Insight into the oligomeric structure of PORA from A. thaliana

Gabruk, Michał; Nowakowska, Zuzanna; Skupień-Rabian, Bożena; Kędracka–Krok, Sylwia; Myśliwa-Kurdziel, Beata; Kruk, Jerzy

doi:10.1016/j.bbapap.2016.09.015

Cited by 15 publications

(28 citation statements)

References 29 publications

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“…In contrast, plant LPORs were found to form oligomers (14,46,50,51). Two regions (residues 85-88 and 240-270 of A. thaliana PORA) were indicated to participate in oligomerization (50). The first region includes the amino end of SyLPOR and TeLPOR; the second region includes the LPORspecific insertion (SI Appendix, Fig.…”

Section: Discussionmentioning

confidence: 99%

Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Dong

Zhang

Wang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) is the penultimate step of chlorophyll biosynthesis. In oxygenic photosynthetic bacteria, algae, and plants, this reaction can be catalyzed by the light-dependent Pchlide oxidoreductase (LPOR), a member of the short-chain dehydrogenase superfamily sharing a conserved Rossmann fold for NAD(P)H binding and the catalytic activity. Whereas modeling and simulation approaches have been used to study the catalytic mechanism of this light-driven reaction, key details of the LPOR structure remain unclear. We determined the crystal structures of LPOR from two cyanobacteria, Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. Structural analysis defines the LPOR core fold, outlines the LPOR–NADPH interaction network, identifies the residues forming the substrate cavity and the proton-relay path, and reveals the role of the LPOR-specific loop. These findings provide a basis for understanding the structure-function relationships of the light-driven Pchlide reduction.

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Section: Discussionmentioning

confidence: 99%

Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Dong

Zhang

Wang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The procedure is based on a previously reported protocol [ 21 ]. First, we injected the heavy-labeled peptide for shotgun LC–MS/MS analysis at 1 pmol.…”

Section: Methodsmentioning

confidence: 99%

Expression of alternatively spliced variants of the Dclk1 gene is regulated by psychotropic drugs

et al. 2018

Self Cite

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BackgroundThe long-term effects of psychotropic drugs are associated with the reversal of disease-related alterations through the reorganization and normalization of neuronal connections. Molecular factors that trigger drug-induced brain plasticity remain only partly understood. Doublecortin-like kinase 1 (Dclk1) possesses microtubule-polymerizing activity during synaptic plasticity and neurogenesis. However, the Dclk1 gene shows a complex profile of transcriptional regulation, with two alternative promoters and exon splicing patterns that suggest the expression of multiple isoforms with different kinase activities.ResultsHere, we applied next-generation sequencing to analyze changes in the expression of Dclk1 gene isoforms in the brain in response to several psychoactive drugs with diverse pharmacological mechanisms of action. We used bioinformatics tools to define the range and levels of Dclk1 transcriptional regulation in the mouse nucleus accumbens and prefrontal cortex. We also sought to investigate the presence of DCLK1-derived peptides using mass spectrometry. We detected 15 transcripts expressed from the Dclk1 locus (FPKM > 1), including 2 drug-regulated variants (fold change > 2). Drugs that act on serotonin receptors (5-HT2A/C) regulate a subset of Dclk1 isoforms in a brain-region-specific manner. The strongest influence was observed for the mianserin-induced expression of an isoform with intron retention. The drug-activated expression of novel alternative Dclk1 isoforms was validated using qPCR. The drug-regulated isoform contains genetic variants of DCLK1 that have been previously associated with schizophrenia and hyperactivity disorder in humans. We identified a short peptide that might originate from the novel DCLK1 protein product. Moreover, protein domains encoded by the regulated variant indicate their potential involvement in the negative regulation of the canonical DCLK1 protein.ConclusionsIn summary, we identified novel isoforms of the neuroplasticity-related gene Dclk1 that are expressed in the brain in response to psychotropic drug treatments.Electronic supplementary materialThe online version of this article (10.1186/s12868-018-0458-4) contains supplementary material, which is available to authorized users.

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“…A pea LPOR / maltose-binding protein (MBP) fusion protein eluted as a dimer in size-exclusion chromatography (SEC) irrespective of substrate and product being present 18 . Arabidopsis thaliana LPOR similarly forms dimers 19 , whereas in vitro cross-linking of recombinant LPOR A of A. thaliana ( At LPOR A) revealed that both apoprotein and holoprotein form tightly packed, higher-order oligomers 20 . Homology modelling and non-denaturing protein blots indicated that barley LPOR forms hexamers with five LPOR A and one LPOR B subunit 19 .…”

Section: Introductionmentioning

confidence: 99%

Consensus model of a cyanobacterial light-dependent protochlorophyllide oxidoreductase in its pigment-free apo-form and photoactive ternary complex

Schneidewind

Krause²,

Bocola

et al. 2019

Commun Biol

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Photosynthetic organisms employ two different enzymes for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide), yielding the chlorophyll precursor chlorophyllide. First, a nitrogenase-like, light-independent (dark-operative) Pchlide oxidoreductase and secondly, a light-dependent Pchlide oxidoreductase (LPOR). For the latter enzyme, despite decades of research, no structural information is available. Here, we use protein structure modelling, molecular dynamics (MD) simulations combined with multi-wavelength analytical ultracentrifugation (MWA-AUC) and small angle X-ray scattering (SAXS) experiments to derive a consensus model of the LPOR apoprotein and the substrate/cofactor/LPOR ternary complex. MWA-AUC and SAXS experiments independently demonstrate that the apoprotein is monomeric, while ternary complex formation induces dimerization. SAXS-guided modelling studies provide a full-length model of the apoprotein and suggest a tentative mode of dimerization for the LPOR ternary complex, supported by published cross-link constraints. Our study provides a first impression of the LPOR structural organization.

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Insight into the oligomeric structure of PORA from A. thaliana

Cited by 15 publications

References 29 publications

Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Expression of alternatively spliced variants of the Dclk1 gene is regulated by psychotropic drugs

Consensus model of a cyanobacterial light-dependent protochlorophyllide oxidoreductase in its pigment-free apo-form and photoactive ternary complex

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