Discover insights from thousands of peer-reviewed papers on microbial electrochemical systems
Pingnan Zhao, Shen Wang, Dong Liu et al.
Research Square · 2021
Abstract In northeastern China, successive years of cultivation have led to a decline in soil quality, a process that is exacerbated by the over-application of chemical fertilizers to ensure staple food production. The large amount of straw produced by cultivation is difficult to effectively use in recent years. There has been an increasing amount of research on the transforming straw into biomass char, but it has often focused on the effects of biomass char addition on soil physicochemical properties, without further exploring the mechanisms of this process and its effects on soil microorganisms. Microorganisms are an important part of the soil system and the process of how biomass char addition affects microorganisms through its effect on soil physicochemical properties should not be overlooked. In this study， the effect of biochar application at different preparation temperatures (300°C, 400°C and 500°C) and addition contents (0.1% and 1%) on ammonia, nitrate and total nitrogen in soil leachates were investigated. The effect of microbial sequencing on the dynamics of carbon and nitrogen was also investigated to reveal the mechanisms contributing to the changes in nitrogen forms. The results showed that biochar had a better adsorption ability on ammonia nitrogen, and biochar promoted the conversion of ammonia nitrogen to nitrate nitrogen by nitrifying bacteria. The addition of 1% biochar (prepared at 500°C) increased nitrate-nitrogen leaching by 86.52% compared to the control treatment. The sequencing of microorganisms also revealed that biochar changed the structure and abundance of the soil microbial community, especially increasing the relative abundance of the Helicobacter nitrification phylum by 2.02%. These results indicates that biochar facilitated the adsorption of ammonium nitrogen and the conversion of nitrate nitrogen, and solving the problem of low nitrogen fertilizer utilization while promoting the formation of beneficial bacteria in the soil.
Stanislav Rudnyckyj, Tanmay Chaturvedi, Mette Hedegaard Thomsen
Biomass Conversion and Biorefinery · 2025
Abstract The study investigated the potential of the organic fraction of municipal solid waste (OFMSW) for microbial biomass production. The compositional analysis of OFMSW showed richness in sugars, proteins, lipids, organic acids, and ethanol, suggesting promising cheap cultivation feedstock if inhibitory compounds are sustainably detoxified. The enzymatic hydrolysis with Cellic® CTec3 and AMG® 300 L BrewQ (Novozymes A/S) demonstrated excellent saccharification of sugar polymer, reaching 92% glucan hydrolysis and 70% xylan hydrolysis. However, higher enzymatic dosages led to a rise in the total organic acids content, potentially causing increased microbial inhibition. Full hydrolysate and hydrolysate after solids removal were cultivated with seven robust microbial strains. Cultivation on hydrolysate with solids showed consumption of sugars and organic acids solely by commercial backer yeast Saccharomyces cerevisiae . Removal of solids from hydrolysate resulted in increased performance of tested strains, showing consumption of measured organic acids and ethanol by S. cerevisiae , Yarrowia lipolytica DSM 8218, and Cutaneotrichosporon oleaginosus ATCC 20509. Remarkably, the investigation of biomass production revealed superior cell mass formation and detoxification by S. cerevisiae , resulting in 18.9 g of biomass/L hydrolysate with 50% of crude protein (w/w) in shake flasks and 13.2 g/L of hydrolase with 46% of crude protein (w/w) in a 5-L bioreactor. Furthermore, bioreactor cultivation confirmed organic acids and ethanol conversion into biomass, highlighting S. cerevisiae ’s suitability for utilizing OFMSW for microbial biomass production. These findings contribute to advancements in biowaste-to-fodder conversion, promoting the development of a more sustainable circular economy. Graphical abstract
Alexandru Dumitrache
· 2021
Recent findings support the concept that Clostridium thermocellum is a cellulose-utilizing specialist having growth benefits with increasing substrate chain length. We developed a continuous-flow system for in-situ detection of cellulose colonization and qualitatively assayed metabolic activities and behaviour of cellulolytic cultures. This study demonstrates the existence of strongly adherent celluloytic cells arranged in monolayers with invariably end-on attached spores. The substrate-cell distance was recorded to be lower than 0.44 pm and a typical EPS matrix was absent. Measurements on carbon dioxide released in continuous-flow cultures was successfully employed to monitor biofilm activity and total carbohydrate assays do not reveal loss of cellulolysis end-products in the effluent. These findings demonstrate the bacteria have optimized access to the cellulosic substrates and suggest that they have an ability to sequester products of substrate hydrolysis which confers benefits over non-adherent cellulolytic or non-cellulolytic organisms.
Tong Zhang, Yufei Liu, xin Sui et al.
Research Square (Research Square) · 2020
Abstract Background : To study the impact of land-use change on soil microbial community structure and diversity in Northeast China, three typical land-use types (plough, grassland, and forest), grassland change to forest land and grassland change to plough, in the Qiqihar region of Heilongjiang Province were taken as research objects. Methods : MiSeq high-throughput sequencing technology based on bacterial 16S rRNA and fungal ITS rRNA was used to study the above community structure of soil bacteria and fungi and to explore the relationship between soil bacteria and soil environmental factors. Results : The results showed that the dominant bacterial phyla changed from Actinobacteria to Acidobacteria , the dominant fungal phyla changed from Ascomycetes to Basidiomycetes , and the ECM functional group increased significantly after the grassland was completely changed to forest land. After the grassland was changed to plough, the dominant phyla changed from Actinomycetes to Proteobacteria . The functional groups of pathogens and parasites increased significantly. There was no significant difference in the diversity of soil bacterial communities, and the diversity of fungal communities increased significantly. CCA showed that pH, MC, NO 3 - -N, TP and AP of soil were important factors affecting the composition of soil microbial communities, and changes in land-use patterns changed the physical and chemical properties of soils, thereby affecting the structure and diversity of microbial communities. Conclusions : Our research results clarify the impact of changes in land use on the characteristics of soil microbial communities and provide basic data on the healthy use of land.
