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five clinical cases of necropsobacter rosorum bacteremia.five cases of bacteremia with necropsobacter rosorum are described, originating from intra-abdominal infections or localized soft tissue infections in the pelvic region. n. rosorum is consistently misidentified by commercial identification systems, which may delay recognition of this organism as a human pathogen.201323390273
genomic and functional analyses of the gentisate and protocatechuate ring-cleavage pathways and related 3-hydroxybenzoate and 4-hydroxybenzoate peripheral pathways in burkholderia xenovorans lb400.in this study, the gentisate and protocatechuate pathways in burkholderia xenovorans lb400 were analyzed by genomic and functional approaches, and their role in 3-hydroxybenzoate (3-hba) and 4-hydroxybenzoate (4-hba) degradation was proposed. the lb400 genome possesses two identical mhbrtdhi gene clusters encoding the gentisate pathway and one mhbm gene encoding a 3-hba 6-hydroxylase that converts 3-hba into gentisate. the pca genes encoding the protocatechuate pathway and the poba gene encoding ...201323418504
specificity in transition state binding: the pauling model revisited.linus pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. the observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. we review experimental results that support the proposal that pauling's model provides a satisfactory explanation for the rate accelerations fo ...201323327224
degradation of the acyl side chain of the steroid compound cholate in pseudomonas sp. strain chol1 proceeds via an aldehyde intermediate.bacterial degradation of steroids is widespread, but the metabolic pathways have rarely been explored. previous studies with pseudomonas sp. strain chol1 and the c(24) steroid cholate have shown that cholate degradation proceeds via oxidation of the a ring, followed by cleavage of the c(5) acyl side chain attached to c-17, with 7α,12β-dihydroxy-androsta-1,4-diene-3,17-dione (12β-dhadd) as the product. in this study, the pathway for degradation of the acyl side chain of cholate was investigated i ...201323204454
ground state destabilization from a positioned general base in the ketosteroid isomerase active site.we compared the binding affinities of ground state analogues for bacterial ketosteroid isomerase (ksi) with a wild-type anionic asp general base and with uncharged asn and ala in the general base position to provide a measure of potential ground state destabilization that could arise from the close juxtaposition of the anionic asp and hydrophobic steroid in the reaction's michaelis complex. the analogue binding affinity increased ~1 order of magnitude for the asp38asn mutation and ~2 orders of m ...201323311398
strong inter-population cooperation leads to partner intermixing in microbial communities.patterns of spatial positioning of individuals within microbial communities are often critical to community function. however, understanding patterning in natural communities is hampered by the multitude of cell-cell and cell-environment interactions as well as environmental variability. here, through simulations and experiments on communities in defined environments, we examined how ecological interactions between two distinct partners impacted community patterning. we found that in strong coop ...201323359860
a pks/nrps/fas hybrid gene cluster from serratia plymuthica rvh1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics.serratia plymuthica strain rvh1, initially isolated from an industrial food processing environment, displays potent antimicrobial activity towards a broad spectrum of gram-positive and gram-negative bacterial pathogens. isolation and subsequent structure determination of bioactive molecules led to the identification of two polyamino antibiotics with the same molecular structure as zeamine and zeamine ii as well as a third, closely related analogue, designated zeamine i. the gene cluster encoding ...201323349809
genome sequence of pseudomonas sp. strain chol1, a model organism for the degradation of bile salts and other steroid compounds.bacterial degradation of steroid compounds is of high ecological and biotechnological relevance. pseudomonas sp. strain chol1 is a model organism for studying the degradation of the steroid compound cholate. its draft genome sequence is presented and reveals one gene cluster responsible for the metabolism of steroid compounds.201323405354
bioanodes/biocathodes formed at optimal potentials enhance subsequent pentachlorophenol degradation and power generation from microbial fuel cells.bioanodes formed at an optimal potential of 200 mv vs. she and biocathodes developed at -300 mv vs. she in bioelectrochemical cells (becs) enhanced the subsequent performances of microbial fuel cells (mfcs) compared to the un-treated controls. while the startup times were reduced to 320 h (bioanodes) and 420-440 h (biocathodes), pcp degradation rates were improved by 28.5% (bioanodes) and 21.5% (biocathodes), and power production by 41.7% (bioanodes) and 44% (biocathodes). accordingly, there wer ...201323747520
a novel transcriptional repressor phar for the steroid-inducible expression of the 3,17β-hydroxysteroid dehydrogenase gene in comamonas testosteroni atcc11996.comamonas testosteroni is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons and might be used in the bioremediation of contaminated environments. 3,17β-hydroxysteroid dehydrogenase (3,17β-hsd) from c. testosteroni is a member of the short-chain dehydrogenase/reductase (sdr) superfamily and a key enzyme in steroid degradation. the genome of c. testosteroni atcc11996 was sequenced in our previous work. in addition to the gene coding for 3,17β-hsd (βhsd), a novel transcr ...201323295223
assimilation of aromatic compounds by comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria.comamonas testosteroni strain cnb-1 was isolated from activated sludge and has been investigated for its ability to degrade 4-chloronitrobenzene. results from this study showed that strain cnb-1 grew on phenol, gentisate, vanillate, 3-hydroxybenzoate (3hb), and 4-hydroxybenzoate (4hb) as carbon and energy sources. proteomic data and enzyme activity assays suggested that vanillate, 3hb, and 4hb were degraded in strain cnb-1 via protocatechuate (pca) 4,5-cleavage pathway. the genetics and biochemi ...201322996279
comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus comamonas.a facultatively anaerobic bacterium, strain cy01(t), isolated from subterranean forest sediment collected from guangdong province, china, was investigated using a polyphasic taxonomic approach. the cells were short rods, gram-negative, non-sporulating and motile. phylogenetic analysis based on 16s rrna gene sequences showed that strain cy01(t) showed highest sequence similarities to comamonas thiooxydans s23(t) (98.0 %), comamonas testosteroni jcm 5832(t) (97.9 %), comamonas koreensis kctc 12005 ...201322581903
comamonas testosteroni uses a chemoreceptor for tricarboxylic acid cycle intermediates to trigger chemotactic responses towards aromatic compounds.bacterial chemotaxis towards aromatic compounds has been frequently observed; however, knowledge of how bacteria sense aromatic compounds is limited. comamonas testosteroni cnb-1 is able to grow on a range of aromatic compounds. this study investigated the chemotactic responses of cnb-1 to 10 aromatic compounds. we constructed a chemoreceptor-free, non-chemotactic mutant, cnb-1δ20, by disruption of all 19 putative methyl-accepting chemotaxis proteins (mcps) and the atypical chemoreceptor in stra ...201324102855
multi-enzymatic one-pot reduction of dehydrocholic acid to 12-keto-ursodeoxycholic acid with whole-cell biocatalysts.ursodeoxycholic acid (udca) is a bile acid of industrial interest as it is used as an agent for the treatment of primary sclerosing cholangitis and the medicamentous, non-surgical dissolution of gallstones. currently, it is prepared industrially from cholic acid following a seven-step chemical procedure with an overall yield of <30%. in this study, we investigated the key enzymatic steps in the chemo-enzymatic preparation of udca-the two-step reduction of dehydrocholic acid (dhca) to 12-keto-urs ...201322806613
degradation of norgestrel by bacteria from activated sludge: comparison to progesterone.natural and synthetic progestagens in the environment have become a concern due to their adverse effects on aquatic organisms. laboratory studies were performed to investigate aerobic biodegradation of norgestrel by bacteria from activated sludge in comparison with progesterone, and to identify their degradation products and biotransformation pathways. the degradation of norgestrel followed first order reaction kinetics (t1/2 = 12.5 d), while progesterone followed zero order reaction kinetics (t ...201323952780
novel whole-cell biocatalysts with recombinant hydroxysteroid dehydrogenases for the asymmetric reduction of dehydrocholic acid.ursodeoxycholic acid is an important pharmaceutical so far chemically synthesized from cholic acid. various biocatalytic alternatives have already been discussed with hydroxysteroid dehydrogenases (hsdh) playing a crucial role. several whole-cell biocatalysts based on a 7α-hsdh-knockout strain of escherichia coli overexpressing a recently identified 7β-hsdh from collinsella aerofaciens and a nad(p)-bispecific formate dehydrogenase mutant from mycobacterium vaccae for internal cofactor regenerati ...201222581067
molecular characterization of three 3-ketosteroid-δ(1)-dehydrogenase isoenzymes of rhodococcus ruber strain chol-4.rhodococcus ruber strain chol-4 isolated from a sewage sludge sample is able to grow on minimal medium supplemented with steroids, showing a broad catabolic capacity. this paper reports the characterization of three different 3-ketosteroid-δ(1)-dehydrogenases (kstds) in the genome of r. ruber strain chol-4. the genome of this strain does not contain any homologues of a 3-keto-5α-steroid-δ(4)-dehydrogenase (kst4d or tesi) that appears in the genomes of rhodococcus erythropolis sq1 or comamonas te ...201222771584
the fe-type nitrile hydratase from comamonas testosteroni ni1 does not require an activator accessory protein for expression in escherichia coli.we report herein the functional expression of an fe-type nitrile hydratase (nhase) without the co-expression of an activator protein or the escherichia coli chaperone proteins groes/el. soluble protein was obtained when the α- and β-subunit genes of the fe-type nhase comamonas testosteroni ni1 (ctnhase) were synthesized with optimized e. coli codon usage and co-expressed. as a control, the fe-type nhase from rhodococcus equi tg328-2 (renhase) was expressed with (renhase(+act)) and without (renha ...201222713452
two cases of bacteremia due to an unusual pathogen, comamonas testosteroni in iran and a review literature.here we describe two cases of bacteremia caused by comamonas testosteroni in two malignant patients, a 10-year-old boy with brain medulloblastoma and a 19-year-old girl with osteosarcoma admitted in the same hospital at short intervals. this is the first report in iran on this low inherent virulence organism as a human pathogen.201222706196
oligomerization and negative autoregulation of the lysr-type transcriptional regulator hsdr from comamonas testosteroni."3α-hydroxysteroid dehydrogenase/carbonyl reductase regulator" (hsdr) from comamonas testosteroni (c. testosteroni) was identified as a member of the lysr-type transcriptional regulator (lttr) family. we have shown previously that hsdr activates the expression of the hsda gene, encoding 3α-hydroxysteroid dehydrogenase/carbonyl reductase (3α-hsd/cr), which is an important enzyme involved in the degradation of steroid compounds. phylogenetic analysis indicated that hsdr is related to the contact-r ...201222684002
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins.the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ...201222192777
Vanillin Catabolism in Rhodococcus jostii RHA1.Genes encoding vanillin dehydrogenase (vdh) and vanillate O-demethylase (vanAB) were identified in Rhodococcus jostii RHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes.201222057861
