. To gain insight into the substrate and cofactor specificity, a structural model was constructed. The catalytic zinc atom is likely coordinated by Cys37, His70, and Glu71, while the structural zinc site is probably composed of Cys100, Cys103, Cys106, and Cys114. Residues determining NADP specificity were predicted as well. The physiological role of Cb-ACR in C. beijerinckii is discussed
DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications
Falcicchio, P. ; Wolterink-van Loo, S. ; Franssen, M.C.R. ; Oost, J. van der - \ 2014
Extremophiles 18 (2014)1. - ISSN 1431-0651 - p. 1 - 13.
l-threonine aldolase - stereochemically complementary biocatalysts - ii fructose-1,6-bisphosphate aldolase - thermus-thermophilus hb8 - escherichia-coli - d-fructose-6-phosphate aldolase - directed evolution - crystal-structure - active-site - l-rhamnulose-1-phosp
Generating new carbon-carbon (C-C) bonds in an enantioselective way is one of the big challenges in organic synthesis. Aldolases are a natural tool for stereoselective C-C bond formation in a green and sustainable way. This review will focus on thermophilic aldolases in general and on dihydroxyacetone phosphate-dependent aldolases in particular. Biochemical properties and applications for synthesis of rare sugars and carbohydrates will be discussed
Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage
Sheng, G. ; Zhao, H. ; Wang, J. ; Rao, Y. ; Tian, W. ; Swarts, D.C. ; Oost, J. van der; Patel, D.J. ; Wang, Y. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)2. - ISSN 0027-8424 - p. 652 - 657.
crystal-structure - rna recognition - silencing complex - substrate-specificity - slicer activity - piwi protein - paz domain - human risc - endonuclease - interference
We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5'-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand
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