Discover insights from thousands of peer-reviewed papers on microbial electrochemical systems
C. J. Jackson, J.-L. Foo, N. Tokuriki et al.
Proceedings of the National Academy of Sciences · 2009
To efficiently catalyze a chemical reaction, enzymes are required to maintain fast rates for formation of the Michaelis complex, the chemical reaction and product release. These distinct demands could be satisfied via fluctuation between different conformational substates (CSs) with unique configurations and catalytic properties. However, there is debate as to how these rapid conformational changes, or dynamics, exactly affect catalysis. As a model system, we have studied bacterial phosphotriesterase (PTE), which catalyzes the hydrolysis of the pesticide paraoxon at rates limited by a physical barrier—either substrate diffusion or conformational change. The mechanism of paraoxon hydrolysis is understood in detail and is based on a single, dominant, enzyme conformation. However, the other aspects of substrate turnover (substrate binding and product release), although possibly rate-limiting, have received relatively little attention. This work identifies “open” and “closed” CSs in PTE and dominant structural transition in the enzyme that links them. The closed state is optimally preorganized for paraoxon hydrolysis, but seems to block access to/from the active site. In contrast, the open CS enables access to the active site but is poorly organized for hydrolysis. Analysis of the structural and kinetic effects of mutations distant from the active site suggests that remote mutations affect the turnover rate by altering the conformational landscape.
Pratima Bajpai
Bacterial Nanocellulose for Papermaking and Packaging · 2024
Bacterial cellulose is recognized as a multifaceted, versatile biomaterial with abundant applications. It is a completely biodegradable, ecological, non-toxic, chemically stable, and biocompatible material. Unlike plant cellulose, it is characterized by high crystallinity, a higher degree of polymerization, and higher tensile strength and Young’s modulus. In addition, bacterial cellulose, unlike vegetable cellulose, has a smaller diameter of fibres and hence possesses higher hydrophilicity. The properties of bacterial cellulose depend on multiple factors, such as culture conditions, the type of microorganisms, and nutrients present in the growth medium. These factors have a huge impact on the properties of the polymer, such as strength, crystallinity, degree of polymerization, or hygroscopicity.
Teunie van Herk, Aloysius F. Hartog, Alida M. van der Burg et al.
Advanced Synthesis & Catalysis · 2005
Abstract Bacterial non‐specific acid phosphatases normally catalyze the dephosphorylation of a variety of substrates. As shown previously the enzymes from Shigella flexneri and Salmonella enterica are also able to catalyze the phosphorylation of inosine to inosine monophosphate and D ‐glucose to D ‐glucose 6‐phosphate (D‐G6P) using cheap pyrophosphate as the phosphate donor. After optimization high yields (95%) are achieved in the latter reaction and we show here that it is possible to use these enzymes in a preparative manner. This prompted us to investigate by using 31 P NMR and HPLC also the phosphorylation of a broad range of carbohydrates and alcohols. Many cyclic carbohydrates are phosphorylated in a regioselective manner. Non‐cyclic carbohydrates are phosphorylated as well. Phosphorylation of linear alcohols, cyclic and aromatic alcohols is also possible. In all cases the acid phosphatase from Shigella prefers a primary alcohol function above a secondary one. We conclude that these enzymes are an attractive alternative to existing chemical and enzymatic methods in the phosphorylation of a broad range of compounds.
luyan ma
· 2020
<p>Microbial nanowires are nanofilaments that could offer an extracellular electron transfer (EET) pathway linking the bacterial respiratory chain to external surfaces, such as oxidized metals in the environment and engineered electrodes in renewable energy devices. Filaments proposed to function as nanowires have been reported in multiple bacteria, yet it remains largely unclear about the composition and electron transfer mechanism of bacterial nanowires. Pseudomonas aeruginosa is an environmental and electrochemically active bacterium. In this study, we found nanotube-like extracellular filaments in P. aeruginosa biofilms, which were bacterial membrane extensions similar to the nanowires reported in Shewanella oneidensis. Remarkably, conductive probe atomic force microscope showed measurable conductivity of these extracellular filaments, suggesting that they may function as nanowires in P. aeruginosa. Our results also indicated that the electron shuttle pyocyanin significantly affected the conductivity of P. aeruginosa nanowires, suggesting that the electron transfer mechanism of P. aeruginosa nanowires was different from S. oneidensis. Furthermore, factors that impact biofilm formation, such as flagella, type IV pili, and exopolysaccharides, were not essential for nanowires formation, while affect the formation and length of nanowires of P. aeruginosa. Taken together, this is the first report that investigated the role of electron shuttle on the conductivity of nanowires and factors that affected nanowires formation.</p>
Pratima Bajpai
Bacterial Nanocellulose for Papermaking and Packaging · 2024
Bacterial nanocellulose (BNC) biosynthesis is a well-organized and strictly controlled process and has two stages: first, the formation of 1,4-glucan linkages, and subsequently the assembly and cellulose crystallization. The process starts with the carbon source, such as glucose and fructose, being transported into the cell, where the cellulose precursor UDPG is produced. Bcs then polymerizes glucose from UDPG into 1,4-glucan strands. Finally, cellulose chains are secreted as sub-fibrils through pores in the cell membrane and then combined into ribbons in a 3D nanofiber network supported by hydrogen bonds.
