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PubMed2003

Comparison of di-n-methyl phthalate biodegradation by free and immobilized microbial cells.

OBJECTIVE: To compare the biodegradation of di-n-methyl pathalate by free and immobilized microbial cells. METHODS: The enrichment and isolation technique was used to isolate the microorganism. The PAV-entrapment method was utilized to immobilize the microorganisms. The scanning electron microscophy (SEM) was used to observe the growth and distribution of microbial cells immobilized inside the PVA bead gels. The GC/MS method was used to identify the main intermediates of DMP degradation. RESULTS: The microbial cells could grow quite well in PVA gel. The metabolic pathway did not change before and after immobilization of the microbial cells. The degradation rate of immobilized cells was higher than that of free cells. CONCLUSION: The immobilized microbial cells possess advantages than free cells when applied to the biodegradation of toxic organic pollutants.

Bacteria↗
PubMed2001

The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolic enzymes and their organization into metabolic pathways. Currently, it contains information on over 400 enzymes. In the last year the enzyme page was enhanced to contain more internal and external links; it also displays the different metabolic pathways in which each enzyme participates. In collaboration with the Nomenclature Commission of the International Union of Biochemistry and Molecular Biology, 35 UM-BBD enzymes were assigned complete EC codes during 2000. Bacterial oxygenases are heavily represented in the UM-BBD; they are known to have broad substrate specificity. A compilation of known reactions of naphthalene and toluene dioxygenases were recently added to the UM-BBD; 73 and 108 were listed respectively. In 2000 the UM-BBD is mirrored by two prestigious groups: the European Bioinformatics Institute and KEGG (the Kyoto Encyclopedia of Genes and Genomes). Collaborations with other groups are being developed. The increased emphasis on UM-BBD enzymes is important for predicting novel metabolic pathways that might exist in nature or could be engineered. It also is important for current efforts in microbial genome annotation.

Bacteria↗
PubMed2026

In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.

BACKGROUND: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison. RESULTS: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence. CONCLUSIONS: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.

Metabolic Networks and Pathways↗
PubMed2004

Creation of a shikimate pathway variant.

The competition between the Escherichia coli carbohydrate phosphotransferase system and 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase for phosphoenolpyruvate limits the concentration and yield of natural products microbially synthesized via the shikimate pathway. To circumvent this competition for phosphoenolpyruvate, a shikimate pathway variant has been created. 2-Keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases encoded by Escherichia coli dgoA and Klebsiella pneumoniae dgoA are subjected to directed evolution. The evolved KDPGal aldolase isozymes exhibit 4-8-fold higher specific activities relative to that for native KDPGal aldolase with respect to catalyzing the condensation of pyruvate and d-erythrose 4-phosphate to produce DAHP. To probe the ability of the created shikimate pathway variant to support microbial growth and metabolism, growth rates and synthesis of 3-dehydroshikimate are examined for E. coli constructs that lack phosphoenolpruvate-based DAHP synthase activity and rely on evolved KDPGal aldolase for biosynthesis of shikimate pathway intermediates and products.

Aldehyde-Lyases↗
PubMed1974

Microbial metabolism of the pyridine ring. Metabolism of 2- and 3-hydroxypyridines by the maleamate pathway in Achromobacter sp.

1. Washed suspensions of two Achromobacter species (G2 and 2L), capable of growth upon 2- and 3-hydroxypyridine respectively as sources of C and N, rapidly oxidized their growth substrate pyridine-2,5-diol (2,5-dihydroxypyridine) and the putative ring-cleavage product maleamate without a lag. Suspensions derived from fumarate plus (NH(4))(2)SO(4) cultures were unable to do so. 2. Extracts of both bacteria oxidized pyridine-2,5-diol with the stoicheiometry of an oxygenase forming 1mol of NH(3)/mol of substrate. 3. Heat-treated extracts, however, formed maleamate and formate with little free NH(3). 4. The conversion of maleamate into maleate plus NH(3) by extracts of strain 2L, fractionated with (NH(4))(2)SO(4), and the metabolism of maleamate and maleate to fumarate by extracts of both strains demonstrated the existence of the enzymes catalysing each reaction of the maleamate pathway in these bacteria. 5. The pyridine-2,5-diol dioxygenase (mol.wt. approx. 340000) in extracts of these Achromobacter species required Fe(2+) (1.7mum) to restore full activity after dialysis or treatment with chelating agents; the enzyme from strain 2L also had a specific requirement for l-cysteine (6.7mm), which could not be replaced by GSH or dithiothreitol. 6. The oxygenase was strongly inhibited in a competitive manner by the isomeric pyridine-2,3- and -3,4-diols.

