| the reca protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of recas and 16s rrnas from the same species. | the evolution of the reca protein was analyzed using molecular phylogenetic techniques. phylogenetic trees of all currently available complete reca proteins were inferred using multiple maximum parsimony and distance matrix methods. comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. the reca trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, ... | 1995 | 8587109 |
| molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility. | paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ... | 1998 | 9841665 |
| distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases. | the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ... | 1999 | 10482517 |
| localization of periplasmic redox proteins of alcaligenes faecalis by a modified general method for fractionating gram-negative bacteria. | a lysozyme-osmotic shock method is described for fractionation of alcaligenes faecalis which uses glucose to adjust osmotic strength and multiple osmotic shocks. during phenylethylamine-dependent growth, aromatic amine dehydrogenase, azurin, and a single cytochrome c were localized in the periplasm. their induction patterns are different from those for the related quinoprotein methylamine dehydrogenase and its associated redox proteins. | 1999 | 10515948 |
| the mitochondrial alcohol dehydrogenase adh3p is involved in a redox shuttle in saccharomyces cerevisiae. | ndi1 is the unique gene encoding the internal mitochondrial nadh dehydrogenase of saccharomyces cerevisiae. the enzyme catalyzes the transfer of electrons from intramitochondrial nadh to ubiquinone. surprisingly, ndi1 is not essential for respiratory growth. here we demonstrate that this is due to in vivo activity of an ethanol-acetaldehyde redox shuttle, which transfers the redox equivalents from the mitochondria to the cytosol. cytosolic nadh can be oxidized by the external nadh dehydrogenases ... | 2000 | 10940011 |
| comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. | in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ... | 2000 | 11055963 |
| urea utilization in the phototrophic bacterium rhodobacter capsulatus is regulated by the transcriptional activator ntrc. | the phototrophic nonsulfur purple bacterium rhodobacter capsulatus can use urea as a sole source of nitrogen. three transposon tn5-induced mutations (xan-9, xan-10, and xan-19), which led to a ure(-) phenotype, were mapped to the uref and urec genes, whereas two other tn5 insertions (xan-20 and xan-22) were located within the ntrc and ntrb genes, respectively. as in klebsiella aerogenes and other bacteria, the genes encoding urease (ureabc) and the genes required for assembly of the nickel metal ... | 2001 | 11133958 |
| novel genes affecting urease acivity in actinobacillus pleuropneumoniae. | characterization of a series of urease-negative transposon mutations of actinobacillus pleuropneumoniae revealed that many of the mutants had insertions 2 to 4 kbp upstream of the urease gene cluster. a 5-kbp upstream region of dna was sequenced and found to contain six open reading frames (orfs) transcribed in the same orientation as the urease genes. as well, a partial orf, apur, 202 bp upstream of these six orfs, is transcribed in the opposite orientation. the predicted product of this partia ... | 2001 | 11157936 |
| chloromethane utilization gene cluster from hyphomicrobium chloromethanicum strain cm2(t) and development of functional gene probes to detect halomethane-degrading bacteria. | hyphomicrobium chloromethanicum cm2(t), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source. h. chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kda cmua and 35-kda cmub) are expressed. previously, four genes, cmua, cmub, cmuc, and puru, were shown to be essential for growth of methylobacterium chloromethanicum on chloromethane. the ... | 2001 | 11133460 |
| effect of model sorptive phases on phenanthrene biodegradation: molecular analysis of enrichments and isolates suggests selection based on bioavailability. | reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. we established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (r. j. grosser, m. friedrich, d. m. ward, and w. p. inskeep, appl. environ. microbiol. 66:2695-2702, 2000). bacteria enriched and isolated from contaminated soils under these conditions were ... | 2000 | 10877758 |
| two distinct alcohol dehydrogenases participate in butane metabolism by pseudomonas butanovora. | the involvement of two primary alcohol dehydrogenases, bdh and boh, in butane utilization in pseudomonas butanovora (atcc 43655) was demonstrated. the genes coding for boh and bdh were isolated and characterized. the deduced amino acid sequence of boh suggests a 67-kda alcohol dehydrogenase containing pyrroloquinoline quinone (pqq) as cofactor and in the periplasm (29-residue leader sequence). the deduced amino acid sequence of bdh is consistent with a 70.9-kda, soluble, periplasmic (37-residue ... | 2002 | 11889098 |
| cloning and heterologous expression of an enantioselective amidase from rhodococcus erythropolis strain mp50. | the gene for an enantioselective amidase was cloned from rhodococcus erythropolis mp50, which utilizes various aromatic nitriles via a nitrile hydratase/amidase system as nitrogen sources. the gene encoded a protein of 525 amino acids which corresponded to a protein with a molecular mass of 55.5 kda. the deduced complete amino acid sequence showed homology to other enantioselective amidases from different bacterial genera. the nucleotide sequence approximately 2.5 kb upstream and downstream of t ... | 2002 | 12089004 |
| rhizobium leguminosarum has a second general amino acid permease with unusually broad substrate specificity and high similarity to branched-chain amino acid transporters (bra/liv) of the abc family. | amino acid uptake by rhizobium leguminosarum is dominated by two abc transporters, the general amino acid permease (aap) and the branched-chain amino acid permease (bra(rl)). characterization of the solute specificity of bra(rl) shows it to be the second general amino acid permease of r. leguminosarum. although bra(rl) has high sequence identity to members of the family of hydrophobic amino acid transporters (haat), it transports a broad range of solutes, including acidic and basic polar amino a ... | 2002 | 12107123 |