in the nadr regulon, adhesins and diverse meningococcal functions are regulated in response to signals in human saliva.the neisseria meningitidis regulator nadr was shown to repress expression of the nada adhesin and play a major role in nada phase-variable expression. in this study, we identified through microarray analysis over 30 genes coregulated with nada in the nadr mutant and defined members of the nadr regulon through in vitro dna-binding assays. two distinct types of promoter architectures (i and ii) were identified for nadr targets, differing in both the number and position of nadr-binding sites. all n ...201222081399
microbial community analysis in biocathode microbial fuel cells packed with different materials.biocathode mfcs using microorganisms as catalysts have important advantages in lowering cost and improving sustainability. electrode materials and microbial synergy determines biocathode mfcs performance. in this study, four materials, granular activated carbon (gac), granular semicoke (gs), granular graphite (gg) and carbon felt cube (cfc) were used as packed cathodic materials. the microbial composition on each material and its correlation with the electricity generation performance of mfcs we ...201222458430
two enzymes of a complete degradation pathway for linear alkylbenzenesulfonate (las) surfactants: 4-sulfoacetophenone baeyer-villiger monooxygenase and 4-sulfophenylacetate esterase in comamonas testosteroni kf-1.complete biodegradation of the surfactant linear alkylbenzenesulfonate (las) is accomplished by complex bacterial communities in two steps. first, all las congeners are degraded into about 50 sulfophenylcarboxylates (spc), one of which is 3-(4-sulfophenyl)butyrate (3-c(4)-spc). second, these spcs are mineralized. 3-c(4)-spc is mineralized by comamonas testosteroni kf-1 in a process involving 4-sulfoacetophenone (sap) as a metabolite and an unknown inducible baeyer-villiger monooxygenase (bvmo) t ...201223001656
characterization of bacteria in ballast water using maldi-tof mass spectrometry.to evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms). since international maritime organization (imo) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of vibrio, enterococci and coliforms. seawater samples collected fr ...201222685576
gene cluster encoding cholate catabolism in rhodococcus spp.bile acids are highly abundant steroids with important functions in vertebrate digestion. their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. we found that rhodococcus jostii rha1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. the transcriptome of rha1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. reverse transcript ...201223024343
analysis of the bacterial diversity existing on animal hide and wool: development of a preliminary pcr-restriction fragment length polymorphism fingerprint database for identifying isolates.twenty-one bacterial strains were isolated from imported cattle hide and rabbit wool using two types of media, nutrient broth, and nutrient broth with serum. the bacteria identified were brevibacillus laterosporus, leclercia adecarboxylata, peptococcus niger, bacillus circulans, raoultella ornithinolytica, bacillus subtilis, bacillus cereus, bacillus thermobacillus, bacillus choshinensis, bacillus sphaericus, acinetobacter haemolyticus, sphingomonas paucimobilis, bacillus thuringiensis, staphylo ...201223451394
role of sex steroid hormones in bacterial-host interactions.sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ...201223509808
role of sex steroid hormones in bacterial-host interactions.sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ...201223509808
novel dehalogenase mechanism for 2,3-dichloro-1-propanol utilization in pseudomonas putida strain mc4.a pseudomonas putida strain (mc4) that can utilize 2,3-dichloro-1-propanol (dcp) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. degradation of dcp was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kda monomeric protein (dppa) that was isolated from cell lysate. the dppa gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that po ...201222752160
reciprocal tripartite interactions between the aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence.dengue virus is one of the most important arboviral pathogens and the causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. it is transmitted between humans by the mosquitoes aedes aegypti and aedes albopictus, and at least 2.5 billion people are at daily risk of infection. during their lifecycle, mosquitoes are exposed to a variety of microbes, some of which are needed for their successful development into adulthood. however, recent studies have suggested that th ...201222413032
surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes.the instrument channels of gastrointestinal (gi) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (hld). the british society of gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (aers) for disinfecting endoscopes. in this study, we aimed to assess the effectiveness of decontamination using reprocessors after hld by comparing the cultured samples obtained from biopsy channels ...201222943739
16th carbonyl metabolism meeting: from enzymology to genomics.the 16th international meeting on the enzymology and molecular biology of carbonyl metabolism, castle of ploen (schleswig-holstein, germany), july 10-15, 2012, covered all aspects of nad(p)-dependent oxido-reductases that are involved in the general metabolism of xenobiotic and physiological carbonyl compounds. starting 30 years ago with enzyme purification, structure elucidation and enzyme kinetics, the carbonyl society members have meanwhile established internationally recognized enzyme nomenc ...201223199258
two transporters essential for reassimilation of novel cholate metabolites by rhodococcus jostii rha1.the bacterial uptake of steroids and their metabolites remains poorly understood. we investigated two transporters associated with cholate catabolism in rhodococcus jostii rha1. reverse transcriptase quantitative-pcr indicated that an atp-binding cassette (abc) transporter and a major facilitator superfamily (mfs) transporter were upregulated 16.7- and 174-fold, respectively, during the exponential phase of growth on cholate compared to growth on pyruvate. gene knockout analysis established that ...201223024344