Norzawani Jaffar
Focus on Bacterial Biofilms · 2022
Most pathogenic bacteria species form biofilm as their protective mode of growth, which helps them survive from the bactericidal effect of the antimicrobials or the killing activity of the host immune cells. The bacteria cells’ survivability via biofilm formation creates challenges in the medical field in terms of the device and also disease-related to biofilm. The impact of the bacterial biofilm issue is worsening over time, and the association to the high tolerance to the antimicrobial agents leads to increased morbidity and mortality worldwide. This review will highlight the main characteristics of the biofilm, the issue of biofilm in clinical practice, which also covered the pertinence of the biofilm in clinical practice, device-related biofilm disease, oral disease, and the significant bacterial species involved in the biofilm-related infections. Knowledge about the vital role of bacterial biofilm in related disorders will give new insight into the best approaches and alternative treatments for biofilm-related disease.
Hammam Antar, Young-Min Soh, Stefano Zamuner et al.
Science Advances · 2021
Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB acts as adaptor protein between the 16–base pair centromeric parS DNA sequences and the DNA segregation proteins ParA and Smc (structural maintenance of chromosomes). Upon cytidine triphosphate (CTP) and parS DNA binding, ParB dimers form DNA clamps that spread onto parS -flanking DNA by sliding, thus assembling the so-called partition complex. We show here that CTP hydrolysis is essential for efficient chromosome segregation by ParABS but largely dispensable for Smc recruitment. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It promotes ParB unloading from DNA to limit the extent of ParB spreading, and it recycles off-target ParB clamps to allow for parS retargeting, together superconcentrating ParB near parS . We also propose a model for clamp closure involving a steric clash when binding ParB protomers to opposing parS half sites.
Roland Weis, Margit Winkler, Matthias Schittmayer et al.
Advanced Synthesis & Catalysis · 2009
Abstract Innovative biohydroxylation catalysts for the preparation of drug metabolites were developed from scratch. A set of bacterial and fungal sequences of putative and already known bifunctional P450 enzymes was identified by protein sequence alignments, expressed in Escherichia coli and characterised. Notably, a fungal self‐sufficient cytochrome P450 (CYP) from Aspergillus fumigatus turned out to be especially stable during catalyst preparation and application and also in presence of organic co‐solvents. To enhance the catalytic activity and broaden the substrate specificity of those variants with high expression levels prominent single mutations were introduced. Selected improved variants were then used as lyophilised bacterial lysates for the synthesis of 4′‐hydroxydiclofenac and 6‐hydroxychlorzoxazone, the two metabolites of active pharmaceutical compounds diclofenac and chlorzoxazone representing the same metabolites as generated by human P450s.
Jacqueline N. Watson, Simon Newstead, Veedeeta Dookhun et al.
FEBS Letters · 2004
A recombinant D92G mutant sialidase from Micromonospora viridifaciens has been cloned, expressed and purified. Kinetic studies reveal that the replacement of the conserved aspartic acid with glycine results in a catalytically competent retaining sialidase that possesses significant activity against activated substrates. The contribution of this aspartate residue to the free energy of hydrolysis for natural substrates is greater than 19 kJ/mol. The three dimensional structure of the D92G mutant shows that the removal of aspartic acid 92 causes no significant re‐arrangement of the active site, and that an ordered water molecule substitutes for the carboxylate group of D92.
Atsuki Nakano, Jun-ichi Kishikawa, Atsuko Nakanishi et al.