Alcaligenes↗
PubMed2026

Genome-resolved analysis reveals disruption of gut microbial vitamin B and K2 biosynthesis during Toxoplasma gondii infection in mice.

UNLABELLED: Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness &#x2265;90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in &#x3b1;-diversity of vitamin biosynthesis pathways during acute infection, and a clear &#x3b2;-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD+ precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD+ metabolism. IMPORTANCE: Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD+ precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD+-related metabolism may contribute to host redox adaptation during T. gondii infection.

B vitamins↗
PubMed1999

Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes.

Computational analysis of complete genomes, followed by experimental testing of emerging hypotheses--the area of research often referred to as 'functional genomics'--aims at deciphering the wealth of information contained in genome sequences and at using it to improve our understanding of the mechanisms of cell function. This review centers on the recent progress in the genome analysis with special emphasis on the new insights in enzyme evolution. Standard methods of predicting functions for new proteins are listed and the common errors in their application are discussed. A new method of improving the functional predictions is introduced, based on a phylogenetic approach to functional prediction, as implemented in the recently constructed Clusters of Orthologous Groups (COG) database (available at http:@www.ncbi.nlm.nih.gov/COG). This approach provides a convenient way to characterize the protein families (and metabolic pathways) that are present or absent in any given organism. Comparative analysis of microbial genomes based on this approach shows that metabolic diversity generally correlates with the genome size-parasitic bacteria code for fewer enzymes and lesser number of metabolic pathways than their free-living relatives. Comparison of different genomes reveals another evolutionary trend, the non-orthologous gene displacement of some enzymes by unrelated proteins with the same cellular function. An examination of the phylogenetic distribution of such cases provides new clues to the problems of biochemical evolution, including evolution of glycolysis and the TCA cycle.

Databases, Factual↗
PubMed1999

Discovery and development of antineoplastic agents from natural sources.

Nature has provided many effective anticancer agents in current use, such as the microbially derived drugs; dactinomycin; bleomycin and doxorubicin; and the plant-derived drugs, vinblastine, irinotecan, topotecan, etoposide, and paclitaxel. The search for novel antitumor agents from natural sources continues through collaboration among scientists worldwide in the investigation of coral reefs, rainforests, and deep subsurface thermal vents for novel bioactive compounds. The potential for drug discovery is being further enhanced by recent advances in procedures for microbial cultivation and the extraction of nucleic acids from environmental samples, resulting in the identification of novel microbes that provide a vast untapped reservoir of genetic and metabolic diversity. Manipulation of the biosynthetic pathways of microbial polyketides through genetic engineering permits the biosynthesis of bioactive polyketides not generated naturally.

Animals↗
PubMed2003

Acetylacetone-cleaving enzyme Dke1: a novel C-C-bond-cleaving enzyme from Acinetobacter johnsonii.

The toxicity of acetylacetone has been demonstrated in various studies. Little is known, however, about metabolic pathways for its detoxification or mineralization. Data presented here describe for the first time the microbial degradation of acetylacetone and the characterization of a novel enzyme that initiates the metabolic pathway. From an Acinetobacter johnsonii strain that grew with acetylacetone as the sole carbon source, an inducible acetylacetone-cleaving enzyme was purified to homogeneity. The corresponding gene, coding for a 153 amino acid sequence that does not show any significant relationship to other known protein sequences, was cloned and overexpressed in Escherichia coli and gave high yields of active enzyme. The enzyme cleaves acetylacetone to equimolar amounts of methylglyoxal and acetate, consuming one equivalent of molecular oxygen. No exogenous cofactor is required, but Fe(2+) is bound to the active protein and essential for its catalytic activity. The enzyme has a high affinity for acetylacetone with a K (m) of 9.1 microM and a k(cat) of 8.5 s(-1). A metabolic pathway for acetylacetone degradation and the putative relationship of this novel enzyme to previously described dioxygenases are discussed.

Acetates↗
PubMed2006

Investigating heavy metal resistance, bioaccumulation and metabolic profile of a metallophile microbial consortium native to an abandoned mine.

