Chemical and structural characterization of SeIV biotransformations by Stenotrophomonas bentonitica into Se0 nanostructures and volatiles Se species

Microorganisms such as Stenotrophomonas bentonitica could influence the safety of the deep geological repository system by producing nanoparticles and volatile compounds of selenium

Allotropy of selenium nanoparticles: Colourful transition, synthesis, and biotechnological applications

Abstract Elemental selenium (Se0) nanomaterials undergo allotropic transition from thermodynamically‐unstable to more stable phases. This process is significantly different when Se0 nanoparticles (NPs) are produced via physico‐chemical and biological pathways. While the allotropic transition of physico‐chemically synthesized Se0 is fast (minutes to hours), the biogenic Se0 takes months to complete. The biopolymer layer covering biogenic Se0 NPs might be the main factor controlling this retardation, but this still remains an open question. Phylogenetically‐diverse bacteria reduce selenium oxyanions to red amorphous Se0 allotrope, which has low market value. Then, red Se0 undergoes allotropic transition to trigonal (metallic grey) allotrope, the end product having important industrial applications (e.g. semiconductors, alloys). Is it not yet clear whether biogenic Se0 presents any biological function, or it is mainly a detoxification and respiratory by‐product. The better understanding of this transition would benefit the recovery of Se0 NPs from secondary resources and its targeted utilization with respect to each allotropic stage. This review article presents and critically discusses the main physico‐chemical methods and biosynthetic pathways of Se0 (bio)mineralization. In addition, the article proposes a conceptual model for the resource recovery potential of trigonal selenium nanomaterials in the context of circular economy

Structural dynamics at the active site of the cancer-associated flavoenzyme NQO1 probed by chemical modification with PMSF

12 pags., 4 figs., 1 tab.A large conformational heterogeneity of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with various human diseases, has been observed to occur in the catalytic site of the enzyme. Here, we report the X-ray structure of NQO1 with phenylmethylsulfonyl fluoride (PMSF) at 1.6 Å resolution. Activity assays confirmed that, despite being covalently bound to the Tyr128 residue at the catalytic site, PMSF did not abolish NQO1 activity. This may indicate that the PMSF molecule does not reduce the high flexibility of Tyr128, thus allowing NADH and DCPIP substrates to bind to the enzyme. Our results show that targeting Tyr128, a key residue in NQO1 function, with small covalently bound molecules could possibly not be a good drug discovery strategy to inhibit this enzyme.The X-ray diffraction experiments presented in this study were carried out at BL13-XALOC at ALBA syn-chrotron under proposal number 2020084437. The following funding is acknowledged: Ayuda de Atracción y Retención de Talento Investigador from the Community of Madrid (No. 2019-T1/BMD-15552); ERDF/Spanish Ministry of Science, Innovation and Universities—State Research Agency (Grant number RTI2018-096246-B-I00), Consejerıa de Economıa, Conocimiento Empresas y Universidad, Junta de Andalucía (Grant number P18-RT-2413), ERDF/Counseling of Economic transformation, Industry, Knowledge and Universities(Grant B-BIO-84-UGR20).Peer reviewe

Combined bioreduction and volatilization of SeVI by Stenotrophomonas bentonitica: Formation of trigonal selenium nanorods and methylated species

Nowadays, metal pollution due to the huge release of toxic elements to the environment has become one of the world's biggest problems. Bioremediation is a promising tool for reducing the mobility and toxicity of these contaminants (e.g. selenium), being an efficient, environmentally friendly, and inexpensive strategy. The present study describes the capacity of Stenotrophomonas bentonitica to biotransform SeVI through enzymatic reduction and volatilization processes. HAADF-STEM analysis showed the bacterium to effectively reduce SeVI (200 mM) into intra- and extracellular crystalline Se0 nanorods, made mainly of two different Se allotropes: monoclinic (m-Se) and trigonal (t-Se). XAS analysis appears to indicate a Se crystallization process based on the biotransformation of amorphous Se0 into stable t-Se nanorods. In addition, results from headspace analysis by gas chromatography-mass spectometry (GC-MS) revealed the formation of methylated volatile Se species such as DMSe (dimethyl selenide), DMDSe (dimethyl diselenide), and DMSeS (dimethyl selenenyl sulphide). The biotransformation pathways and tolerance are remarkably different from those reported with this bacterium in the presence of SeIV. The formation of crystalline Se0 nanorods could have positive environmental implications (e.g. bioremediation) through the production of Se of lower toxicity and higher settleability with potential industrial applications

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

18 pags. 7 figs., 1 tab. -- This article is part of the themed collection: Lab on a Chip HOT Articles 2023Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.Financial support from the STC Program of the National Science Foundation through BioXFEL (under agreement # 1231306), ABI Innovations award (NSF # 1565180), IIBR award (# 1943448), MCB award (1817862), and the National Institutes of Health award # R01GM095583 is gratefully acknowledged. The use of the Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, is generously supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract # DE-AC02-76SF00515. The authors would like to acknowledge the instrument group and facility staff for their assistance in the use of the MFX instrument during proposal MFXLW7919 at LCLS. The HERA system for in-helium experiments at MFX was developed by Bruce Doak and funded by the Max Planck Institute for Medical Research. This work was also supported by The Center for Structural Dynamics in Biology, NIH grant P41GM139687. Alice Grieco and Jose M. Martin-Garcia were supported by the “Ayuda de Atracción y Retención de Talento Investigador” from the Community of Madrid, Spain (REF: 2019-T1/BMD-15552). JLPG and ALP acknowledge funding from the ERDF/Spanish Ministry of Science, Innovation, and Universities—State Research Agency (grant RTI2018-096246-BI00), Consejería de Economía, Conocimiento, Empresas, y Universidad, Junta de Andalucía (grant P18-RT-2413), and ERDF/Counseling of Economic transformation, Industry, Knowledge, and Universities (grant B-BIO-84-UGR20).Peer reviewe