PNAS Nexus · 2022
Abstract Adenosine triphosphate (ATP) synthases (F0F1-ATPases) are crucial for all aerobic organisms. F1, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central γε rotor inside a cylinder made of α3β3 in three different conformations (referred to as βE, βTP, and βDP). In this study, we determined multiple cryo-electron microscopy structures of bacterial F0F1 exposed to different reaction conditions. The structures of nucleotide-depleted F0F1 indicate that the ε subunit directly forces βTP to adopt a closed form independent of the nucleotide binding to βTP. The structure of F0F1 under conditions that permit only a single catalytic β subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on βTP instead of βDP, where ATP hydrolysis proceeds in the steady-state catalysis of F0F1. This indicates that the unisite catalysis of bacterial F0F1 significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.
Florian Rudroff, Joanna Rydz, Freek H. Ogink et al.
Advanced Synthesis & Catalysis · 2007
Abstract Microbial Baeyer–Villiger oxidation of representative prochiral ketones with a cyclobutanone structural motif was investigated using a collection of eight monooxygenases of different bacterial origin. This platform of enzymes is able to perform stereoselective biotransformations on an array of structurally diverse substrates. With several ketone precursors, biooxidations yielded enantiocomplementary butyrolactones as key intermediates for the synthesis of natural products and bioactive compounds. The microbial Baeyer–Villiger oxidation allows a facile and rapid entry to several compound classes in a desymmetrization reaction upon de novo generation of chirality.
María Maneiro, Antonio Peón, Emilio Lence et al.
Biochemical Journal · 2014
Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu46, Phe145 and Met205 and Gln236, Pro234 and Ala233 residues, with the latter three being located in the flexible substrate-covering loop. Gln236 was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agents.
Ronja Driller, Sophie Janke, Monika Fuchs et al.
Nature Communications · 2018
Abstract Terpenes constitute the largest and structurally most diverse natural product family. Most terpenoids exhibit a stereochemically complex macrocyclic core, which is generated by C–C bond forming of aliphatic oligo-prenyl precursors. This reaction is catalysed by terpene synthases (TPSs), which are capable of chaperoning highly reactive carbocation intermediates through an enzyme-specific reaction. Due to the instability of carbocation intermediates, the proteins’ structural dynamics and enzyme:substrate interactions during TPS catalysis remain elusive. Here, we present the structure of the diterpene synthase CotB2, in complex with an in crystallo cyclised abrupt reaction product and a substrate-derived diphosphate. We captured additional snapshots of the reaction to gain an overview of CotB2’s catalytic mechanism. To enhance insights into catalysis, structural information is augmented with multiscale molecular dynamic simulations. Our data represent fundamental TPS structure dynamics during catalysis, which ultimately enable rational engineering towards tailored terpene macrocycles that are inaccessible by conventional chemical synthesis.
D Ralt, J S Wishnok, R Fitts et al.
Journal of Bacteriology · 1988
We have developed a rapid and sensitive fluorimetric method, based on the formation of a fluorescent product from nitrosation of 2,3-diaminonaphthalene, for measuring the ability of bacteria to catalyze nitrosation of amines. We have shown in Escherichia coli that nitrosation can be induced under anaerobic conditions by nitrite and nitrate, that formate is the most efficient electron donor for this reaction, and that nitrosation may be catalyzed by nitrate reductase (EC 1.7.99.4). The narG mutants defective in nitrate reductase do not catalyze nitrosation, and the fnr gene is essential for nitrosation. Induction by nitrite or nitrate of nitrosation, N2O production, and nitrate reductase activity all require the narL gene.
Carolyn M.C. Lam, María Suárez Diez, Miguel Godinho et al.
FEBS Letters · 2012
Bacteria have long been used for the synthesis of a wide range of useful proteins and compounds. The developments of new bioprocesses and improvements of existing strategies for syntheses of valuable products in various bacterial cell hosts have their own challenges and limitations. The field of synthetic biology has combined knowledge from different science and engineering disciplines and facilitated the advancement of novel biological components which has inspired the design of targeted biosynthesis. Here we discuss recent advances in synthetic biology with relevance to biosynthesis in bacteria and the applications of computational algorithms and tools for manipulation of cellular components. Continuous improvements are necessary to keep up with increasing demands in terms of complexity, scale, and predictability of biosynthesis products.