| identification by genetic suppression of escherichia coli tolb residues important for tolb-pal interaction. | the tol-pal system of escherichia coli is involved in maintaining outer membrane stability. mutations in tolq, tolr, tola, tolb, or pal genes result in sensitivity to bile salts and the leakage of periplasmic proteins. moreover, some of the tol genes are necessary for the entry of group a colicins and the dna of filamentous bacteriophages. tolq, tolr, and tola are located in the cytoplasmic membrane where they interact with each other via their transmembrane domains. tolb and pal form a periplas ... | 2000 | 10633120 |
| improved large scale culture of methylophilus methylotrophus for 13c/15n labeling and random fractional deuteration of ribonucleotides. | isotopic labeling of rna with 13c and 15n has become a routine procedure in structural studies by nmr spectroscopy. the methodology in this paper describes the random fractional deuteration of rna using the obligate methylotropic bacterium, methylophilus methylotrophus. this bacterium was grown using a non-deuterated carbon source in 52:48 d20/h20 and we have shown that all protons in the ribonucleotides except for the ribose h1 become 52% randomly fractionally deuterated. improved growth condit ... | 1996 | 8972874 |
| three-dimensional structure of human electron transfer flavoprotein to 2.1-a resolution. | mammalian electron transfer flavoproteins (etf) are heterodimers containing a single equivalent of flavin adenine dinucleotide (fad). they function as electron shuttles between primary flavoprotein dehydrogenases involved in mitochondrial fatty acid and amino acid catabolism and the membrane-bound electron transfer flavoprotein ubiquinone oxidoreductase. the structure of human etf solved to 2.1-a resolution reveals that the etf molecule is comprised of three distinct domains: two domains are con ... | 1996 | 8962055 |
| physical, biochemical, and immunological characterization of a thermostable amidase from klebsiella pneumoniae nctr 1. | an amidase capable of degrading acrylamide and aliphatic amides was purified to apparent homogeneity from klebsiella pneumoniae nctr 1. the enzyme is a monomer with an apparent molecular weight of 62,000. the ph and temperature optima of the enzyme were 7.0 and 65 degrees c, respectively. the purified amidase contained 11 5,5-dithiobis(2-nitrobenzoate) (dtnb)-titratable sulfhydryl (sh) groups. in the native enzyme 1.0 sh group readily reacted with dtnb with no detectable loss of activity. titrat ... | 1996 | 8636044 |
| organization of the methylamine utilization (mau) genes in methylophilus methylotrophus w3a1-ns. | the organization of genes involved in utilization of methylamine (mau genes) was studied in methylophilus methylotrophus w3a1. the strain used was a nonmucoid variant termed ns (nonslimy). the original mucoid strain was shown to be identical to the ns strains on the basis of chromosomal digest and hybridization patterns. an 8-kb psti fragment of the chromosome from m. methylotrophus w3a1-ns encoding the mau genes was cloned and a 6,533-bp region was sequenced. eight open reading frames were foun ... | 1994 | 8021188 |
| genetic organization of the mau gene cluster in methylobacterium extorquens am1: complete nucleotide sequence and generation and characteristics of mau mutants. | the nucleotide sequence of the methylamine utilization (mau) gene region from methylobacterium extorquens am1 was determined. open reading frames for 11 genes (maufbedacjglmn) were found, all transcribed in the same orientation. the maub, maua, and mauc genes encode the periplasmic methylamine dehydrogenase (madh) large and small subunit polypeptides and amicyanin, respectively. the products of maud, maug, maul, and maum were also predicted to be periplasmic. the products of mauf, maue, and maun ... | 1994 | 8021187 |
| cloning, sequencing, and mutation of a gene for azurin in methylobacillus flagellatum kt. | the gene cluster for methylamine utilization (mau genes) has been cloned from the obligate methylotrophic bacterium methylobacillus flagellatum kt. partial sequence data showed that the organization of these genes was similar to that found in methylophilus methylotrophus w3a1-ns, including the lack of a gene for amicyanin, which had been thought to be the electron acceptor for methylamine dehydrogenase in m. flagellatum kt. however, a gene encoding azurin was discovered at the 3' end of the mau ... | 1995 | 7635847 |
| the electron-transport chains of the obligate methylotroph methylophilus methylotrophus. | the cytochrome complement of methylophilus methylotrophus and its respiratory properties were determined during batch culture and in continuous culture under conditions of methanol-, nitrogen- and o(2)-limitation. about 35% of the cytochrome c produced by the bacteria was released into the growth medium, and of the remaining cytochrome c about half was membrane-bound and half was soluble. two cytochromes c were always present on membranes (redox potentials 375mv and 310mv), and these probably co ... | 1980 | 7236221 |
| purification and properties of the methanol dehydrogenase from methylophilus methylotrophus. | 1. a dye-linked methanol dehydrogenase, resembling many others from a variety of methylotrophic bacteria, was purified to homogeneity from extracts of methanol-grown methylophilus methylotrophus. 2. the enzyme was very stable in the presence of methanol; in the absence of methanol it had a half-life of 1-2 days at 4 degrees c. 3. the value of a1% 1cm,280 was 17.5. 4. the enzyme retained bound methanol after passage through sephadex g-25. this tightly-bound methanol slowly exchanged with free [14 ... | 1981 | 6802134 |
| the autoreducible cytochromes c of the methylotrophs methylophilus methylotrophus and pseudomonas am1. | the two types of soluble cytochrome c (cytochrome ch and cytochrome cl) found in methylotrophs are completely distinct proteins; one type is not a dimer or degradation product of the other. free thiol groups are probably not involved in the unusually rapid autoreduction of the cytochromes at high ph. the axial ligands to the haem iron, histidine and methionine, are the same as in other low-spin cytochromes c. the methionine ligand is displaced at high ph by an alternative strong-field ligand. th ... | 1982 | 6295363 |