self-subunit swapping occurs in another gene type of cobalt nitrile hydratase.self-subunit swapping is one of the post-translational maturation of the cobalt-containing nitrile hydratase (co-nhase) family of enzymes. all of these nhases possess a gene organization of <β-subunit> <α-subunit> <activator protein>, which allows the activator protein to easily form a mediatory complex with the α-subunit of the nhase after translation. here, we discovered that the incorporation of cobalt into another type of co-nhase, with a gene organization of <α-subunit> <β-subunit> <activat ...201223226397
denitrification performance and microbial community structure of a combined wla-obco system.the contamination of surface water by nitrogen due to fertilizer application and discharge of wastewater is an increasingly serious problem. a multifunctional device, which combines water-lifting and aeration (wla) with oligotrophic biological contact oxidation (obco), was developed for pretreatment of raw water to reduce nitrogen. the performance of nitrogen removal and changes in microbial community structure were investigated. the results showed that the combined technique of wla-obco was fea ...201223152768
application of a battery of biotests for the determination of leachate toxicity to bacteria and invertebrates from sewage sludge-amended soil.the objective of the study was to determine the leachates toxicity from sewage sludge-amended soils (sandy and loamy). samples originated from a plot experiment realized over a period of 29 months. two types of soil were fertilized with sewage sludges at the dose of 3 % (90 t/ha). soil samples were taken after 0, 7, 17, and 29 months from the application of sewage sludges. leachates were obtained according to the en 12457-2 protocol. the following commercial tests were applied for the estimation ...201223132406
application of a battery of biotests for the determination of leachate toxicity to bacteria and invertebrates from sewage sludge-amended soil.the objective of the study was to determine the leachates toxicity from sewage sludge-amended soils (sandy and loamy). samples originated from a plot experiment realized over a period of 29 months. two types of soil were fertilized with sewage sludges at the dose of 3 % (90 t/ha). soil samples were taken after 0, 7, 17, and 29 months from the application of sewage sludges. leachates were obtained according to the en 12457-2 protocol. the following commercial tests were applied for the estimation ...201223132406
acute infective endocarditis caused by delftia acidovorans, a rare pathogen complicating intravenous drug use.gram-negative bacilli causing infective endocarditis (ie) is rare, even in intravenous drug users. this case report underscores several clinically important aspects of delftia acidovorans ie: the organism's ability to cause rapid destruction of normal native valves and to cause embolic occlusion of large arteries and its resistance to all aminoglycosides.201222933597
nitrilases in nitrile biocatalysis: recent progress and forthcoming research.over the past decades, nitrilases have drawn considerable attention because of their application in nitrile degradation as prominent biocatalysts. nitrilases are derived from bacteria, filamentous fungi, yeasts, and plants. in-depth investigations on their natural sources function mechanisms, enzyme structure, screening pathways, and biocatalytic properties have been conducted. moreover, the immobilization, purification, gene cloning and modifications of nitrilase have been dwelt upon. some nitr ...201223106943
crystallization and preliminary crystallographic analysis of 2-aminophenol 1,6-dioxygenase complexed with substrate and with an inhibitor.dioxygen activation implemented by nonhaem fe(ii) enzymes containing the 2-his-1-carboxylate facial triad has been extensively studied in recent years. extradiol dioxygenase is the archetypal member of this superfamily and catalyzes the oxygenolytic ring opening of catechol analogues. here, the crystallization and preliminary x-ray analysis of 2-aminophenol 1,6-dioxygenase, an enzyme representing a minor subset of extradiol dioxygenases that catalyze the fission of 2-aminophenol rather than cate ...201223143244
catabolism and biotechnological applications of cholesterol degrading bacteria.cholesterol is a steroid commonly found in nature with a great relevance in biology, medicine and chemistry, playing an essential role as a structural component of animal cell membranes. the ubiquity of cholesterol in the environment has made it a reference biomarker for environmental pollution analysis and a common carbon source for different microorganisms, some of them being important pathogens such as mycobacterium tuberculosis. this work revises the accumulated biochemical and genetic knowl ...201222309478
proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, arhodomonas sp. strain rozel, isolated from a hypersaline environment.lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. the focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. the extremely halophilic bacteria arhodomonas sp. strain seminole and arhodomonas sp. strain rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 m nacl), were is ...201222885747
role of serine140 in the mode of action of mycobacterium tuberculosis β-ketoacyl-acp reductase (maba).tuberculosis (tb) still remains one of the most deadly infectious diseases in the world. mycobacterium tuberculosis β-ketoacyl-acp reductase (maba) is a member of the fatty acid elongation system type ii, providing precursors of mycolic acids that are essential to the bacterial cell growth and survival. maba has been shown to be essential for m. tuberculosis survival and to play a role in intracellular signal transduction of bacilli.201223006410
characterization of a novel phenol hydroxylase in indoles biotransformation from a strain arthrobacter sp. w1 [corrected].indigoids, as popular dyes, can be produced by microbial strains or enzymes catalysis. however, the new valuable products with their transformation mechanisms, especially inter-conversion among the intermediates and products have not been clearly identified yet. therefore, it is necessary to investigate novel microbial catalytic processes for indigoids production systematically.201223028517