Anastasiia Afanasenko, Tao Yan, Katalin Barta
Communications Chemistry · 2019
Abstract β-amino acid esters are important scaffolds in medicinal chemistry and valuable building blocks for materials synthesis. Surprisingly, the waste-free construction of such moieties from readily available or renewable starting materials has not yet been addressed. Here we report on a robust and versatile method for obtaining β-amino acid esters by direct amination of β-hydroxyl acid esters via the borrowing hydrogen methodology using a cooperative catalytic system that comprises a homogeneous ruthenium catalyst and an appropriate Brønsted acid additive. This method allows for the direct amination of esters of 3-hydroxypropionic acid, a top value-added bio-based platform chemical, opening a simple route to access β-amino acid esters from a range of renewable polyols including sugars and glycerol.
Yue-Ming Wang, Fabio Lorenzini, Martin Rebros et al.
Green Chemistry · 2016
The hydrogen transfer initiated dehydration of 1,3-propanadiol to propionaldehyde, catalysed by a highly recyclable, air and water stable, soluble Ir( iii ) complex, in an ionic liquid, was demonstrated.
Xu Zhang, Siquan Xu, Qinfang Li et al.
RSC Advances · 2021
Furfural is a promising renewable platform molecule derived from hemi-cellulose, which can be further converted to fossil fuel alternatives and valuable chemicals due to its highly functionalized molecular structure.
Andrew C. Marr
Advanced Synthesis & Catalysis · 2024
Abstract This opinionated review underlines the increasing production of 1,3‐propanediol (1,3‐PDO) by whole cell biocatalytic fermentation of biomass and highlights how production has transitioned from petrochemicals to bio‐renewables. Current uses of 1,3‐PDO are listed. Some future prospects for evolving the current technology and expanding the chemical uses of 1,3‐PDO are discussed, with emphasis on catalytic and atom efficient chemistries. Lessons from the success of biomass derived 1,3‐PDO are noted that may be applied to other bio‐based organic platform chemicals.
Urs Hackbarth, Christos Argirusis, Georgia Sourkouni
Journal of Bio-catalysis and Photocatalysis · 2025
Aims: The aim of the present manuscript is the preparation of g-C3N4 using different methods and educts and the use of the prepared materials for the decoloration of dermacid red. Background: Graphitic carbon nitride (g-C3N4) is a promising photocatalytic material due to its unique structural and electronic properties that enhance photocatalytic activity under UV light. Its layered structure and suitable electronic configuration facilitate the generation of reactive species necessary for catalyzing reactions, such as the degradation of azo dyes, organic pollutants, and hydrogen production. Objective: The objective of this research is to evaluate the photocatalytic efficiency of g-C3N4 materials, focusing on the impact of different synthesis and exfoliation methods on their performance, particularly in the degradation of the azo dye Dermacid Red. Method: Characterization techniques such as Powder X-ray Diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy, and Scanning Electron Microscopy (SEM) were employed to confirm the successful synthesis of the materials and to outline structural differences originating from variations in the synthesis process. The photocatalytic performance was assessed using a customdesigned photocatalytic reactor equipped with UV lamps. Results: The study reveals that photocatalytic efficiency significantly depends on the material's properties, with chemical and ultrasonic exfoliation methods resulting in a substantial increase in efficiency. Notably, after just four minutes of exposure, complete degradation of the azo dye was achieved, highlighting the g-C3N4 material's potential for practical applications in wastewater treatment and environmental remediation processes. Conclusion: The consistent results obtained across varying sample preparations further substantiate the reliability of the synthesized materials. This research contributes valuable insights into the development of effective photocatalysts, paving the way for their integration into various industrial processes aimed at pollution reduction and sustainable practices.
Sophie Hameury, Hana Bensalem, Karine De Oliveira Vigier
Catalysts · 2022
In this review, we aim to give an overview of the use of the Borrowing Hydrogen (BH) methodology with bio-based alcohols. This methodology only forms water as a by-product, thus providing a sustainable way to amines, which have a large range of applications. This process is of particular interest when related to biomass due to the high abundance of alcohol functions in natural compounds. However, natural compounds often comprise multiple chemical functions that can change the reactivity of the substrate. This comprehensive review, comprising both homogeneous and heterogeneous catalysts, aims at summarizing the recent advancements in biomass amination for every class of substrate, highlighting the key parameters governing their reactivity and the remaining scientific hurdles. Even though most substrates have successfully been converted into the corresponding amines, reaction selectivity and functional group tolerance still need to be improved.