| l-selective amidase with extremely broad substrate specificity from ochrobactrum anthropi ncimb 40321. | an industrially attractive l-specific amidase was purified to homogeneity from ochrobactrum anthropi ncimb 40321 wild-type cells. the purified amidase displayed maximum initial activity between ph 6 and 8.5 and was fully stable for at least 1 h up to 60 degrees c. the purified enzyme was strongly inhibited by the metal-chelating compounds edta and 1,10-phenanthroline. the activity of the edta-treated enzyme could be restored by the addition of zn2+ (to 80%), mn2+ (to 400%), and mg2+ (to 560%). s ... | 2005 | 16332774 |
| isolation of auxotrophic mutants of methylophilus methylotrophus by modified-marker exchange. | a method for stabilizing a transposon (tn5) has been developed which allows the isolation of stable auxotrophic mutants of methylophilus methylotrophus asi. insertion of tn5 into a cloned m. methylotrophus asi dna fragment encoding anthranilate synthase followed by transfer of the vector with the modified trpe gene to m. methylotrophus asi resulted in unstable auxotrophs among the recombinants. deletion of is50r, which encodes transposase production from tn5, stabilized the transposon after mobi ... | 1988 | 16347531 |
| respiration-linked proton translocation in the obligate methylotroph methylophilus methylotrophus. | the stoicheiometries of respiration-linked proton translocation in methylophilus methylotrophus were determined by using both the oxygen-pulse and initial-rate methods. the latter has also been used to determine leads to charge/o quotients (measured as yield k+/o quotients) in order to ascertain whether the leads to h+/o quotients might be underestimated by h+/anion symport. the results suggest that 6h+/o are translocated during nadh oxidation, and that 2h+/o are translocated during the oxidatio ... | 1981 | 6272739 |
| the purification and properties of the soluble cytochromes c of the obligate methylotroph methylophilus methylotrophus. | the obligate methylotroph methylophilus methylotrophus contains three distinct soluble cytochromes c. the major cytochromes, cytochrome ch (about 50% of the total) and cytochrome cl (about 42%), were similar in most respects to the cytochromes ch and cl of the facultative methylotroph pseudomonas am1 [o'keeffe & anthony (1980) biochem. j. 192, 411-419]. cytochrome ch had a high isoelectric point, a midpoint redox potential at ph 7.0 of 373 mv and a low molecular weight (8500). the cytochrome cl ... | 1980 | 6263254 |
| expression of a chemically synthesized human alpha 1 interferon gene. | cells of escherichia coli containing a chemically synthesized human alpha 1 interferon (ifn-alpha 1) gene, under control of the lac promoter, make a product with biological properties indistinguishable from those of the natural ifn-alpha 1 [antiviral activity, acid stability, species crossreactivity, inactivation by antisera directed against leukocyte or namalwa cell interferon, and stimulation of (2'-5')oligoadenylate synthetase activity]. similar levels of ifn synthesis were obtained when the ... | 1982 | 6181502 |
| electron transfer flavoprotein from methylophilus methylotrophus: properties, comparison with other electron transfer flavoproteins, and regulation of expression by carbon source. | when grown on methylated amines as a carbon source, methylophilus methylotrophus synthesizes an electron transfer flavoprotein (etf) which is the natural electron acceptor of trimethylamine dehydrogenase. it is composed of two dissimilar subunits of 38,000 and 42,000 daltons and 1 mol of flavin adenine dinucleotide. it was reduced by trimethylamine dehydrogenase to a stable anionic semiquinone form, which could not be converted, either enzymatically or chemically, to the fully reduced dihydroqui ... | 1986 | 3711024 |
| isolation and computer-aided characterization of mmei, a type ii restriction endonuclease from methylophilus methylotrophus. | a type ii restriction endonuclease, mmei, has been purified from the obligate methylotroph, methylophilus methylotrophus. the enzyme was shown to have the non-palindromic recognition sequence 5'-t c c pu a c (n)20-3', 3'-a g g py t g (n)18-5' and to cleave (as indicated) on the 3' side, generating a two nucleotide 3' projection. determination of the recognition sequence was achieved using two new computer programs; recog, which predicts recognition sequences from the pattern of restriction fragm ... | 1986 | 3016643 |
| studies on electron transfer from methanol dehydrogenase to cytochrome cl, both purified from hyphomicrobium x. | ferricytochrome cl isolated from hyphomicrobium x is an electron acceptor in assays for homologous methanol dehydrogenase (mdh), albeit a poor one compared with artificial dyes. the intermediates of mdh seen during the reaction are identical with those observed with wurster's blue as electron acceptor, indicating that the reaction cycles are similar. the assay showed a ph optimum of approx. 7.0 and scarcely any stimulation by nh4cl, this being in contrast with assays with artificial dyes, where ... | 1989 | 2537627 |
| cytochrome c'' isolated from methylophilus methylotrophus. an example of bis-histidine-co-ordinated fe3+ haem, with near-perpendicular orientation of the ligands. | cytochrome c'' (methylophilus methylotrophus) is a soluble protein, mr 15,000, possessing one haem which is high-spin in the reduced state but switches to a low-spin form on oxidation. low-temperature electron-paramagnetic-resonance spectroscopy of the oxidized state shows a low-spin signal at gz = 3.65 with a folded line-shape typical of a haem of low rhombicity, and the near-infrared magnetic-circular-dichroism (m.c.d.) spectra reveal an unusually intense (delta epsilon = 400 m-1.cm-1 at 5 t, ... | 1990 | 2169241 |
| preparation of isotopically labeled ribonucleotides for multidimensional nmr spectroscopy of rna. | a general method for large scale preparation of uniformly isotopically labeled ribonucleotides and rnas is described. bacteria are grown on isotopic growth medium, and their nucleic acids are harvested and degraded to mononucleotides. these are enzymatically converted into ribonucleoside triphosphates, which are used in transcription reactions in vitro to prepare rnas for nmr studies. for 15n-labeling, e.coli is grown on 15n-ammonium sulfate, whereas for 13c-labeling, methylophilus methylotrophu ... | 1992 | 1383928 |
| expression, purification, crystallization and preliminary x-ray studies of histamine dehydrogenase from nocardioides simplex. | histamine dehydrogenase (hadh) from nocardioides simplex catalyzes the oxidative deamination of histamine to produce imidazole acetaldehyde and an ammonium ion. hadh is functionally related to trimethylamine dehydrogenase (tmadh), but hadh has strict substrate specificity towards histamine. hadh is a homodimer, with each 76 kda subunit containing two redox cofactors: a [4fe-4s] cluster and an unusual covalently bound flavin mononucleotide, 6-s-cysteinyl-fmn. in order to understand the substrate ... | 2008 | 18765904 |