Hammam Antar, Young-Min Soh, Stefano Zamuer et al.
bioRxiv (Cold Spring Harbor Laboratory) · 2021
Abstract Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB protein acts as an adaptor between the 16 bp centromeric parS DNA sequences and the DNA segregation ATPase ParA. It accumulates at high concentrations at and near a parS site by assembling a partition complex. ParB dimers form a DNA sliding clamp whose closure at parS requires CTP binding. The mechanism underlying ParB loading and the role of CTP hydrolysis however remain unclear. We show that CTP hydrolysis is dispensable for Smc recruitment to parS sites in Bacillus subtilis but is essential for chromosome segregation by ParABS in the absence of Smc. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It recycles off-target ParB clamps to allow for new attempts at parS targeting and it limits the extent of spreading from parS by promoting DNA unloading. We also propose a model for how parS DNA catalyzes ParB clamp closure involving a steric clash between ParB protomers binding to opposing parS half sites.
J. Kristin Smith, John Hsieh, Carol A. Fierke
Biopolymers · 2007
Abstract Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) complex that catalyzes the metal‐dependent maturation of the 5′ end of precursor tRNAs (pre‐tRNAs) in all organisms. RNase P is comprised of a catalytic RNA (P RNA), and at least one essential protein (P protein). Although P RNA is the catalytic subunit of the enzyme and is active in the absence of P protein under high salt concentrations in vitro, the protein is still required for enzyme activity in vivo. Therefore, the function of the P protein and how it interacts with both P RNA and pre‐tRNA have been the focus of much ongoing research. RNA‐protein interactions in RNase P serve a number of critical roles in the RNP including stabilizing the structure, and enhancing the affinity for substrates and metal ions. This review examines the role of RNA‐protein interactions in bacterial RNase P from both structural and mechanistic perspectives. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 329–338, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Aloysius F. Hartog, Ron Wever
Advanced Synthesis & Catalysis · 2015
Abstract The use of substrate engineering allowed the enzymatic sulfation by an arylsulfotransferase from Desulfitobacterium hafniense of a number of carbohydrate derivatives. Specific sulfation of carbohydrates chemically or enzymatically is notoriously difficult or complex. As we have shown previously, the arylsulfotransferase is able to sulfate a variety of phenolic alcohols as well as non‐phenolic alcohols, albeit the conversion in the latter case is limited and in general less than a few percent. Here we used the strategy of substrate engineering to increase the conversion by attaching a hydrophobic group to the carbohydrate. The formed sulfated intermediates may be used as building blocks in the formation of more complex sulfated carbohydrates via a transglycosylation reaction. magnified image
Henning Kirst, Cheryl A. Kerfeld
BMC Biology · 2019
Abstract Bacterial cells have long been thought to be simple cells with little spatial organization, but recent research has shown that they exhibit a remarkable degree of subcellular differentiation. Indeed, bacteria even have organelles such as magnetosomes for sensing magnetic fields or gas vesicles controlling cell buoyancy. A functionally diverse group of bacterial organelles are the bacterial microcompartments (BMCs) that fulfill specialized metabolic needs. Modification and reengineering of these BMCs enable innovative approaches for metabolic engineering and nanomedicine.
S. Kambourakis, K. Draths, J. W. Frost
Journal of the American Chemical Society · 2000
Among a spectrum of uses, 1 gallic acid and pyrogallol are often incorporated into chemical syntheses to provide the trihydrox-ylated aromatic ring of biologically active molecules such as the antibiotic trimethoprim 1 , the muscle relaxant gallamine tri-ethiodide 2 , and the insecticide bendiocarb 3 . The availability of gallic acid is restricted by its current isolation from insect carapices (gall nuts) harvested in China, and an isolate (tara powder) derived from the ground seed pod of a tree found in Peru. 1 Thermal decarboxylation of gallic acid in copper autoclaves affords pyrogallol. 1 As part of a larger effort 2 to supplant isolation of natural products from scarce natural sources, gallic acid and pyrogallol were targeted for microbe-catalyzed synthesis from abundant glucose. In lieu of an elaborated biosynthetic pathway leading to gallic acid, a pathway had to be created. The result is Escherichia coli KL7/pSK6.161, which synthesizes 20 g/L of gallic acid in 12% yield from glucose. E. coli RB791 serA :: aroB / pSK6.234 then converts gallic acid into pyrogallol in yields of 93 - 97%
A. Ugo, Arazu Vivian Amara, Igwe Cn et al.
Fermentation Technology · 2017
Microbes have been novel hosts for suitable industrial enzymes including lipases. With the rapid increase in biotechnological industries, there is need for improvement of bioproducts, enhance environmental safety and product yield. Microbes are qualified biological arsenal for the achievement of the above mentioned targets in the industrial sectors. Lipases as versatile biological catalyst has given a promising prospect in meeting the needs for most industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. Catalytic importance of lipases includes hydrolysis, esterification and transesterification. Each of the mentioned reactions has their industrial applications. Lipases exhibit various properties, with respect to its source. Immobilization has made the use of microbial lipases attain its optimum performance and hence suitable for various reaction and the need to add flavor to the immobilization processes.