Contaminated sites represent new ecological niches where historical pollution has originated an unusual microbial biodiversity. The knowledge of these microorganisms contributes to the discovery of new pathways and metabolic networks and may offer potential solutions for damaged areas. In the present work seven microbial consortia have been isolated from an abandoned mine of blend and galena (Ingurtosu, Italy) through a selection for resistance to zinc (tested up to 40 mM in solution). All the consortia were able to accumulate zinc and the best accumulator, named Ing5, has been studied for the following characteristics: resistance and accumulation of Zn, Cd, Hg, bioaccumulation mechanisms of Zn, and influence of Zn and Cd on the metabolic profile. The results indicate that the consortium Ing5 bears resistance systems for Cd and Hg as well as Zn and that, for some of the 5 isolates belonging to Ing5, the resistance thresholds are higher in consortium than in pure culture. The prevalent mechanism for zinc accumulation can be reasonably considered to be metabolism-dependent, inducible and regulated by metal concentrations. The study on the metabolic profile, carried out by the Biolog system, shows that Zn exerts a very low influence on the metabolic profile and that this influence can also be positive; Cd has a stronger negative influence but that, despite this, the consortium is able to maintain a wide metabolic potential in the presence of heavy metals. These features of Ing5 make it a good candidate for biotechnological applications and for further investigation of the degradation of organic pollutants in the presence of metals.

Biodegradation, Environmental↗
PubMed2026

Associations between gut microbiota on carcass traits and meat quality in Neijiang pigs, Yorkshire pigs, and their hybrids.

This study was designed as an exploratory analysis to compare carcass performance, meat quality traits, and gut microbiota of Neijiang pigs (NN), Yorkshire pigs (YY), and Yorkshire &#xd7; Neijiang hybrid pigs (YN), with the goal of generating testable hypotheses regarding potential links between gut microbial composition and production phenotypes. Compared with NN pigs, YN hybrids exhibited improved carcass performance while inheriting the favorable meat quality characteristics of Neijiang pigs. The results of 16S rRNA sequencing analysis showed that the relative abundance of the microbiota was similar to that of NN pigs. LDA effect size (LEfSe) results showed that Streptococcus, Treponema, probable_genus_10 and Fibrobacter were the differentially enriched taxa in YN pigs (p < 0.05). Correlation analysis was performed on carcass, meat quality and intestinal microbiota screened out by LEfSe. The results showed that Akkermansia tended to positively associate with body length and oblique length in YN pigs; Dialister correlated positively with dressing rate and pH45min; Treponema showed positive trends with a*45min and a*24h (p < 0.05). Finally, the correlation network model preliminarily mapped associations among production traits, gut microbiota, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for exploratory screening. Nine core microbial taxa exhibited close correlations with phenotypic indicators, which implied that these microbes might modulate metabolic pathways to shape pig performance. Overall, hybrids inherited superior parental carcass and meat quality but harbored unique gut microbial communities relative to purebreds-these preliminary correlative observations generate new hypotheses that gut microbiota may contribute to heterosis-associated phenotypic advantages, which require further targeted validation.

Animals↗
PubMed1989

Evolutionary aspects of urea cycle enzyme genes.

The functions and expression pattern of urea cycle enzymes have undergone considerable changes during the course of evolution. Sequence analyses shows that urea cycle enzymes from mammals are homologous to microbial enzymes of the arginine-metabolic pathway. Recently, an unexpected relationship was found between argininosuccinate lyase (EC 4.3.2.1), the fourth enzyme of the cycle, and delta-crystallin, a lens structural protein of birds and reptiles.

Animals↗
PubMed2002

Environmental fate of triclopyr.

Triclopyr is nonpersistent in surface water. It has limited mobility and low to medium persistence in soil. Considering its adsorptive characteristics and that it dissipates via multiple pathways, such as photolysis, plant metabolism, and microbial degradation, its potential to leach to depth in soil and to contaminate groundwater is low. This conclusion is corroborated by field leaching and groundwater monitoring data, both derived from use areas in several states in the U.S. and sites directly near handling/mixing facilities. Even when detected in the groundwater, e.g., five reported detections in two states in the U.S., the highest concentration was well below the estimated HAL of the USEPA.

Absorption↗
PubMed2003

The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining.

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.

Biodegradation, Environmental↗
PubMed2001

Update on antifolate drugs targets.