| characterization of mutant forms of the quinoprotein methanol dehydrogenase lacking an essential calcium ion. | methanol dehydrogenase (mdh) from methylobacterium extorquens, methylophilus methylotrophus, paracoccus denitrificans and hyphomicrobium x all contained a single atom of ca2+ per alpha 2 beta 2 tetramer. the role of ca2+ was investigated using the mdh from methylobacterium extorquens. this was shown to be similar to the mdh from hyphomicrobium x in having 2 mol of prosthetic group (pyrroloquinoline quinine; pqq) per mol of tetramer, the pqq being predominantly in the semiquinone form. mdh isolat ... | 1992 | 1332681 |
| multiphasic kinetics of transformation of 1,2,4-trichlorobenzene at nano- and micromolar concentrations by burkholderia sp. strain ps14. | the transformation of 1,2,4-trichlorobenzene (1,2,4-tcb) at initial concentrations in nano- and micromolar ranges was studied in batch experiments with burkholderia sp. strain ps14. 1,2,4-tcb was metabolized from nano- and micromolar concentrations to below its detection limit of 0.5 nm. at low initial 1,2,4-tcb concentrations, a first-order relationship between specific transformation rate and substrate concentration was observed with a specific affinity (a(0)(a)) of 0.32 liter. mg (dry weight) ... | 2001 | 11472925 |
| overproduction of l-lysine from methanol by methylobacillus glycogenes derivatives carrying a plasmid with a mutated dapa gene. | the dapa gene, encoding dihydrodipicolinate synthase (ddps) partially desensitized to inhibition by l-lysine, was cloned from an l-threonine- and l-lysine-coproducing mutant of the obligate methylotroph methylobacillus glycogenes dhl122 by complementation of the nutritional requirement of an escherichia coli dapa mutant. introduction of the dapa gene into dhl122 and al119, which is the parent of dhl122 and an l-threonine producing mutant, elevated the specific activity of ddps 20-fold and l-lysi ... | 2001 | 11425723 |
| characterization of bsemii, a new type iv restriction-modification system, which recognizes the pentanucleotide sequence 5'-ctcag(n)(10/8)/. | we report the properties of the new bsemii restriction and modification enzymes from bacillus stearothermophilus isl 15-111, which recognize the 5'-ctcag sequence, and the nucleotide sequence of the genes encoding them. the restriction endonuclease r.bsemii makes a staggered cut at the tenth base pair downstream of the recognition sequence on the upper strand, producing a two base 3'-protruding end. magnesium ions and s:-adenosyl-l-methionine (adomet) are required for cleavage. s:-adenosylhomocy ... | 2001 | 11160921 |
| catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and x-ray crystallographic investigation. | the catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (mdh) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (pqq). a crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. a theoretical an ... | 2001 | 11149955 |
| amia is a negative regulator of acetamidase expression in mycobacterium smegmatis. | the acetamidase of mycobacterium smegmatis is a highly inducible enzyme. expression of this enzyme is increased 100-fold when the substrate acetamide is present. the acetamidase gene is found immediately downstream of three open reading frames. two of these are proposed to be involved in regulation. | 2001 | 11570974 |
| genomic signature tags (gsts): a system for profiling genomic dna. | genomic signature tags (gsts) are the products of a method we have developed for identifying and quantitatively analyzing genomic dnas. the dna is initially fragmented with a type ii restriction enzyme. an oligonucleotide adaptor containing a recognition site for mmei, a type iis restriction enzyme, is then used to release 21-bp tags from fixed positions in the dna relative to the sites recognized by the fragmenting enzyme. these tags are pcr-amplified, purified, concatenated, and then cloned an ... | 2002 | 12421763 |
| bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. | seasonal shifts in bacterioplankton community composition in toolik lake, a tundra lake on the north slope of alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (dom). a shift in community composition, measured by denaturing gradient gel electrophoresis (dgge) of 16s rrna genes, occurred at 4 degrees c in near-surface waters beneath seasonal ice and snow cover in spring. this shift was associated with an annual peak in bacteri ... | 2003 | 12676708 |
| a mutant of paracoccus denitrificans with disrupted genes coding for cytochrome c550 and pseudoazurin establishes these two proteins as the in vivo electron donors to cytochrome cd1 nitrite reductase. | in paracoccus denitrificans, electrons pass from the membrane-bound cytochrome bc(1) complex to the periplasmic nitrite reductase, cytochrome cd(1). the periplasmic protein cytochrome c(550) has often been implicated in this electron transfer, but its absence, as a consequence of mutation, has previously been shown to result in almost no attenuation in the ability of the nitrite reductase to function in intact cells. here, the hypothesis that cytochrome c(550) and pseudoazurin are alternative el ... | 2003 | 14563865 |
| crystal structure of histamine dehydrogenase from nocardioides simplex. | histamine dehydrogenase (hadh) isolated from nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. hadh is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. we describe the first crystal structure of a recombinant form of hadh (hadh) to 2.7-a resolution. hadh is a homodimer, where each 76-kda subunit contains an iron-sulfur cluster ([4fe-4s](2+)) and a 6-s-cysteinyl flavin mononuc ... | 2010 | 20538584 |
| flow sorting of marine bacterioplankton after fluorescence in situ hybridization. | we describe an approach to sort cells from coastal north sea bacterioplankton by flow cytometry after in situ hybridization with rrna-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (card-fish). in a sample from spring 2003 >90% of the cells were detected by card-fish with a bacterial probe (eub338). approximately 30% of the microbial assemblage was affiliated with the cytophaga-flavobacterium lineage of the bacteroidetes (cfb group) ( ... | 2004 | 15466568 |