R. Jha, C. Strauss
ACS Synthetic Biology · 2020
Enzyme engineering for gain-of-function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements while a single 'bad' mutation can inactivate the enzyme. To establish high throughput screening and achieve enhanced resolution between two variants, genetic libraries of organophos-phate hydrolase enzyme (PON1) were rapidly screened via an engineered positive feedback circuit: a PNP-specific transcrip-tion factor (TF) regulated expression of PON1, which catalyzed paraoxon breakdown and PNP production. Rare active mu-tant colonies, picked by simple visual fluorescence of a PON1-GFP (Green Fluorescent Protein) fusion, were characterized. In a single screening round, high (library-scale) throughput enabled discovery of enhanced paraoxon degradation activity in PON1 including structurally unexpected mutations.
L. Wackett, McKnight
Microbial Biotechnology · 2023
Polymer biof i lms for biocatalysis https://www.ncbi.nlm.nih.gov/pmc/artic les/PMC95 28183/ In some cases, the most catalytically useful bacteria are not adept at forming biofilms naturally. This study addressed that issue by demonstrating different methods of making polymerinduced biofilms. Anammox biof i lm reactor https://pubs.acs.org/doi/10.1021/acsestwater.0c00107 Anammox microbes have been shown to be very useful in industrial nitrogen removal from wastewaters. This paper describes the development and operation of a flowthrough Anammox biofilm reactor.
Pengfei Gong, Jiali Tang, Jiaying Wang et al.
International Journal of Molecular Sciences · 2023
Hydroxytyrosol, a valuable plant-derived phenolic compound, is increasingly produced from microbial fermentation. However, the promiscuity of the key enzyme HpaBC, the two-component flavin-dependent monooxygenase from Escherichia coli, often leads to low yields. To address this limitation, we developed a novel strategy utilizing microbial consortia catalysis for hydroxytyrosol production. We designed a biosynthetic pathway using tyrosine as the substrate and selected enzymes and overexpressing glutamate dehydrogenase GdhA to realize the cofactor cycling by coupling reactions catalyzed by the transaminase and the reductase. Additionally, the biosynthetic pathway was divided into two parts and performed by separate E. coli strains. Furthermore, we optimized the inoculation time, strain ratio, and pH to maximize the hydroxytyrosol yield. Glycerol and ascorbic acid were added to the co-culture, resulting in a 92% increase in hydroxytyrosol yield. Using this approach, the production of 9.2 mM hydroxytyrosol was achieved from 10 mM tyrosine. This study presents a practical approach for the microbial production of hydroxytyrosol that can be promoted to produce other value-added compounds.
Iris Hilker, Véronique Alphand, Roland Wohlgemuth et al.
Advanced Synthesis & Catalysis · 2004
Abstract An efficient preparative scale process for achieving asymmetric Baeyer–Villiger oxidation – a reaction still very difficult to perform using conventional chemistry – is described. This process is based on a biocatalytic whole cells strategy – using a recombinant E. coli strain overexpressing cyclohexanone monooxygenase (CHMO) – combined with a “two‐in‐one” in situ “substrate feeding and product removal” concept (SFPR) using an adsorbent resin. The most efficient resin out of fourteen tested was used in three types of bioreactors (conventional, recycle and bubble column) that were compared. The best one proved to be the bubble column reactor, where 25 g (0.23 M) of rac ‐bicyclo[3.2.0]hept‐2‐en‐6‐one could be totally transformed using a one‐litre vessel with a volumetric productivity of about 1 g L −1 h −1 (i.e., 7.7 mmol L −1 h −1 ). This led to the production of the two corresponding regioisomeric lactones, which were both obtained in excellent enantiomeric purity (ee>98%) and high preparative yield (84%). To our knowledge, these results represent the best example of a (highly productive) preparative scale asymmetric Baeyer–Villiger oxidation.
Yuhua Sheng, Yaokang Wu, Linpei Zhang et al.