surviving chytridiomycosis: differential anti-batrachochytrium dendrobatidis activity in bacterial isolates from three lowland species of atelopus.in the neotropics, almost every species of the stream-dwelling harlequin toads (genus atelopus) have experienced catastrophic declines. the persistence of lowland species of atelopus could be explained by the lower growth rate of batrachochytrium dendrobatidis (bd) at temperatures above 25 °c. we tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis. w ...201222970314
inactivation of chloramphenicol and florfenicol by a novel chloramphenicol hydrolase.chloramphenicol and florfenicol are broad-spectrum antibiotics. although the bacterial resistance mechanisms to these antibiotics have been well documented, hydrolysis of these antibiotics has not been reported in detail. this study reports the hydrolysis of these two antibiotics by a specific hydrolase that is encoded by a gene identified from a soil metagenome. hydrolysis of chloramphenicol has been recognized in cell extracts of escherichia coli expressing a chloramphenicol acetate esterase g ...201222752166
inferring the evolutionary history of incp-1 plasmids despite incongruence among backbone gene trees.plasmids of the incompatibility group incp-1 can transfer and replicate in many genera of the proteobacteria. they are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of incp-1 plasmids. as a conseque ...201222936717
inferring the evolutionary history of incp-1 plasmids despite incongruence among backbone gene trees.plasmids of the incompatibility group incp-1 can transfer and replicate in many genera of the proteobacteria. they are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of incp-1 plasmids. as a conseque ...201222936717
biodegradation of mono-hydroxylated pcbs by burkholderia xenovorans.three hydroxylated derivatives of pcbs, 2'-hydroxy-4-chlorobiphenyl (2'-oh-4-cb), 3'-hydroxy-4-chlorobiphenyl (3'-oh-4-cb), and 4'-hydroxy-4-chlorobiphenyl (4'-oh-4-cb), were transformed by the pcb degrader, burkholderia xenovorans. when the bacterium was growing on biphenyl (biphenyl pathway-inducing conditions), all three hydroxylated isomers were transformed. however, only 2'-oh-4-cb was transformed by the bacterium growing on succinate (conditions non-inductive of the biphenyl pathway). gene ...201222918793
recurrent microvirgula aerodenitrificans bacteremia.microvirgula aerodenitrificans is a denitrifying gram-negative organism first described by patureau et al. in 1998 (d. patureau et al., int. j. syst. bacteriol. 48:775-782, 1998). the organism has been isolated globally but has never been described as causative of clinical infection. we describe the first human case of bacteremia attributed to m. aerodenitrificans in an infant with pompe's disease.201222692735
isolation of a gene responsible for the oxidation of trans-anethole to para-anisaldehyde by pseudomonas putida jyr-1 and its expression in escherichia coli.a plasmid, pta163, in escherichia coli contained an approximately 34-kb gene fragment from pseudomonas putida jyr-1 that included the genes responsible for the metabolism of trans-anethole to protocatechuic acid. three tn5-disrupted open reading frame 10 (orf 10) mutants of plasmid pta163 lost their abilities to catalyze trans-anethole. heterologously expressed orf 10 (1,047 nucleotides [nt]) under a t7 promoter in e. coli catalyzed oxidative cleavage of a propenyl group of trans-anethole to an ...201222610435
identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil.bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. in order to avoid biases of culture-based approaches, stable isotope probing was applied in combination with sequence analysis of 16 s rrna gene pyrotags amplified from (13)c-enriched dna fractions. special attention was paid to pyrosequencing data analysis in order to eliminate the errors cause ...201222808223
marine crude-oil biodegradation: a central role for interspecies interactions.the marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. the diverse array of hydrocarbons present in crude oil requires resource partition ...201222591596
the phn island: a new genomic island encoding catabolism of polynuclear aromatic hydrocarbons.bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (pah), which are widespread environmental pollutants. at least six genotypes of pah degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (rhd) that initiates bacterial pah metabolism. a given rhd genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (hgt) is an important process for dissemination of pah-degrading genes. but, mechanisms of hgt for mos ...201222493593
ring-cleaving dioxygenases with a cupin fold.ring-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. many pathways converge to catecholic intermediates, which are subject to ortho or meta cleavage by intradiol or extradiol dioxygenases, respectively. however, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. the ring-cleaving dioxygenases active toward the ...201222287012
dynamics of the linuron hydrolase liba gene pool size in response to linuron application and environmental perturbations in agricultural soil and on-farm biopurification systems.liba, a gene encoding a novel type of linuron hydrolase, was recently identified in the linuron-mineralizing variovorax sp. strain srs16. in order to assess the contribution of liba to linuron degradation in environmental settings, liba abundance was monitored in response to the application of linuron and to environmental perturbations in agricultural soil microcosms and microcosms simulating the matrix of on-farm biopurification systems. liba numbers were measured by real-time pcr and linked to ...201222307296
biochemical characterization of the cdp-d-arabinitol biosynthetic pathway in streptococcus pneumoniae 17f.streptococcus pneumoniae is a major human pathogen associated with many diseases worldwide. capsular polysaccharides (cpss) are the major virulence factor. the biosynthetic pathway of d-arabinitol, which is present in the cpss of several s. pneumoniae serotypes, has never been identified. in this study, the genes abpa (previously known as abp1) and abpb (previously known as abp2), which have previously been reported to be responsible for nucleoside diphosphate (ndp)-d-arabinitol (the nucleotide- ...201222328666