Günther Knör
ECS Meeting Abstracts · 2016
Light-induced substrate transformations in artificial photosynthetic devices and functional enzyme model systems strongly depend on the feasibility of multielectron transfer catalysis [1,2]. The crucial advantage of coupling multiple redox equivalents and proton transfer steps in photocatalysis is to avoid free radical reaction pathways and energetic constraints due to charge accumulation, as these processes can decrease both the long-term stability and the efficiency of the corresponding systems. In this context, certain coordination compounds including tetrapyrrole-based derivatives such as porphyrin, corrole and phthalocyanine complexes have been shown to achieve an efficient fusion of the complementary functions of a light-harvester, a photoredox interface, a substrate recognition site and a mediator for chemical reactions [3-6]. To further improve the performance of such systems, the design of long-term stable processes for artificial photosynthetic energy storage and green synthetic chemistry using artificial (photo)enzymes has to be achieved with sustainable, environmentally benign and earth-abundant bulding blocks. Another crucial aspect in the context of solar chemistry and catalysis is not only the requirement for using visible light, but also to shift the threshold wavelength of the photosensitizers as far as possible to the red and NIR-spectral regions. Some of our recent developments in this direction will be presented in this contribution. [1] G. Knör, Chem. Eur. J. 2009 , 15 , 568 [2] G. Knör, Coord. Chem. Rev. 2015 , 304-305 , 102 [3] M. Hajimohammadi, C. Schwarzinger, G. Knör, RSC Advances 2012 , 2 , 3257 [4] C. Uslan, K. T. Oppelt, L. M. Reith, B. Ş. Sesalan, G. Knör, Chem. Commun. 2013 , 49 , 8108 [5] K. T. Oppelt, E. Wöß, M. Stiftinger, W. Schöfberger, W. Buchberger, G. Knör, Inorg. Chem. 2013 , 52 , 11910 [6] M. Ertl, E. Wöß, G. Knör, Photochem. Photobiol. Sci. 2015 , 14 , 1826
Yingxuan Wang
Applied and Computational Engineering · 2025
The creation of efficient water oxidation catalysts (WOCs) is a key area of advancement in sustainable energy researches, particularly for enabling large-scale hydrogen production through water electrolysis. Recent advances in molecular catalyst design have highlighted the prominence of multi-site ruthenium-based systems, with Ru(bda) (bda = 2,2-bipyridine-6,6-dicarboxylate) complexes emerging as a benchmark due to their mechanistic versatility and tunable reactivity. Substantial progress has been achieved through strategic modifications of Ru(bda) catalysts, including dimerization, macrocyclization, and integration into covalent organic frameworks (COFs). Dimeric Ru(bda) systems, for instance, exhibit exceptional turnover frequencies (TOFs) by leveraging intramolecular radical coupling to circumvent the concentration limitations typical of bimolecular O-O bond formation pathways. Meanwhile, macrocyclic Ru(bda) derivatives, inspired by the natural oxygen-evolving complex (OEC), demonstrate enhanced proton-coupled electron transfer (PCET) kinetics, with TOFs reaching 7.9 s-1, attributed to the preorganization of water molecules within their confined cavities. Further innovations include embedding Ru(bda) units into COFs or immobilizing them on carbon nanotubes (CNTs). These hybrid architectures combine the precision of molecular catalysis with the stability of heterogeneous systems, enabling efficient water oxidation via the I2M mechanism. Notably, Ru(bda)-CNT assemblies achieve record-breaking performance with TOFs exceeding 3200 s-1. This review underscores the transformative potential of multi-site Ru(bda) catalysts and outlines a roadmap for rational catalyst design. However, challenges such as long-term stability under oxidative conditions and the scalability of noble-metal-based systems remain to be addressed. Future research directions may focus on elucidating structure-activity relationships and exploring earth-abundant alternatives to further advance practical applications in renewable energy technologies.
Greg Mann, Frédéric V. Stanger
CHIMIA · 2020
Enzymes have the potential to catalyse complex chemical reactions with unprecedented selectivity, under mild conditions in aqueous media. Accordingly, there is serious interest from the pharmaceutical industry to utilize enzymes as biocatalysts to produce medicines in an environmentally sustainable and economic manner. Prominent advances in the field of biotechnology have transformed this potential into a reality. Using modern protein engineering techniques, in a matter of months it is possible to evolve an enzyme, which fits the demands of a chemical process, or even to catalyse entirely novel chemistry. Consequently, biocatalysis is routinely applied throughout the pharmaceutical industry for a variety of applications, ranging from the manufacture of large volumes of high value blockbuster drugs to expanding the chemical space available for drug discovery.
Xia Hua, Jian Han, Xin Zhou et al.
· 2022
Oxygen, as a terminal electron acceptor, is an essential substrate in the aerobic bio-oxidation process, affecting bacterial vitality and bio-oxidation performance. In this study, a new and smart platform biotechnology of sealed-oxygen supply bioreactor (SOS-BR) was developed by improving gas pressure to significantly intensify oxygen transfer rate and resolving the formidable barriers of aerobic catalysis. In virtue of SOS-BR, the bio-productivity was greatly improved for three representative substrates (xylose, furfural, glycerol) bio-oxidation with the whole-cell catalysis of Gluconobacter oxydans. The determination of oxygen transfer coefficient (KLα) established an upgraded theoretical dynamic model for gas pressure intersification biosystem. Additionally, viscosity measurement and combined pressure control strategy explained the inflection point phenomenon of productivity and confirmed the intensify mechanism. The new strategy of significantly intensifying oxygen transfer provided insightful ideas for overcoming the subbon obstacle of obligate aerobic catalysis, and further promoted industrial practicability of bio-oxidation.
Gabriella Garbarino, Giovanni Pampararo, Thanh Khoa Phung et al.
Energies · 2020
In gas/solid conditions, different chemicals, such as diethylether, ethylene, butadiene, higher hydrocarbons, acetaldehyde, acetone and hydrogen, can be produced from ethanol with heterogeneous catalytic processes. The focus of this paper is the interplay of different reaction paths, which depend on thermodynamic factors as well as on kinetic factors, thus mainly from catalyst functionalities and reaction temperatures. Strategies for selectivity improvements in heterogeneously catalyzed processes converting (bio)ethanol into renewable chemicals and biofuels are also considered.
Andree Iemhoff, James Sherwood, Con R. McElroy et al.
Green Chemistry · 2018
The esterification of 2-phenylpropionic acid was investigated as a model system for enzyme catalysed (CALB, Novozyme 435) reactions in bio-based solvents.
Jie Yu
Heterogeneous Catalysis for Energy Applications · 2020
Today, the conversion of biomass in sub- or super-critical water has been extensively studied to produce liquid fuels or synthesis gas (syngas). Given the extreme conditions of water at high pressure and temperature, along with the complex structure of biomass, the development of such processes remains a challenge. In order to realize the complete decomposition of biomass and a high yield of desired products, such as CH4 and H2, at relatively mild conditions, various catalysts have been synthesized and employed. Different metals (such as Cr, Ni, Zn, Ru and Rh) have been incorporated into various supports, such as mineral compounds of Al2O3, SiO2, TiO2, ZrO2, MgO, Y2O3, CeO2, silica-alumina, zeolites and carbon-based supports (e.g. carbon nanotubes, activated carbon). The stability of various support materials and the function of active metals have been extensively tested to obtain an ideal catalyst support. Therefore, this chapter focuses on the discussion of the catalytic gasification of biomass in supercritical water using heterogeneous catalysts. The stability of the catalyst support, the mechanism of cracking, the methanation and water gas shift reaction of intermediates over catalysts and the deactivation of catalysts in supercritical water are discussed.