| pcogr: phylogenetic cog ranking as an online tool to judge the specificity of cogs with respect to freely definable groups of organisms. | the rapidly increasing number of completely sequenced genomes led to the establishment of the cog-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of orthologous groups (cogs). there are several bioinformatic studies that made use of this database to determine (hyper)thermophile-specific proteins by searching for cogs containing (almost) exclusively proteins from (hyper)thermophilic genomes. however, public software to perform individual ... | 2004 | 15488147 |
| kinetic isotope effects and ligand binding in pqq-dependent methanol dehydrogenase. | the reaction of pqq (2,7,9-tricarboxypyrroloquinoline quinone)-dependent mdh (methanol dehydrogenase) from methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [gee (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of mdh). studies of initial velocity with methanol (protiated methanol, c1h3o1h) and [2h]methanol (deuteriated methanol, c2 ... | 2005 | 15617516 |
| soluble expression of recombinant proteins in the cytoplasm of escherichia coli. | pure, soluble and functional proteins are of high demand in modern biotechnology. natural protein sources rarely meet the requirements for quantity, ease of isolation or price and hence recombinant technology is often the method of choice. recombinant cell factories are constantly employed for the production of protein preparations bound for downstream purification and processing. eschericia coli is a frequently used host, since it facilitates protein expression by its relative simplicity, its i ... | 2005 | 15629064 |
| characterization of a bifunctional puta homologue from bradyrhizobium japonicum and identification of an active site residue that modulates proline reduction of the flavin adenine dinucleotide cofactor. | puta is a bifunctional flavoenzyme in bacteria that catalyzes the four-electron oxidation of proline to glutamate. in certain prokaryotes such as escherichia coli, puta is also a transcriptional repressor of the proline utilization (put) genes and thus is trifunctional. in this work, we have begun to assess differences between bifunctional and trifunctional puta enzymes by examining the puta protein from bradyrhizobium japonicum (bjputa). primary structure analysis of bjputa shows it lacks the d ... | 2005 | 15966737 |
| functional annotation by identification of local surface similarities: a novel tool for structural genomics. | protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. hence, functional annotation by means of sequence or fold similarity is not adequate for such cases. | 2005 | 16076399 |
| application of the bacteriophage mu-driven system for the integration/amplification of target genes in the chromosomes of engineered gram-negative bacteria--mini review. | the advantages of phage mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. the cis and trans requirements for mu phage-mediated transposition, which include the l/r ends of the mu dna, the transposition factors mua and mub, and the cis/trans functioning of the e element as an enhancer, are presented. mini-mu(lr)/(ler) units are mu derivatives that lack most of the mu genes but contain the l/r ends or a properly arranged e element in cis to the l/r en ... | 2011 | 21698377 |
| specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. | high-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. a total of 570 bacterial cultures were obtained by employing the most probable number and microdrop techniques. the majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the alpha-proteobacteria, beta-proteobacteria, actinobacteria, firmicutes, or flavobacteria-c ... | 2005 | 16204504 |
| Biochemical and Mutational Studies of the Bacillus cereus CECT 5050T Formamidase Support the Existence of a C-E-E-K Tetrad in Several Members of the Nitrilase Superfamily. | Formamidases (EC 3.5.1.49) are poorly characterized proteins. In spite of this scarce knowledge, ammonia has been described as playing a central role in the pathogenesis of human pathogens such as Helicobacter pylori, for which formamidase has been shown to participate in the nitrogen metabolic pathway. Sequence analysis has revealed that at least two different groups of formamidases are classified as EC 3.5.1.49: on the one hand, the derivatives of the FmdA-AmdA superfamily, which are the best ... | 2011 | 21705545 |
| primer extension enrichment reaction (peer): a new subtraction method for identification of genetic differences between biological specimens. | we developed a conceptually new subtraction strategy for the detection and isolation of target dna and/or rna from complex nucleic acid mixtures, called primer extension enrichment reaction (peer). peer uses adapters and class iis restriction enzymes to generate tagged oligonucleotides from dsdna fragments derived from specimens containing an unknown target ('tester'). subtraction is achieved by selectively disabling these oligonucleotides by extension reaction using ddntps and a double stranded ... | 2006 | 16790564 |
| clonothrix fusca roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. | crenothrix polyspora cohn 1870 and clonothrix fusca roze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. very recently, dna sequencing data from uncultured c. polyspora-enriched material have suggested that crenothrix is a methane-oxidizing gamma-proteobacterium (39). in contrast, the possible ecological function of c. fusca, originally cons ... | 2007 | 17416684 |
| integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. | integrons are horizontal gene transfer (hgt) systems containing elements necessary for site-specific recombination and expression of foreign dna. the overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. this report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. first, using culture-independent techniques, we explored the diversity of integrons and integron-tran ... | 2004 | 14766601 |
| composition and dynamics of bacterial communities of a drinking water supply system as assessed by rna- and dna-based 16s rrna gene fingerprinting. | bacterial community dynamics of a whole drinking water supply system (dwss) were studied from source to tap. raw water for this dwss is provided by two reservoirs with different water characteristics in the harz mountains of northern germany. samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. rna and dna were extracted from the sampled water. the 16s rrna or its gen ... | 2006 | 16517632 |