Microbial Biotechnology · 2025
ABSTRACT Creatine (CR) is a naturally occurring amino acid derivative that plays a key role in cellular energy homeostasis, which has wide‐ranging applications in food and medicine. Currently, the lack of green and sustainable CR biomanufacturing methods has led to reliance on chemical methods for industrial CR synthesis. This study presents a biological approach to synthesising CR using whole‐cell catalysis by engineered Escherichia coli . First, through screening of critical enzymes from different sources and dual‐enzyme co‐expression strategies, arginine: glycine amidinotransferase (AGAT) from Amycolatopsis kentuckyensis and guanidinoacetate N‐methyltransferase (GAMT) from Mus caroli were introduced to construct the CR biosynthesis pathway, yielding 0.83 g/L CR production. Then, the expression level of GAMT, the critical rate‐limiting enzyme, was optimised by screening the ribosome binding site and N‐terminal coding sequences, resulting in a 92% enhancement of CR production, reaching 1.59 g/L. Next, the endogenous ornithine and methionine cycles were further engineered to boost the synthesis of the precursor guanidinoacetate (GAA) and methyl donor S‐adenosylmethionine (SAM), leading to a 68% increase in CR production, reaching 2.67 g/L. Finally, considering adenosine triphosphate (ATP) is required as a cofactor for SAM biosynthesis, we integrated the reconstitution methionine cycle with a polyphosphate kinase‐based ATP regeneration system, achieving a CR titre of 5.27 g/L with a productivity of 0.22 g/L/h, and the molar conversion of substrate arginine was 71 mol% over 24 h following the engineering process. This study is the first report achieving whole‐cell catalysis of CR production in engineered E. coli with a dual enzyme cascade using arginine as substrate, providing a new platform for CR production and insights into the biosynthesis of high‐value metabolites that rely on ATP consumption.
Mark J. Pallen
Microbial Biotechnology · 2016
Summary Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever‐growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale‐up to the million‐microbial‐genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user‐friendly outputs. The “internet of things” will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd‐sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand‐held sequencers will be analysed on mobile devices. Open‐source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty‐first century, microbial sequence space will remain the final frontier!
Ji‐Won Song, Jung‐Hoo Lee, Uwe T. Bornscheuer et al.
Advanced Synthesis & Catalysis · 2014
Abstract Biotransformation of long‐chain fatty acids into medium‐chain α,ω‐dicarboxylic acids or ω‐aminocarboxylic acids could be achieved with biocatalysts. This study presents the production of α,ω‐dicarboxylic acids (e.g., C 9 , C 11 , C 12 , C 13 ) and ω‐aminocarboxylic acids (e.g., C 11 , C 12 , C 13 ) directly from fatty acids (e.g., oleic acid, ricinoleic acid, lesquerolic acid) using recombinant Escherichia coli ‐based biocatalysts. ω‐Hydroxycarboxylic acids, which were produced from oxidative cleavage of fatty acids via enzymatic reactions involving a fatty acid double bond hydratase, an alcohol dehydrogenase, a Baeyer–Villiger monooxygenase and an esterase, were then oxidized to α,ω‐dicarboxylic acids by alcohol dehydrogenase (ADH, AlkJ) from Pseudomonas putida GPo1 or converted into ω‐aminocarboxylic acids by a serial combination of ADH from P. putida GPo1 and an ω‐transaminase of Silicibacter pomeroyi . The double bonds present in the fatty acids such as ricinoleic acid and lesquerolic acid were reduced by E. coli ‐native enzymes during the biotransformations. This study demonstrates that the industrially relevant building blocks (C 9 to C 13 saturated α,ω‐dicarboxylic acids and ω‐aminocarboxylic acids) can be produced from renewable fatty acids using biocatalysis. magnified image
Abebe Tadesse
Microbial journal · 2023
Microbial communities play a pivotal role in shaping various aspects of human health. Understanding the intricate relationship between humans and microorganisms is crucial for advancing our knowledge in microbiology and developing novel therapeutic strategies. This review article provides a comprehensive overview of the current research on the impact of microbial communities on human health. It covers a wide range of topics, including the gut microbiome, skin microbiota, oral microbiota, and the role of microorganisms in infectious diseases. The article also highlights emerging research areas such as the microbiome-brain axis and the potential therapeutic applications of manipulating microbial communities. Through a critical analysis of the existing literature, this review aims to contribute to the advancement of microbial research and promote the exploration of new avenues for improving human health.