Mpumelelo T. Matsena, Evans M. N. Chirwa
Scientific Reports · 2021
Abstract The discharge of hexavalent chromium [Cr(VI)] from several anthropogenic activities leads to environmental pollution. In this study, we explore a simple yet cost effective method for the synthesis of palladium (Pd) nanoparticles for the treatment of Cr(VI). The presence of elemental Pd [Pd(0)] was confirmed by scanning electron microscope (SEM), electron dispersive spectroscopy and X-ray diffraction (XRD). We show here that the biologically synthesized nanoparticles (Bio-PdNPs) exhibit improved catalytic reduction of Cr(VI) due to their size being smaller and also being highly dispersed as compared to chemically synthesized nanoparticles (Chem-PdNPs). The Langmuir–Hinshelwood mechanism was successfully used to model the kinetics. Using this model, the Bio-PdNPs were shown to perform better than Chem-PdNPs due to the rate constant (k bio = 6.37 mmol s −1 m −2 ) and Cr(VI) adsorption constant (K Cr(VI),bio = 3.11 × 10 −2 L mmol −1 ) of Bio-PdNPs being higher than the rate constant (k chem = 3.83 mmol s −1 m −2 ) and Cr(VI) adsorption constant (K Cr(VI),chem = 1.14 × 10 −2 L mmol −1 ) of Chem-PdNPs. In addition, product inhibition by trivalent chromium [Cr(III)] was high in Chem-PdNPs as indicated by the high adsorption constant of Cr(III) in Chem-PdNPs of K Cr(III),chem = 52.9 L mmol −1 as compared to the one for Bio-PdNPs of K Cr(III),bio = 2.76 L mmol −1 .
John Warcup Cornforth
Proceedings of the Royal Society of London. Series B. Biological Sciences · 1978
This lecture is a report of progress in work that began at Shell Research Ltd’s Milstead Laboratory and has continued at the University of Sussex. I had spent some ten years studying the substrate sterochemistry of enzymes. No one who has done this could fail to be impressed by the stereochemical precision with which enzymes handle their substrates, even when the nature of the product does not exact a stereospecific treatment. It is hard to resist the conclusion that this specificity is an integral and not an incidental feature of the enormous efficiency of enzymes as catalysts. Naturally, like everyone who has worked with enzymes, I form hypotheses about this or that enzymic catalysis; some of these ideas have been testable by stereochemical methods or by various types of isotopic labelling. Further progress can be, and is being, made by the intensive study of particular enzymes, but to someone like myself who is interested in chemical reactions and chemical synthesis it was more attractive to attempt, on the basis of knowledge and conjecture about the nature of enzymic catalysis, to devise synthetic catalysts having the properties of stereospecificity, positional specificity and high efficiency. Without at present presuming to excel or even equal catalytic powers that are thought to have evolved by trial and error over thousands of millions of years, one can, by making the assumption that catalytic activity of this type is not uniquely a property of proteins, substitute the resources of organic chemistry as a whole for the rigours of polypeptide synthesis.
J. Lubkowski, J. Vanegas, W. Chan et al.
Biochemistry · 2020
Two bacterial type II L-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have been playing a critical role for over 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II L-asparaginase (EcAII). Our model was developed based on new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory (DFT). We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed based only on data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) L-asparaginases.
Henrik Almblad, Trevor E Randall, Fanny Liu et al.
Nature Communications · 2021
Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, we identify a thermosensory diguanylate cyclase (TdcA) that modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa. TdcA synthesizes c-di-GMP with catalytic rates that increase more than a hundred-fold over a ten-degree Celsius change. Analyses using protein chimeras indicate that heat-sensing is mediated by a thermosensitive Per-Arnt-SIM (PAS) domain. TdcA homologs are widespread in sequence databases, and a distantly related, heterologously expressed homolog from the Betaproteobacteria order Gallionellales also displayed thermosensitive diguanylate cyclase activity. We propose, therefore, that thermotransduction is a conserved function of c-di-GMP signaling networks, and that thermosensitive catalysis of a second messenger constitutes a mechanism for thermal sensing in bacteria. Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, the authors identify a thermosensitive enzyme that synthesizes c-di-GMP and modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa.
Cherian Gloria Susan, Raja Madhan
Journal of Natural Products and Resources · 2021
Tannin degradation by bacteria has not been studied much as tannins are commonly known to be bacteriostatic due to enzyme inhibition, substrate deprivation, and the enzyme activity on the bacterial cell wall. However, about a handful of bacteria have been found to tolerate certain concentrations of tannin. This study focuses on isolating and identifying bacteria from decaying portions of tree bark for tannase production and effective catalysis of ester bond hydrolysis in tannins. Different concentrations of commercial tannic acid were used as the sole carbon source on mineral salt medium (MSM) agar plates, to test the maximum tolerable concentrations (MTCs) by the isolates. Tannin degradation was confirmed by a visual reading method and bacterial tannase activity and the biodegradation percentage were determined. One particular isolate was identified to have 50 g/L MTC of tannin, with a tannase activity of 51.61 U/mL that is optimum after 96 hours of incubation. The 16s rRNA sequencing results showed that the isolate belonged to Bacillus genus and the resulting bacterial strain isolate was found to be a new strain of Bacillus subtilis which was submitted to GenBank under the accession number MH330408.