| insights into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effects on the reaction of n-methyltryptophan oxidase. | the mechanism of n-methyltryptophan oxidase, a flavin-dependent amine oxidase from escherichia coli, was studied using a combination of kinetic isotope effects and theoretical calculations. the 15(kcat/km) kinetic isotope effect for sarcosine oxidation is ph-dependent with a limiting value of 0.994-0.995 at high ph. density functional theory calculations on model systems were used to interpret these isotope effects. the isotope effects are inconsistent with proposed mechanisms involving covalent ... | 2007 | 17542620 |
| molecular basis of bacterial outer membrane permeability revisited. | gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. this review summarizes the development in the field since ... | 2003 | 14665678 |
| protein aq_1862 from the hyperthermophilic bacterium aquifex aeolicus is a porin and contains two conductance pathways of different selectivity. | the "hypothetical protein" aq_1862 was isolated from the membrane fraction of aquifex aeolicus and identified as the major porin. in experiments with one conducting unit (molecule) a conductance of 1.4 ns was observed in 0.1 m kcl at ph 7.5. this stable (basic) conductance was superimposed by conductance fluctuations of approximately 0.25 ns. because both events were always observed simultaneously, it is suggested that they are caused by the same molecular entity. nonetheless they show very diff ... | 2007 | 17586565 |
| dissection of the caffeate respiratory chain in the acetogen acetobacterium woodii: identification of an rnf-type nadh dehydrogenase as a potential coupling site. | the anaerobic acetogenic bacterium acetobacterium woodii couples caffeate reduction with electrons derived from hydrogen to the synthesis of atp by a chemiosmotic mechanism with sodium ions as coupling ions, a process referred to as caffeate respiration. we addressed the nature of the hitherto unknown enzymatic activities involved in this process and their cellular localization. cell extract of a. woodii catalyzes h(2)-dependent caffeate reduction. this reaction is strictly atp dependent but can ... | 2007 | 17873051 |
| determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. | molecular dynamics (md) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (mdh), and soluble glucose dehydrogenase (sgdh). the mechanisms of reduction of the orthoquinone cofactor (pqq) of mdh and sgdh involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon c5 of pqq. the products of methan ... | 2004 | 15273299 |
| investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rrna analysis, and fluorescent in situ hybridization-microautoradiography. | the acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (sip). [13c]acetate was used in sip to label the dna of the denitrifiers. the [13c]dna fraction that was extracted was subjected to a full-cycle rrna analysis. the dominant 16s rrna gene phylotypes in the 13c library were closely related to the bacterial families comamonadaceae and rhodocyclaceae in the class betaproteobacteria. seven oligonuc ... | 2005 | 16332863 |
| construction of stably maintained non-mobilizable derivatives of rsf1010 lacking all known elements essential for mobilization. | rsf1010 is a well-studied broad-host-range plasmid able to be mobilized to different bacteria and plants. rsf1010-derived plasmid vectors are widely used in both basic research and industrial applications. in the latter case, exploiting of mobilizable plasmids or even the plasmids possessing negligible mobilization frequency, but containing dna fragments that could promote conjugal transfer, is undesirable because of biosafety considerations. previously, several mutations significantly decreasin ... | 2007 | 18028554 |
| characterization of a novel methanol dehydrogenase in representatives of burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. | some members of burkholderiales are able to grow on methanol but lack the genes (mxafi) responsible for the well-characterized two-subunit pyrroloquinoline quinone-dependent quinoprotein methanol dehydrogenase that is widespread in methylotrophic proteobacteria. here, we characterized novel, mono-subunit enzymes responsible for methanol oxidation in four strains, methyloversatilis universalis fam5, methylibium petroleiphilum pm1, and unclassified burkholderiales strains rz18-153 and fam1. the en ... | 2008 | 18390659 |
| a comparison of random sequence reads versus 16s rdna sequences for estimating the biodiversity of a metagenomic library. | the construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16s rdna sequences has been used for over two decades to examine bacterial biodiversity. here, we show that the analysis of random sequence reads (rsrs) instead of 16s is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. we generated 10,010 rsrs from a metagenomic library of microorganisms found in human faecal samples. ... | 2008 | 18682527 |
| functional analysis of mmei from methanol utilizer methylophilus methylotrophus, a subtype iic restriction-modification enzyme related to type i enzymes. | mmei from methylophilus methylotrophus belongs to the type ii restriction-modification enzymes. it recognizes an asymmetric dna sequence, 5'-tccrac-3' (r indicates g or a), and cuts both strands at fixed positions downstream of the specific site. this particular feature has been exploited in transcript profiling of complex genomes (using serial analysis of gene expression technology). we have shown previously that the endonucleolytic activity of mmei is strongly dependent on the presence of s-ad ... | 2009 | 18997032 |
| functional analysis of mmei from methanol utilizer methylophilus methylotrophus, a subtype iic restriction-modification enzyme related to type i enzymes. | mmei from methylophilus methylotrophus belongs to the type ii restriction-modification enzymes. it recognizes an asymmetric dna sequence, 5'-tccrac-3' (r indicates g or a), and cuts both strands at fixed positions downstream of the specific site. this particular feature has been exploited in transcript profiling of complex genomes (using serial analysis of gene expression technology). we have shown previously that the endonucleolytic activity of mmei is strongly dependent on the presence of s-ad ... | 2009 | 18997032 |