molecular characterizations of cytolethal distending toxin produced by providencia alcalifaciens strains isolated from patients with diarrhea.cytolethal distending toxins (cdts), which block eukaryotic cell proliferation by acting as inhibitory cyclomodulins, are produced by diverse groups of gram-negative bacteria. active cdt is composed of three polypeptides--cdta, cdtb, and cdtc--encoded by the genes cdta, cdtb, and cdtc, respectively. we developed a pcr-restriction fragment length polymorphism assay for the detection and differentiation of five alleles of cdtb (cdt-i through cdt-v) in escherichia coli and used the assay to investi ...201222252871
phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.in petrochemical refinery wastewater treatment plants (wwtp), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. in the present work, the microbial sludge from a refinery wwtp was enriched for phenol, cloned into fosmid vectors and pyrosequenced. the fosmid libraries yielded 13,200 ...201222452812
culturable gut microbiota diversity in zebrafish.the zebrafish (danio rerio) is an increasingly used laboratory animal model in basic biology and biomedicine, novel drug development, and toxicology. the wide use has increased the demand for optimized husbandry protocols to ensure animal health care and welfare. the knowledge about the correlation between culturable zebrafish intestinal microbiota and health in relation to environmental factors and management procedures is very limited. a semi-quantitative level of growth of individual types of ...201222428747
genome sequence of comamonas testosteroni atcc 11996, a representative strain involved in steroid degradation.comamonas testosteroni strains belong to the family of comamonadaceae and are known for their ability to utilize steroid compounds as carbon source. here, we present the draft genome sequence of strain atcc 11996, with a g+c content of 61.48%.201222374961
genes that influence swarming motility and biofilm formation in variovorax paradoxus eps.variovorax paradoxus is an aerobic soil bacterium associated with important biodegradative processes in nature. we use v. paradoxus eps to study multicellular behaviors on surfaces.201222363744
quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. to quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate v ...201222308339
microbes and asthma: the missing cellular and molecular links.in this review, we describe the 'state-of-the-art' in our knowledge of asthma and what gaps exist, which can be exploited in the future for effective translation of our knowledge from the bench or population studies to diagnosis and therapy.201222113000
distribution of genes encoding nucleoid-associated protein homologs in plasmids.bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...201121350637
across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage.the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ...201121423704
role of incp-1β plasmids pwdl7::rfp and pnb8c in chloroaniline catabolism as determined by genomic and functional analyses.broad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. to gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an incp-1 chloroaniline degradation plasmid, pwdl7::rfp and its close relative pnb8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-ca) oxidation genes. based on phylogenetic analysis of backbon ...201122101050
a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16.the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ...201122003008
Identification and Characterization of the LysR-type Transcriptional Regulator HsdR for Steroid-inducible Expression of the 3a-Hydroxysteroid Dehydrogenase/Carbonyl Reductase Gene in Comamonas testosteroni.3a-hydroxysteroid dehydrogenase/carbonyl reductase (3a-HSD/CR) from Comamonas testosteroni (C. testosteroni) is a key enzyme in steroid degradation in soil and water. 3a-HSD/CR gene (hsdA) expression can be induced by steroids like testosterone and progesterone. Previously, we have shown that induction of hsdA expression by steroids is a derepression where steroidal inducers bind to two repressors, RepA and RepB, thereby preventing blocking of hsdA transcription and translation, respectively. In ...201122156416
nonlinear changes in the activity of the oxygen-dependent demethylase system in rhodococcus erythropolis cells in the presence of low and very low doses of formaldehyde.abstract: the effect of exogenous, highly diluted formaldehyde on the rate of demethylation/re-methylation of veratric acid by the bacteria rhodococcus erythropolis was studied using electrophoretic and microscopic techniques. the activity of 4-o-demethylase, responsible for accumulation of vanillic acid, and the levels of veratric and vanillic acids were determined using capillary electrophoresis. formaldehyde was serially diluted at 1:100 ratios, and the total number of iterations was 20. afte ...201122104369
Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011.Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods.201122022434
isolation and partial characterization of extracellular nadph-dependent phenol hydroxylase oxidizing phenol to catechol in comamonas testosteroni.comamonas testosteroni pb50 is a microorganism that possesses high tolerance for phenol and shows strong phenol degrading activity. this bacterial strain is capable of utilizing phenol as the sole carbon and energy source. although examples are known in which the c. testosteroni utilizes phenol for growth or metabolism, much less information are known on the nature of the phenol-oxidizing enzymes in this microorganism. therefore, the occurrence and cellular location of phenol hydroxylase (ec 1.1 ...201122167219
why two are not enough: degradation of p-toluenesulfonate by a bacterial community from a pristine site in moorea, french polynesia.in previous work, only one culture (strain ta12) from a pristine site was reported to utilize the xenobiotic compound p-toluenesulfonate (tsa) as a sole source of carbon and energy for aerobic growth. 'strain ta12' has now been recognized as a community of three bacteria: achromobacter xylosoxidans ta12-a, ensifer adhaerens ta12-b and pseudomonas nitroreducens ta12-c. achromobacter xylosoxidans ta12-a and e. adhaerens ta12-b were identified as the tsa degraders. these two organisms contain sever ...201121204940