D. Balchin, M. Hayer-Hartl, F. Hartl
FEBS Letters · 2020
Molecular chaperones are highly conserved proteins that promote proper folding of other proteins in vivo. Diverse chaperone systems assist de novo protein folding and trafficking, the assembly of oligomeric complexes, and recovery from stress‐induced unfolding. A fundamental function of molecular chaperones is to inhibit unproductive protein interactions by recognizing and protecting hydrophobic surfaces that are exposed during folding or following proteotoxic stress. Beyond this basic principle, it is now clear that chaperones can also actively and specifically accelerate folding reactions in an ATP‐dependent manner. We focus on the bacterial Hsp70 and chaperonin systems as paradigms, and review recent work that has advanced our understanding of how these chaperones act as catalysts of protein folding.
M. Sutter, Matthew R Melnicki, Frederik Schulz et al.
Nature Communications · 2021
Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications. Bacterial microcompartments (BMCs) are organelles consisting of a protein shell in which certain metabolic reactions take place separated from the cytoplasm. Here, Sutter et al. present a comprehensive catalog of BMC loci, substantially expanding the number of known BMCs and describing distinct types and compartmentalized reactions.
L. Hor, R. Dobson, M. Downton et al.
Journal of Biological Chemistry · 2013
Background: Diaminopimelate epimerase catalyzes a key step in the synthesis of meso-diaminopimelate and lysine. Results: Solution and crystal studies show that diaminopimelate epimerase exists as an active dimer, whereas a monomeric mutant is catalytically inactive. Conclusion: The diaminopimelate epimerase dimer is essential for function with evidence suggesting that dimerization attenuates subunit dynamics. Significance: Structural insights into the design of antimicrobial agents to disrupt diaminopimelate epimerase dimerization are provided. Diaminopimelate (DAP) epimerase is involved in the biosynthesis of meso-DAP and lysine, which are important precursors for the synthesis of peptidoglycan, housekeeping proteins, and virulence factors in bacteria. Accordingly, DAP epimerase is a promising antimicrobial target. Previous studies report that DAP epimerase exists as a monomeric enzyme. However, we show using analytical ultracentrifugation, X-ray crystallography, and enzyme kinetic analyses that DAP epimerase from Escherichia coli exists as a functional dimer in solution and the crystal state. Furthermore, the 2.0-Å X-ray crystal structure of the E. coli DAP epimerase dimer shows for the first time that the enzyme exists in an open, active conformation. The importance of dimerization was subsequently probed by using site-directed mutagenesis to generate a monomeric mutant (Y268A). Our studies show that Y268A is catalytically inactive, thus demonstrating that dimerization of DAP epimerase is essential for catalysis. Molecular dynamics simulations indicate that the DAP epimerase monomer is inherently more flexible than the dimer, suggesting that dimerization optimizes protein dynamics to support function. Our findings offer insight into the development of novel antimicrobial agents targeting the dimeric antibiotic target DAP epimerase.
Xia Hua, Jian Han, Xin Zhou et al.
AIChE Journal · 2022
Oxygen, as a terminal electron acceptor, is an essential substrate in the aerobic bio-oxidation process, affecting bacterial vitality and bio-oxidation performance. In this study, a new and smart platform biotechnology of sealed-oxygen supply bioreactor (SOS-BR) was developed by improving gas pressure to significantly intensify oxygen transfer rate and resolving the formidable barriers of aerobic catalysis. In virtue of SOS-BR, the bio-productivity was greatly improved for three representative substrates (xylose, furfural, glycerol) bio-oxidation with the whole-cell catalysis of Gluconobacter oxydans. The determination of oxygen transfer coefficient (KL α ) established an upgraded theoretical dynamic model for gas pressure intersification biosystem. Additionally, viscosity measurement and combined pressure control strategy explained the inflection point phenomenon of productivity and confirmed the intensify mechanism. The new strategy of significantly intensifying oxygen transfer provided insightful ideas for overcoming the subbon obstacle of obligate aerobic catalysis, and further promoted industrial practicability of bio-oxidation.
Ping-Yi Li, P. Ji, Chunyang Li et al.
Journal of Biological Chemistry · 2014
Background: Catalytic mechanisms of GTSAG motif subfamily enzymes of the bacterial hormone-sensitive lipases (HSLs) family are largely unknown. Results: E25, a GTSAG motif subfamily esterase, adopts a novel dimerization pattern. Dimerization keeps the catalytic Asp282 orientation for E25 catalysis. Conclusion: Dimerization and some catalytic profiles of E25 are distinctive from other HSLs. Significance: Our study sheds light on protein folding and evolution of HSLs. Hormone-sensitive lipases (HSLs) are widely distributed in microorganisms, plants, and animals. Microbial HSLs are classified into two subfamilies, an unnamed new subfamily and the GDSAG motif subfamily. Due to the lack of structural information, the detailed catalytic mechanism of the new subfamily is not yet clarified. Based on sequence analysis, we propose to name the new subfamily as the GTSAG motif subfamily. We identified a novel HSL esterase E25, a member of the GTSAG motif subfamily, by functional metagenomic screening, and resolved its structure at 2.05 Å. E25 is mesophilic (optimum temperature at 50 °C), salt-tolerant, slightly alkaline (optimum pH at 8.5) for its activity, and capable of hydrolyzing short chain monoesters (C2–C10). E25 tends to form dimers both in the crystal and in solution. An E25 monomer contains an N-terminal CAP domain, and a classical α/β hydrolase-fold domain. Residues Ser186, Asp282, and His312 comprise the catalytic triad. Structural and mutational analyses indicated that E25 adopts a dimerization pattern distinct from other HSLs. E25 dimer is mainly stabilized by an N-terminal loop intersection from the CAP domains and hydrogen bonds and salt bridges involving seven highly conserved hydrophilic residues from the catalytic domains. Further analysis indicated that E25 also has some catalytic profiles different from other HSLs. Dimerization is essential for E25 to exert its catalytic activity by keeping the accurate orientation of the catalytic Asp282 within the catalytic triad. Our results reveal the structural basis for dimerization and catalysis of an esterase from the GTSAG motif subfamily of the HSL family.