Antifolate drugs are molecules directed to interfere with the folate metabolic pathway at some level. They can be recognized among the first rationally designed compounds applying the principle of structural analogy with the substrate developing the antimetabolite strategy. This strategy has taken advantage of the basic different features of the microbial and human folate metabolism and therefore allows targeting the pathway at different steps generating a specificity tools for Medicinal Chemists. Two main problems are giving renewed importance to such targets and therefore improving the efforts to discover new targets in the folate metabolism area. The first one is the increasing resistance to the present drugs due to different mechanisms such as the enzyme modification and the increased production of enzymes with not well recognized importance. The second one is the development of techniques directed to highlight the interference at genetic level of molecular probes as antifolate drug to develop new enzymes previously unknown. This approach is defined as genetic approach to drug discovery, from gene to drugs. The present article describes the importance in drug design and discovery of some antifolate targets among the best known at the present status of research such as thymidylate synthase (TS), dhydrofolate reductases, (DHFR) serine hydroxymethyltransferase (SHMT), folyilpolyglutamyl synthetase (FPGS), gamma-glutamyl hydrolase (gamma-GH), glycinamide-ribonucleotide transformylase (GARTfase), amino-imidazole-carboxamide-ribonucleotide transformylase (AICARTfase) and Folate transporters. Discovery, known functions, structure/function studies and inhibition will be described.

Carrier Proteins↗
PubMed2004

Bacterial responses to neutrophil phagocytosis.

PURPOSE OF REVIEW: This review focuses on adaptive bacterial interactions with neutrophils, emphasizing information communicated within the past year about bacterial factors that respond to contact with or phagocytosis by PMN. RECENT FINDINGS: Since the discovery of type III and IV secretion, progress in the analysis of bacterial interactions with host phagocytes has been extensive but largely focused on the macrophage. The remarkable growth of information about bacterial subversion of macrophage metabolism has been summarized in several excellent reviews. The scope of progress on neutrophil-bacteria interactions is more limited and dominated by recent studies of the granulocyte pathogen, Anaplasma phagocytophilum, the agent of granulocytic ehrlichiosis. SUMMARY: For many pathogens, contact with or ingestion by phagocytes elicits a vigorous but varied microbial response. The response repertoire includes activation of type III and type IV secretion systems that inject effector molecules into the host cell. Effectors modify host cell signaling and metabolic pathways to favor survival of the microbe. Whereas microbial secretory structures are few in kind and relatively conserved, effector molecules are numerous and variable. Effectors may promote phagocytosis by nonphagocytic cells or suppress phagocytosis by macrophages and neutrophils. They may suppress assembly or misdirect localization of the phagocyte NADPH oxidase that is responsible for generating toxic oxidants, and they may suppress phagosome-lysosome fusion. Phagocytosed bacteria may also up-regulate the expression of defensive proteins that attenuate the effects of phagocyte-derived antimicrobial toxins. These pathogenic stratagems probably have their origins in the competition among single-celled organisms, eukaryotes versus prokaryotes, that arose early in evolution.

Anaplasma phagocytophilum↗
PubMed2002

Microbial sensors on a respiratory basis for wastewater monitoring.

In respect of their rapidity, their online capabilities, and their moderate costs, biosensing systems generally offer an attractive alternative to the existing methods of water analysis. Additionally, one particular advantage of microbial biosensors is the ability to measure direct effects on living cells, e.g., their respiratory activity and its alteration caused by environmental pollutants. It is true that microbial sensors, often do not provide the optimum solution for the determination of individual analytes when compared to established physico-chemical analysis methods. However, these biosensing devices are predestined for the summary determination of environmentally relevant compounds and their complex effects, respectively. For this reason, microbial sensors allow an integral evaluation of the degree of environmental pollution including the interaction of various compounds. Moreover, in some cases specific metabolic pathways in microorganisms are used, resulting in the development of microbial sensors for the more selective analysis for those compounds or pollutants, which cannot be measured by simple enzyme reactions, e.g., the determination of aromatic compounds and heavy metals. This chapter gives an overview of microbiological biosensors on respiratory basis for the measurement of the following environmentally relevant compounds: inorganic N-compounds, heavy metals, organic xenobiotics and the estimation of sum parameters or so-called complex parameters such as BOD, ADOC, N-BOD, and the inhibition of nitrification.

Bacteria↗