catheter-related bacteremia caused by comamonas testosteroni in a hemodialysis patient.comamonas testosteroni has rarely been implicated as a human pathogen. in general, the outcome of c. testosteroni infections is favorable. we report a case of fatal bacteremia caused by c. testosteroni in a 64-year-old woman on hemodialysis.201121223488
steroid degradation and two steroid-inducible enzymes in the marine bacterium h5.natural and synthetic steroid hormones excreted into the environment are potentially threatening the population dynamics of all kinds of animals and public health. we have previously isolated a steroid degrading bacterial strain (h5) from the baltic sea, at kiel, germany. 16s-rrna analysis showed that bacterial strain h5 belongs to the genus vibrio, family vibrionaceae and class gamma-proteobacteria. bacterial strain h5 can degrade steroids such as testosterone and estrogens, which was shown in ...201121281621
identification of a new steroid degrading bacterial strain h5 from the baltic sea and isolation of two estradiol inducible genes.the presence of steroid hormones in the aquatic environment is potentially threatening the population dynamics of all kinds of sea animals and public health. environmental estrogens in water have been reported to be associated with abnormal sexual development and abnormal feminizing responses in some animals. new approaches for the bioremediation of steroid hormones from the environment are therefore urgently sought. we have previously isolated a steroid degrading bacterial strain (h5) from the ...201121310233
identification of a thiolase gene essential for ß-oxidation of the acyl side chain of the steroid compound cholate in pseudomonas sp. strain chol1.bile salts such as cholate are steroid compounds occurring ubiquitously in the environment through excretion by animals. cholate degradation by pseudomonas sp. strain chol1 is initiated by a-ring oxidation and ß-oxidation of the acyl side chain. a transposon mutant of strain chol1 was isolated that could not grow with cholate, but transformed it into several steroid compounds accumulating in culture supernatants. the main product was identified as (22e)-7a,12a-dihydroxy-3-oxochola-1,4,22-triene- ...201121362022
novel regulator mphx represses activation of phenol hydroxylase genes caused by a xylr/dmpr-type regulator mphr in acinetobacter calcoaceticus.acinetobacter calcoaceticus phea-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphklmnop) for phenol degradation. two additional genes, mphr and mphx, were found upstream and downstream of mphklmnop, respectively. the mphr gene encodes a xylr/dmpr-type regulator-like protein and is transcribed in the opposite direction to mphklmnop. the mphx gene is transcribed in the same direction as mphklmnop and encodes a protein wit ...201121455294
bioinformatic characterization of the trimeric intracellular cation-specific channel protein family.trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ...201121519847
isomerization of the phytohormone precursor opda in the insect gut: a mechanistic and computational study.12-oxophytodienoic acid (opda) is isomerized in the gut of herbivorous insects to tetrahydrodicranenone b (iso-opda). the transformation is achieved by a glutathione-s-transferase present in the gut epithelium. experiments with 9-[2h]-iso-opda demonstrated the complete retention of the deuterium atom in the product 11-[2h]-opda consistent with an intramolecular 1,3-hydrogen shift. homology-modeling based on the x-ray structure of a glutathione s-trans-ferase from anopheles gambiae revealed that ...201121527631
comamonas testosteroni infection in taiwan: reported two cases and literature review.comamonas testosteroni is a widely distributed aerobic gram-negative bacillus. infection by c testosteroni is infrequent, and no such cases have been reported in taiwan. here, we would like to present a 54-year-old alcoholic patient from taiwan, and his left leg was injured during a fishing trip, resulting in left leg cellulitis and c testosteroni bacteremia. the patient's fever subsided after initial treatment with extended-spectrum cephalosporin, whereas his erythematous swelling did not resol ...201121531356
patchwork assembly of nag-like nitroarene dioxygenase genes and 3-chlorocatechol degradation cluster for the pathway evolution of 2-chloronitrobenzene catabolism in pseudomonas stutzeri zwlr2-1.pseudomonas stutzeri zwlr2-1 utilizes 2-chloronitrobenzene (2cnb) as a sole source of carbon, nitrogen and energy. to identify genes involved in this pathway, a 16.2-kb dna fragment containing putative 2-chloronitrobenzene dioxygenase genes was cloned and sequenced. of the products from the 19 open reading frames that resulted from this fragment, cnbac and cnbad exhibited striking identities to the respective α- and β- subunits of the nag-like ring-hydroxylating dioxygenases involved in the meta ...201121602392
comamonas testosteronan synthase, a bifunctional glycosyltransferase that produces a unique heparosan polysaccharide analog.glycosaminoglycans [gags] are linear hexosamine-containing polysaccharides. these polysaccharides are synthesized by some pathogenic bacteria to form an extracellular coating or capsule. this strategy forms the basis of molecular camouflage since vertebrates possess naturally-occurring gags that are essential for life. a recent sequence database search identified a putative protein from the opportunistic pathogen comamonas testosteroni that exhibits similarity to the pasteurella multocida glycos ...201121610195
effects of entrapment on nucleic acid content, cell morphology, cell surface property, and stress of pure cultures commonly found in biological wastewater treatment.the effects of cell entrapment on nucleic acid content, cell morphology, cell surface property, and stress of major groups of bacteria (betaproteobacteria and gammaproteobacteria) in biological municipal wastewater treatment were investigated. three different entrapment media (alginate, carrageenan, and polyvinyl alcohol) were examined. results indicated that the entrapment and type of entrapment media affected nucleic acid content, cell morphology, cell surface property, and stress of the three ...201121660542