D. Parsonage, K. Nelson, G. Ferrer-Sueta et al.
Biochemistry · 2015
Peroxiredoxins make up a ubiquitous family of cysteine-dependent peroxidases that reduce hydroperoxide or peroxynitrite substrates through formation of a cysteine sulfenic acid (R-SOH) at the active site. In the 2-Cys peroxiredoxins, a second (resolving) cysteine reacts with the sulfenic acid to form a disulfide bond. For all peroxiredoxins, structural rearrangements in the vicinity of the active site cysteine(s) are necessary to allow disulfide bond formation and subsequent reductive recycling. In this study, we evaluated the rate constants for individual steps in the catalytic cycle of Salmonella typhimurium AhpC. Conserved Trp residues situated close to both peroxidatic and resolving cysteines in AhpC give rise to large changes in fluorescence during the catalytic cycle. For recycling, AhpF very efficiently reduces the AhpC disulfide, with a single discernible step and a rate constant of 2.3 × 10(7) M(-1) s(-1). Peroxide reduction was more complex and could be modeled as three steps, beginning with a reversible binding of H2O2 to the enzyme (k1 = 1.36 × 10(8) M(-1) s(-1), and k-1 = 53 s(-1)), followed by rapid sulfenic acid generation (620 s(-1)) and then rate-limiting disulfide bond formation (75 s(-1)). Using bulkier hydroperoxide substrates with higher Km values, we found that different efficiencies (kcat/Km) for turnover of AhpC with these substrates are primarily caused by their slower rates of binding. Our findings indicate that this bacterial peroxiredoxin exhibits rates for both reducing and oxidizing parts of the catalytic cycle that are among the fastest observed so far for this diverse family of enzymes.
Yonghai Feng, Yi Yu, Hui Shi et al.
Science Advances · 2024
The unique bacterial infection microenvironment (IME) usually requires complicated design of nanomaterials to adapt to IME for enhancing antibacterial therapy. Here, an alternative IME adaptative nitrite reductase–mimicking nanozyme is constructed by in situ growth of ultrasmall copper sulfide clusters on the surface of a nanofibrillar lysozyme assembly (NFLA/CuS NHs), which can temporally regulate nitric oxide (NO) gradient concentration to kill bacteria initially and promote tissue regeneration subsequently. Benefiting from a copper nitrite reductase (CuNIR)–inspired structure with CuS cluster as active center and NFLA as skeleton, NFLA/CuS NHs efficiently boost the catalytic reduction of nitrite to NO. The inherent supramolecular fibrillar networks displays excellent bacterial capture capability, facilitating initial high-concentration NO attacks on the bacteria. The subsequent catalytic release of low-concentration NO by NFLA/CuS NHs–mediated nitrite reduction remarkably promotes cell migration and angiogenesis. This work paves the way for dynamically eliminating MDR bacterial infection and promoting tissue regeneration in a simple and smart way through CuNIR-mimicking catalysis.
Martin G. Peverelli, T. P. Soares da Costa, N. Kirby et al.
Journal of Biological Chemistry · 2016
Diaminopimelate decarboxylase (DAPDC) catalyzes the final step in the diaminopimelate biosynthesis pathway of bacteria. The product of the reaction is the essential amino acid l-lysine, which is an important precursor for the synthesis of the peptidoglycan cell wall, housekeeping proteins, and virulence factors of bacteria. Accordingly, the enzyme is a promising antibacterial target. Previous structural studies demonstrate that DAPDC exists as monomers, dimers, and tetramers in the crystal state. However, the active oligomeric form has not yet been determined. We show using analytical ultracentrifugation, small angle x-ray scattering, and enzyme kinetic analyses in solution that the active form of DAPDC from Bacillus anthracis, Escherichia coli, Mycobacterium tuberculosis, and Vibrio cholerae is a dimer. The importance of dimerization was probed further by generating dimerization interface mutants (N381A and R385A) of V. cholerae DAPDC. Our studies indicate that N381A and R385A are significantly attenuated in catalytic activity, thus confirming that dimerization of DAPDC is essential for function. These findings provide scope for the development of new antibacterial agents that prevent DAPDC dimerization.
Blair Ney, Carlo R. Carere, R. Sparling et al.
Frontiers in Microbiology · 2017
F420 is a microbial cofactor that mediates a wide range of physiologically important and industrially relevant redox reactions, including in methanogenesis and tetracycline biosynthesis. This deazaflavin comprises a redox-active isoalloxazine headgroup conjugated to a lactyloligoglutamyl tail. Here we studied the catalytic significance of the oligoglutamate chain, which differs in length between bacteria and archaea. We purified short-chain F420 (two glutamates) from a methanogen isolate and long-chain F420 (five to eight glutamates) from a recombinant mycobacterium, confirming their different chain lengths by HPLC and LC/MS analysis. F420 purified from both sources was catalytically compatible with purified enzymes from the three major bacterial families of F420-dependent oxidoreductases. However, long-chain F420 bound to these enzymes with a six- to ten-fold higher affinity than short-chain F420. The cofactor side chain also significantly modulated the kinetics of the enzymes, with long-chain F420 increasing the substrate affinity (lower Km) but reducing the turnover rate (lower kcat) of the enzymes. Molecular dynamics simulations and comparative structural analysis suggest that the oligoglutamate chain of F420 makes dynamic electrostatic interactions with conserved surface residues of the oxidoreductases while the headgroup binds the catalytic site. In conjunction with the kinetic data, this suggests that electrostatic interactions made by the oligoglutamate tail result in higher-affinity, lower-turnover catalysis. Physiologically, we propose that bacteria have selected for long-chain F420 to better control cellular redox reactions despite tradeoffs in catalytic rate. Conversely, this suggests that industrial use of shorter-length F420 will greatly increase the rates of bioremediation and biocatalysis processes relying on purified F420-dependent oxidoreductases.