Adrian John
Microbial journal · 2023
Context: The sporadic introduction of deceased plant and animal matter into soils is pivotal in reincorporating organic carbon (C) and nitrogen (N) compounds into biogeochemical cycles. The breakdown of animal remains offers a rich reservoir of C and N, stimulating both local environmental microbial communities and introducing external microbes stemming from the carcasses. Nonetheless, the interactions within these blended microbial communities and the respective impacts of environment- and carcass-originating microbes on C and N cycling remain uncertain. To determine whether environment-derived, carcass-derived, or the merged microbial communities exerted a greater influence on C and N cycling, we conducted controlled laboratory experiments mimicking carcass decomposition hotspots by combining carcass decomposition fluids with soils. We selectively sterilized the decomposition fluid and/or soil to remove microbial communities, creating distinct combinations of environment- and carcass-derived communities, and incubated the treatments at three temperatures (around 15, 25, and 35 °C). Findings: Carcass-sourced bacteria persisted in soils in our simulated decomposition scenarios, albeit in modest quantities. Hybrid communities demonstrated increased respiration rates at around 15 and 35 °C compared to singular soil or carcass communities. Interestingly, at higher temperatures, mixed communities exhibited reduced diversity but higher respiration, suggesting functional overlap. Additionally, mixed community treatments furnished evidence that microbes linked with carcasses might play a role in ammonification and denitrification, while nitrification was mainly carried out by indigenous soil organisms. Conclusions: Our investigation yields valuable insights into the dynamics of microbial communities converging during carcass decomposition and their functions in the recycling of carcasses within terrestrial ecosystems.
Michael R. Hoffmann, Bruce C. Faust, Fern A. Panda et al.
Applied and Environmental Microbiology · 1981
Different strains of Thiobacillus ferrooxidans and Thiobacillus thiooxidans were used to catalyze the oxidative dissolution of iron pyrite, FeS 2 , in nine different coal samples. Kinetic variables and parametric factors that were determined to have a pronounced effect on the rate and extent of oxidative dissolution at a fixed Po 2 were: the bacterial strain, the nitrogen/phosphorus molar ratio, the partial pressure of CO 2 , the coal source, and the total reactive surface area of FeS 2 . The overall rate of leaching, which exhibited a first-order dependence on the total surface area of FeS 2 , was analyzed mathematically in terms of the sum of a biochemical rate, ν 1 , and a chemical rate, ν 2 . Results of this study show that bacterial desulfurization (90 to 98%) of coal samples which are relatively high in pyritic sulfur can be achieved within a time-frame of 8 to 12 days when pulp densities are ≤20% and particle sizes are ≤74 μm. The most effective strains of T. ferrooxidans were those that were isolated from natural systems, and T. ferrooxidans ATCC 19859 was the most effective pure strain. The most effective nutrient media contained relatively low phosphate concentrations, with an optimal N/P molar ratio of 90:1. These results suggest that minimal nutrient additions may be required for a commercial desulfurization process.
Wolfgang Stampfer, Klaus Edegger, Birgit Kosjek et al.
Advanced Synthesis & Catalysis · 2004
Abstract Lyophilised cells of various Rhodococcus spp. were employed in an efficient hydrogen transfer‐like process for the asymmetric bioreduction of heteroaryl methyl ketones using 2‐propanol as hydrogen donor. Besides the genus Rhodococcus , only Mycoplana rubra R14 showed a comparable stability towards elevated concentrations of the co‐substrate 2‐propanol. Among the organisms tested, Rhodococcus ruber DSM 44541 and DSM 43338 showed best activity and selectivity. With these strains, the reaction proceeded with high stereoselectivity (ee>99%) and predictable stereochemical outcome regardless of the nature of the heteroaromatic ring system. The reaction could be performed at the exceptional substrate concentration of up to 0.4 mol L −1 in an environmentally friendly aqueous‐organic solvent mixture at room temperature and is easy to handle, thus providing a very practical tool to access enantiopure 1‐heteroarylethanols.
Bin Gu, Haisheng Xie, Xuehong Zhang et al.
Reaction Chemistry & Engineering · 2019
Cascade reactions, i.e. , biosynthesis of OMPs and chemical modification of hydrophobic OMPs with water-soluble MSG, are carried out successfully by IPTC.
Chukwuemeka Kingsley John, Jaan H. Pu, Rodrigo Moruzzi et al.