| oligomeric structure and functional characterization of the urea transporter from actinobacillus pleuropneumoniae. | urea transporters (uts) facilitate urea permeation across cell membranes in prokaryotes and eukaryotes. bacteria use urea as a means to survive in acidic environments and/or as a nitrogen source. the ut from actinobacillus pleuropneumoniae, aput, the pathogen that causes porcine pleurisy and pneumonia, was expressed in escherichia coli and purified. analysis of the recombinant protein using cross-linking and blue-native gel electrophoresis established that aput is a dimer in detergent solution. ... | 2009 | 19361419 |
| functional characterization of the re-face loop spanning residues 536-541 and its interactions with the cofactor in the flavin mononucleotide-binding domain of flavocytochrome p450 from bacillus megaterium. | flavocytochrome p450bm-3, a bacterial monooxygenase, contains a flavin mononucleotide-binding domain bearing a strong structural homology to the bacterial flavodoxin. the flavin mononucleotide (fmn) serves as the one-electron donor to the heme iron, but in contrast to the electron transfer mechanism of mammalian cytochrome p450 reductase, the fmn semiquinone state is not thermodynamically stable and appears transiently as the anionic rather than the neutral form. a unique loop region comprised o ... | 2009 | 19432415 |
| cloning and analysis of a bifunctional methyltransferase/restriction endonuclease tspgwi, the prototype of a thermus sp. enzyme family. | restriction-modification systems are a diverse class of enzymes. they are classified into four major types: i, ii, iii and iv. we have previously proposed the existence of a thermus sp. enzyme family, which belongs to type ii restriction endonucleases (reases), however, it features also some characteristics of types i and iii. members include related thermophilic endonucleases: tspgwi, taqii, tspdti, and tth111ii. | 2009 | 19480701 |
| aromatic amino acid auxotrophs constructed by recombinant marker exchange in methylophilus methylotrophus as1 cells expressing the arop-encoded transporter of escherichia coli. | the isolation of auxotrophic mutants, which is a prerequisite for a substantial genetic analysis and metabolic engineering of obligate methylotrophs, remains a rather complicated task. we describe a novel method of constructing mutants of the bacterium methylophilus methylotrophus as1 that are auxotrophic for aromatic amino acids. the procedure begins with the mu-driven integration of the escherichia coli gene arop, which encodes the common aromatic amino acid transporter, into the genome of m. ... | 2010 | 19880640 |
| aromatic amino acid auxotrophs constructed by recombinant marker exchange in methylophilus methylotrophus as1 cells expressing the arop-encoded transporter of escherichia coli. | the isolation of auxotrophic mutants, which is a prerequisite for a substantial genetic analysis and metabolic engineering of obligate methylotrophs, remains a rather complicated task. we describe a novel method of constructing mutants of the bacterium methylophilus methylotrophus as1 that are auxotrophic for aromatic amino acids. the procedure begins with the mu-driven integration of the escherichia coli gene arop, which encodes the common aromatic amino acid transporter, into the genome of m. ... | 2010 | 19880640 |
| occurrence and sequence of sphaeroides heme protein and diheme cytochrome c in purple photosynthetic bacteria in the family rhodobacteraceae. | sphaeroides heme protein (shp) was discovered in the purple photosynthetic bacterium, rhodobacter sphaeroides, and is the only known c-type heme protein that binds oxygen. although initially not believed to be widespread among the photosynthetic bacteria, the gene has now been found in more than 40 species of proteobacteria and generally appears to be regulated. rb. sphaeroides is exceptional in not having regulatory genes associated with the operon. we have thus analyzed additional purple bacte ... | 2010 | 20587053 |
| growth of wildtype and mutant e. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides. | since rnas lie at the center of most cellular processes, there is a need for synthesizing large amounts of rnas made from stable isotope-labeled nucleotides to advance the study of their structure and dynamics by nuclear magnetic resonance (nmr) spectroscopy. a particularly effective means of obtaining labeled nucleotides is to harvest these nucleotides from bacteria grown in defined minimal media supplemented with 15nh4cl and various carbon sources. given the high cost of carbon precursors requ ... | 2010 | 20730533 |
| impact of the n5-proximal asn on the thermodynamic and kinetic stability of the semiquinone radical in photolyase. | flavoproteins can dramatically adjust the thermodynamics and kinetics of electron transfer at their flavin cofactor. a versatile regulatory tool is proton transfer. here, we demonstrate the significance of proton-coupled electron transfer to redox tuning and semiquinone (sq) stability in photolyases (pls) and cryptochromes (crys). these light-responsive proteins share homologous overall architectures and fad-binding pockets, yet they have evolved divergent functions that include dna repair, phot ... | 2010 | 21131361 |
| impact of the n5-proximal asn on the thermodynamic and kinetic stability of the semiquinone radical in photolyase. | flavoproteins can dramatically adjust the thermodynamics and kinetics of electron transfer at their flavin cofactor. a versatile regulatory tool is proton transfer. here, we demonstrate the significance of proton-coupled electron transfer to redox tuning and semiquinone (sq) stability in photolyases (pls) and cryptochromes (crys). these light-responsive proteins share homologous overall architectures and fad-binding pockets, yet they have evolved divergent functions that include dna repair, phot ... | 2010 | 21131361 |
| purification, crystallization and preliminary x-ray crystallographic analysis of a methanol dehydrogenase from the marine bacterium methylophaga aminisulfidivorans mp(t). | methylophaga aminisulfidivorans mp(t) is a marine methylotrophic bacterium that utilizes c(1) compounds such as methanol as a carbon and energy source. the released electron from oxidation flows through a methanol-oxidizing system (mox) consisting of a series of electron-transfer proteins encoded by the mox operon. one of the key enzymes in the pathway is methanol dehydrogenase (mdh), which contains the prosthetic group pyrroloquinoline quinone (pqq) and converts methanol to formaldehyde in the ... | 2011 | 21505255 |