Lihua Wu, Yue Luo, Chaofeng Wang et al.
ACS Nano · 2023
In this work, a biomimetic nanozyme catalyst with rapid and efficient self-bacteria-killing and wound-healing performances was synthesized. Through an in situ reduction reaction, a PCN-222 metal organic framework (MOF) was doped with bismuth nanoparticles (Bi NPs) to form Bi-PCN-222, an interfacial Schottky heterojunction biomimetic nanozyme catalyst, which can kill 99.9% of Staphylococcus aureus (S. aureus). The underlying mechanism was that Bi NP doping can endow Bi-PCN-222 MOF with self-driven charge transfer through the Schottky interface and the capability of oxidase-like and peroxidase-like activity, because a large number of free electrons can be captured by surrounding oxygen species to produce radical oxygen species (ROS). Furthermore, once bacteria contact Bi-PCN-222 in a physiological environment, its appropriate redox potential can trigger electron transfer through the electron transport pathway in bacterial membranes and then the interior of the bacteria, which disturbs the bacterial respiration process and subsequent metabolism. Additionally, Bi-PCN-222 can also accelerate tissue regeneration by upregulating fibroblast proliferation and angiogenesis genes (bFGF, VEGF, and HIF-1α), thereby promoting wound healing. This biomimetic enzyme-catalyzed strategy will bring enlightenment to the design of self-bacterial agents for efficient disinfection and tissue reconstruction simultaneously.
Hacksung Kim, P. Pastén, J. Gaillard et al.
Journal of the American Chemical Society · 2003
We describe the characterization of an unknown and difficult to identify but geochemically and environmentally significant MnOx structure produced by a freshwater bacterium, Leptothrix discophora SP-6, using combined transmission electron microscopy (TEM), extended X-ray absorption fine structure (EXAFS), and UV Raman spectroscopy. The large surface-to-volume ratio of the needle-shaped nanocrystalline MnO2 formed around the bacterial cells coupled to the porous, zeolite-like structure has the potential to catalyze reactions and oxidize and adsorb metals.
V. Karuppiah, K. Ranaghan, Nicole G H Leferink et al.
ACS Catalysis · 2017
Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances. We report here structures for the recently discovered Streptomyces clavuligerus monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthase (bCinS), and we show that these are active biocatalysts for monoterpene production using biocatalysis and metabolic engineering platforms. In metabolically engineered monoterpene-producing E. coli strains, use of bLinS leads to 300-fold higher linalool production compared with the corresponding plant monoterpene synthase. With bCinS, 1,8-cineole is produced with 96% purity compared to 67% from plant species. Structures of bLinS and bCinS, and their complexes with fluorinated substrate analogues, show that these bacterial monoterpene synthases are similar to previously characterized sesquiterpene synthases. Molecular dynamics simulations suggest that these monoterpene synthases do not undergo large-scale conformational changes during the reaction cycle, making them attractive targets for structured-based protein engineering to expand the catalytic scope of these enzymes toward alternative monoterpene scaffolds. Comparison of the bLinS and bCinS structures indicates how their active sites steer reactive carbocation intermediates to the desired acyclic linalool (bLinS) or bicyclic 1,8-cineole (bCinS) products. The work reported here provides the analysis of structures for this important class of monoterpene synthase. This should now guide exploitation of the bacterial enzymes as gateway biocatalysts for the production of other monoterpenes and monoterpenoids.
Yong Wang, Qi Zhan, Xinlu Wang et al.
Nature Communications · 2020
The bacterial effector MavC catalyzes non-canonical ubiquitination of host E2 enzyme UBE2N without engaging any of the conventional ubiquitination machinery, thereby abolishing UBE2N’s function in forming K63-linked ubiquitin (Ub) chains and dampening NF-кB signaling. We now report the structures of MavC in complex with conjugated UBE2N~Ub and an inhibitor protein Lpg2149, as well as the structure of its ortholog, MvcA, bound to Lpg2149. Recognition of UBE2N and Ub depends on several unique features of MavC, which explains the inability of MvcA to catalyze ubiquitination. Unexpectedly, MavC and MvcA also possess deubiquitinase activity against MavC-mediated ubiquitination, highlighting MavC as a unique enzyme possessing deamidation, ubiquitination, and deubiquitination activities. Further, Lpg2149 directly binds and inhibits both MavC and MvcA by disrupting the interactions between enzymes and Ub. These results provide detailed insights into catalysis and regulation of MavC-type enzymes and the molecular mechanisms of this non-canonical ubiquitination machinery. The bacterial effector MavC can ubiquitinate the host E2 enzyme UBE2N to dampen the host immune response. Here, the authors provide mechanistic insight into this non-canonical ubiquitination machinery and reveal the structural basis for the functional differences between MavC and its close homolog MvcA.
Jian Yang, Yuqun Xu, T. Miyakawa et al.