most mutant occr proteins that are defective in positive control hold operator dna in a locked high angle bend.occr is a lysr-type transcriptional regulator of agrobacterium tumefaciens that positively regulates the octopine catabolism operon of the ti plasmid. positive control of the occ genes occurs in response to octopine, a nutrient released from crown gall tumors. occr also functions as an autorepressor in the presence or absence of octopine. occr binds to a site between occq and occr in the presence or absence of octopine, although octopine triggers a conformational change that shortens the dna foo ...201121804007
recurrent intravascular catheter-related bacteremia caused by delftia acidovorans in a hemodialysis patient.we report the first case of recurrent intravascular catheter-related bacteremia in a pediatric hemodialysis patient caused by delftia acidovorans, previously called comamonas acidovorans or pseudomonas acidovorans. the patient had a history of multiple infections of central vascular catheters with other organisms, requiring courses of antibiotics and catheter replacements. previously reported cases of d. acidovorans infections are reviewed. in vitro susceptibility testing for cephalosporins is n ...201121775546
effects of microbial species, organic loading and substrate degradation rate on the power generation capability of microbial fuel cells.four microbial fuel cells (mfcs) inoculated with different bacterial species were constructed. the species were pseudomonas putida, comamonas testosteroni, corynebacterium gultamicum, and arthrobacter polychromogenes. the mfcs were operated under identical continuous flow conditions. the factors affecting the capabilities of the mfcs for treating organic matter and generating power were evaluated and compared. the factors include microbial species type, organic loading, and substrate degradation ...201121750995
a novel testosterone catabolic pathway in bacteria.forty years ago, coulter and talalay (a. w. coulter and p. talalay, j. biol. chem. 243:3238-3247, 1968) established the oxygenase-dependent pathway for the degradation of testosterone by aerobes. the oxic testosterone catabolic pathway involves several oxygen-dependent reactions and is not available for anaerobes. since then, a variety of anaerobic bacteria have been described for the ability to degrade testosterone in the absence of oxygen. here, a novel, oxygenase-independent testosterone cata ...201121725000
virulence determinants, drug resistance and mobile genetic elements of laribacter hongkongensis: a genome-wide analysis. 201121711902
emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism.all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ...201121823229
genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, comamonas testosteroni s44.a novel and multiple metal(loid)-resistant strain comamonas testosteroni s44 with a high zn(2+) resistance level (10-ámm) was isolated. to understand the molecular basis for the high zinc resistance, whole genome sequencing was performed and revealed a large number of genes encoding putative metal(loid) resistance proteins, mobile genetic elements (mges) and horizontal gene transfer (hgt) events that may have occurred to adapt to a metal(loid)-contaminated environment. in particular, 9 putative ...201121704702
the steroid catabolic pathway of the intracellular pathogen rhodococcus equi is important for pathogenesis and a target for vaccine development.rhodococcus equi causes fatal pyogranulomatous pneumonia in foals and immunocompromised animals and humans. despite its importance, there is currently no effective vaccine against the disease. the actinobacteria r. equi and the human pathogen mycobacterium tuberculosis are related, and both cause pulmonary diseases. recently, we have shown that essential steps in the cholesterol catabolic pathway are involved in the pathogenicity of m. tuberculosis. bioinformatic analysis revealed the presence o ...201121901092
glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ...201122194940
Cloning, overexpression, purification, crystallization and preliminary X-ray analysis of 3-ketosteroid ?(4)-(5a)-dehydrogenase from Rhodococcus jostii RHA1.3-Ketosteroid dehydrogenases are flavoproteins which play key roles in steroid ring degradation. The enzymes are abundantly present in actinobacteria, including the catabolic powerhouse Rhodococcus jostii and the pathogenic species R. equi and Mycobacterium tuberculosis. The gene for 3-ketosteroid ?(4)-(5a)-dehydrogenase [?(4)-(5a)-KSTD] from R. jostii RHA1 was cloned and overexpressed in Escherichia coli. His-tagged ?(4)-(5a)-KSTD enzyme was purified by Ni(2+)-NTA affinity chromatography, anion ...201122102045
evaluation of the energetics of the concerted acid-base mechanism in enzymatic catalysis: the case of ketosteroid isomerase.structures of enzymes invariably reveal the proximity of acidic and basic residues to reactive sites on the substrate, so it is natural and common to suggest that enzymes employ concerted mechanisms to catalyze their difficult reactions. ketosteroid isomerase (ksi) has served as a paradigm of enzymatic proton transfer chemistry, and its catalytic effect has previously been attributed to concerted proton transfer. we employ a specific inhibitor that contains an ir probe that reports directly and ...201122148842
evaluation of the energetics of the concerted acid-base mechanism in enzymatic catalysis: the case of ketosteroid isomerase.structures of enzymes invariably reveal the proximity of acidic and basic residues to reactive sites on the substrate, so it is natural and common to suggest that enzymes employ concerted mechanisms to catalyze their difficult reactions. ketosteroid isomerase (ksi) has served as a paradigm of enzymatic proton transfer chemistry, and its catalytic effect has previously been attributed to concerted proton transfer. we employ a specific inhibitor that contains an ir probe that reports directly and ...201122148842
evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase.prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (ksi) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to ksi catalysis. but these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potenti ...201122053826
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