Topics in Catalysis · 2024
Abstract Since the building roof acts as hub for atmospheric sediment deposition, the attached microbes can enter rainwater storage tank with ease to cause health issue for rainwater users. This study aims to explore the trend of roof-top deposited microbes in the different areas of Ikorodu local Government Area at Lagos, Nigeria. This paper also tests the hypothesis that the roof sediment deposition being a significant source to home bacteria. The total deposition rate on the roof for 34 weeks, which include 17 rainy and 17 dry weeks, were investigated. The enumerated bacteria was obtained from the roof deposit samples, where four representative different sites have been analysed to study the solid depositions and microbes within the area thoroughly. The sites were selected judging by their levels of sanitation and vegetation rate. The experimental investigations showed that enumerated microbes and total suspended solid (TSS) depositions in the different areas were higher in the dry season compared to rainy season, and the highest deposition was experienced in the Harmattan period. In addition, the results showed that areas with poor drainage infrastructure and poor sanitation have the roof-top deposition with higher bacterial count than good sanitation areas; while the unpaved and unvegetated areas produced higher deposits than the paved and vegetated areas. In terms of contamination sources, this study has illustrated that the particulate deposition on the roof-top prior to collection has further contaminated the roof-harvested rainwater.
Armaan Patel, David W. Mulder, Dieter Söll et al.
Frontiers in Catalysis · 2022
Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.
Haisheng Xie, Wenyu Zhao, Daniel Chikere Ali et al.
Catalysis Science & Technology · 2021
The Pickering emulsion interface is an exceptional habitat for bacteria to grow by simultaneously utilizing hydrophobic and hydrophilic chemicals.
Charles J. Sih, Ching‐Shih Chen
Angewandte Chemie International Edition in English · 1984
Abstract Microbial asymmetric reduction of ketones is a method widely used for the preparation of chiral alcohols. The present progress report deals with the basic concepts that govern enantioselectivity of enzymes and intact cells. Strategies to control the stereochemical course of microbial reductions of carbonyl compounds and the relationship of substrate structure to enantioselectivity are considered.
Julia M. West, Ian G. McKinley, Simcha Stroes-Gascoyne
ASME 2009 12th International Conference on Environmental Remediation and Radioactive Waste Management, Volume 2 · 2009
A detailed assessment of studies of oxidising redox fronts around fractures at depth in otherwise “reducing” environments suggests that the usual explanation, in terms of past disturbances that have resulted in deep penetration of oxidising water, are incompatible with hydrogeological and/or geochemical observations. An alternative hypothesis, microbial catalysis of kinetically slow or hindered reactions involving oxyanions such as sulphate or carbonate, appears potentially more credible. Although still not always taken into account by the geochemical community, the role of microbial metabolism in low temperature geochemistry is supported by the rapidly expanding database on subsurface microbial populations. These populations are demonstrated to be viable and, therefore, could potentially be active at levels close to or below current detection limits in deep geological systems. Indeed, inspection of information available from several analogue studies or repository site characterisation programmes suggests that such activity may explain some of the geochemical anomalies encountered. This paper examines the current (indirect) evidence for microbial redox catalysis in relevant subsurface rock matrix environments and considers the implications that this would have for the development of site understanding — and in particular the identification of factors that may distinguish between different locations during site selection. Further, it examines the wider implications of more extensive roles of microbes in repository systems on the overall post-closure safety case and the need for further focused analogue studies to develop answers to these open questions.
Menno J. Sorgedrager, Fred van Rantwijk, Gjalt W. Huisman et al.
Advanced Synthesis & Catalysis · 2008
Abstract The biocatalytic reduction of β‐keto esters and some aromatic ketones in the presence of a variety of ketoreductases from different microbial origins was investigated. The prochiral selectivity was generally high and both product enantiomers could be obtained by a proper choice of enzyme. Aromatic ketones reacted slower than the esters but the prochiral selectivity was often high. The organic cosolvent tolerance of these enzymes was rather variable but useful activity could be maintained in a number of cases. Reduction of the oxidized cofactors NAD and NADP, employing 2‐propanol as a sacrificial reductant, was catalyzed by the ketoreductases from Rhodococcus erythropolis and Lactobacillus kefir , respectively.
Chunling Ma, Yuhua Wang, Kun Guo et al.
Catalysis Science & Technology · 2025
This review summarizes state-of-the-art and future development of enzymatic electrosynthesis systems based on multi-enzyme catalysis or coupled with microbial transformation.