Applied and Environmental Microbiology · 2020
Heterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of β-1,3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine Flavobacterium. The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling. ABSTRACT Laminarin is an abundant algal polysaccharide that serves as carbon storage and fuel to meet the nutrition demands of heterotrophic microbes. Laminarin depolymerization catalyzed by microbial extracellular enzymes initiates remineralization, a key process in ocean biogeochemical cycles. Here, we described a glycoside hydrolase 16 (GH16) family laminarinase from a marine alga-associated Flavobacterium at the biochemical and structural levels. We found that the endolytic enzyme cleaved laminarin with a preference for β-1,3-glycoside linkages and showed transglycosylation activity across a broad range of acceptors. We also solved and compared high-resolution crystal structures of laminarinase in the apo form and in complex with β-1,3-tetrasaccharides, revealing an expanded catalytic cleft formed following substrate binding. Moreover, structure and mutagenesis studies identified multiple specific contacts between the enzyme and glucosyl residues essential for the substrate specificity for β-1,3-glucan. These results provide novel insights into the structural requirements for substrate binding and catalysis of GH16 family laminarinase, enriching our understanding of bacterial utilization of algal laminarin. IMPORTANCE Heterotrophic bacterial communities are key players in marine biogeochemical cycling due to their ability to remineralize organic carbon. Processing of complex organic matter requires heterotrophic bacteria to produce extracellular enzymes with precise specificity to depolymerize substrates to sizes sufficiently small for uptake. Thus, extracellular enzymatic hydrolysis initiates microbe-driven heterotrophic carbon cycling. In this study, based on biochemical and structural analyses, we revealed the depolymerization mechanism of β-1,3-glucan, a carbon reserve in algae, by laminarinase from an alga-associated marine Flavobacterium. The findings provide new insights into the substrate recognition and catalysis of bacterial laminarinase and promote a better understanding of how extracellular enzymes are involved in organic matter cycling.
Godwin E. Oyiwona, J. Ogbonna, C. Anyanwu
Bio-Research · 2019
Two H-type dual-chambered glucose-fed MFC reactors, each with a working volume of 250 ml designated as GPWW (enriched from garri wastewater) and the other as DWW (enriched from domestic wastewater) were constructed under same conditions and the anodes were continuously fed with synthetic medium (SM) at a flow rate of 0.7 ml min -1 . An average power density (Pd) of 1.5 ± 1.39 W/m 3 for GPWW and 0.6 ± 0.6 W/m 3 for DWW was observed in 150 days of operation. The peak biomass density for DWW was significantly (P < 0.05 T-test) higher than that of GPWW by a factor of 2 (8.99mg versus 3.4 BSA/total anode respectively) on day 120 suggesting that more biomass was formed on DWW than GPWW reactor. This indicates that exo-electrogens in DWW reactor directed more of electron flow to cell synthesis rather than to current. The archaea footprints detected on the anodes were limiting factors in current generation. One vital milestone in this study is the discovery of the potential of garri-processing wastewater as a veritable substrate in microbial fuel cell technology. Keywords: Biomass density, Dissimilatory metal reducing bacteria, Current density, Microbial fuel cell, Power density
Jessica A Gable, T. Poulos, A. Follmer
Journal of the American Chemical Society · 2023
Despite being one of the most well-studied aspects of cytochrome P450 chemistry, important questions remain regarding the nature and ubiquity of allosteric regulation of catalysis. The crystal structure of a bacterial P450, P450terp, in the presence of substrate reveals two binding sites, one above the heme in position for regioselective hydroxylation and another in the substrate access channel. Unlike many bacterial P450s, P450terp does not exhibit an open to closed conformational change when substrate binds; instead, P450terp uses the second substrate molecule to hold the first substrate molecule in position for catalysis. Spectral titrations clearly show that substrate binding to P450terp is cooperative with a Hill coefficient of 1.4 and is supported by isothermal titration calorimetry. The importance of the allosteric site was explored by a series of mutations that weaken the second site and that help hold the first substrate in position for proper catalysis. We further measured the coupling efficiency of both the wild-type (WT) enzyme and the mutant enzymes. While the WT enzyme exhibits 97% efficiency, each of the variants showed lower catalytic efficiency. Additionally, the variants show decreased spin shifts upon binding of substrate. These results are the first clear example of positive homotropic allostery in a class 1 bacterial P450 with its natural substrate. Combined with our recent results from P450cam showing complex substrate allostery and conformational dynamics, our present study with P450terp indicates that bacterial P450s may not be as simple as once thought and share complex substrate binding properties usually associated with only mammalian P450s.
Yanli Huang, Xufeng Wan, Qiang Su et al.
Nature Communications · 2024
Implant-associated infections due to the formation of bacterial biofilms pose a serious threat in medical healthcare, which needs effective therapeutic methods. Here, we propose a multifunctional nanoreactor by spatiotemporal ultrasound-driven tandem catalysis to amplify the efficacy of sonodynamic and chemodynamic therapy. By combining piezoelectric barium titanate with polydopamine and copper, the ultrasound-activated piezo-hot carriers transfer easily to copper by polydopamine. It boosts reactive oxygen species production by piezoelectrics, and facilitates the interconversion between Cu2+ and Cu+ to promote hydroxyl radical generation via Cu+ -catalyzed chemodynamic reactions. Finally, the elevated reactive oxygen species cause bacterial membrane structure loosening and DNA damage. Transcriptomics and metabolomics analysis reveal that intracellular copper overload restricts the tricarboxylic acid cycle, promoting bacterial cuproptosis-like death. Therefore, the polyetherketoneketone scaffold engineered with the designed nanoreactor shows excellent antibacterial performance with ultrasound stimulation and promotes angiogenesis and osteogenesis on-demand in vivo.
Yan Ni, Chun‐Xiu Li, Jie Zhang et al.
Advanced Synthesis & Catalysis · 2011
Abstract A β‐ketoacyl‐ACP reductase (FabG) gene from Bacillus sp. ECU0013 was heterologously overexpressed in Escherichia coli and the encoded protein was purified to homogeneity. The recombinant reductase could reduce a broad spectrum of prochiral ketones including aromatic ketones and keto esters and showed the highest activity in the asymmetric reduction of ethyl 2‐oxo‐4‐phenylbutyrate (OPBE). Using E. coli cells coexpressing both FabG and glucose dehydrogenase (GDH) genes, as much as 620 g⋅L −1 of OPBE was almost stoichiometrically converted to ethyl ( S )‐2‐hydroxy‐4‐phenylbutyrate [( S )‐HPBE] with excellent (>99%) enantiomeric excess. More importantly, the process could be performed smoothly without external addition of an expensive cofactor as usually done and could be scaled up very easily. All these positive features demonstrate the applicability of this reductase for the large‐scale production of optically active α‐hydroxy acids/esters.