| methylotrophy in a lake: from metagenomics to single organism physiology. | this review provides a brief summary of on-going studies in lake washington (seattle, usa) directed at understanding of the content and activities of microbial communities involved in methylotrophy. one of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of methylotenera species in the site and their inferred activity in c1 metabolism, highlighting the local environmental importance of this group. comparative analyses of individual ge ... | 2011 | 21622781 |
| analysis and manipulation of aspartate pathway genes for l-lysine overproduction from methanol by bacillus methanolicus. | we investigated the regulation and roles of six aspartate pathway genes in l-lysine overproduction in bacillus methanolicus: dapg, encoding aspartokinase i (aki); lysc, encoding akii; yclm, encoding akiii; asd, encoding aspartate semialdehyde dehydrogenase; dapa, encoding dihydrodipicolinate synthase; and lysa, encoding meso-diaminopimelate decarboxylase. analysis of the wild-type strain revealed that in vivo lysc transcription was repressed 5-fold by l-lysine and induced 2-fold by dl-methionine ... | 2011 | 21724876 |
| gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the atlantic ocean. | methanol biogeochemistry and its importance as a carbon source in seawater is relatively unexplored. we report the first microbial methanol carbon assimilation rates (k) in productive coastal upwelling waters of up to 0.117±0.002 d(-1) (~10 nmol l(-1 )d(-1)). on average, coastal upwelling waters were 11 times greater than open ocean northern temperate (nt) waters, eight times greater than gyre waters and four times greater than equatorial upwelling (eu) waters; suggesting that all upwelling wate ... | 2013 | 23178665 |
| gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the atlantic ocean. | methanol biogeochemistry and its importance as a carbon source in seawater is relatively unexplored. we report the first microbial methanol carbon assimilation rates (k) in productive coastal upwelling waters of up to 0.117±0.002 d(-1) (~10 nmol l(-1 )d(-1)). on average, coastal upwelling waters were 11 times greater than open ocean northern temperate (nt) waters, eight times greater than gyre waters and four times greater than equatorial upwelling (eu) waters; suggesting that all upwelling wate ... | 2013 | 23178665 |
| the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. | the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ... | 2013 | 23451130 |
| prokaryotic diversity in zostera noltii-colonized marine sediments. | the diversity of microorganisms present in a sediment colonized by the phanerogam zostera noltii has been analyzed. microbial dna was extracted and used for constructing two 16s rdna clone libraries for bacteria and archaea. bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. eight major lineages of the domain bacteria were represented in the library. the most frequently retrieved bacterial group (36% of the clones) was delta- ... | 2000 | 10742267 |
| isolation and metabolic characteristics of previously uncultured members of the order aquificales in a subsurface gold mine. | culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order aquificales from a subsurface hot aquifer of a japanese gold mine. thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of aquificales were successfully isolated. 16s ribosomal dna clone analysis of the entire microbial dna assemblage and fluorescence in situ whole-ce ... | 2002 | 12039766 |
| quantitative rrna-targeted solution-based hybridization assay using peptide nucleic acid molecular beacons. | the potential of a solution-based hybridization assay using peptide nucleic acid (pna) molecular beacon (mb) probes to quantify 16s rrna of specific populations in rna extracts of environmental samples was evaluated by designing pna mb probes for the genera dechloromonas and dechlorosoma. in a kinetic study with 16s rrna from pure cultures, the hybridization of pna mb to target 16s rrna exhibited a higher final hybridization signal and a lower apparent rate constant than the hybridizations to no ... | 2008 | 18820054 |
| mmei: a minimal type ii restriction-modification system that only modifies one dna strand for host protection. | mmei is an unusual type ii restriction enzyme that is useful for generating long sequence tags. we have cloned the mmei restriction-modification (r-m) system and found it to consist of a single protein having both endonuclease and dna methyltransferase activities. the protein comprises an amino-terminal endonuclease domain, a central dna methyltransferase domain and c-terminal dna recognition domain. the endonuclease cuts the two dna strands at one site simultaneously, with enzyme bound at two s ... | 2008 | 18931376 |
| relative axial ligand orientation in bis(imidazole)iron(ii) porphyrinates: are "picket fence" derivatives different? | the synthesis of three new bis(imidazole)-ligated iron(ii) picket fence porphyrin derivatives, [fe(tpivpp)(1-rim) 2] 1-rim = 1-methyl-, 1-ethyl-, or 1-vinylimidazole) are reported. x-ray structure determinations reveal that the steric requirements of the four alpha,alpha,alpha,alpha-o-pivalamidophenyl groups lead to very restricted rotation of the imidazole ligand on the picket side of the porphyrin plane; the crowding leads to an imidazole plane orientation eclipsing an iron-porphyrin nitrogen ... | 2008 | 18351735 |
| the mmei family: type ii restriction-modification enzymes that employ single-strand modification for host protection. | the type ii restriction endonucleases form one of the largest families of biochemically-characterized proteins. these endonucleases typically share little sequence similarity, except among isoschizomers that recognize the same sequence. mmei is an unusual type ii restriction endonuclease that combines endonuclease and methyltransferase activities in a single polypeptide. mmei cuts dna 20 bases from its recognition sequence and modifies just one dna strand for host protection. using mmei as query ... | 2009 | 19578066 |
| functional and shunt states of bacteriorhodopsin resolved by 250 ghz dynamic nuclear polarization-enhanced solid-state nmr. | observation and structural studies of reaction intermediates of proteins are challenging because of the mixtures of states usually present at low concentrations. here, we use a 250 ghz gyrotron (cyclotron resonance maser) and cryogenic temperatures to perform high-frequency dynamic nuclear polarization (dnp) nmr experiments that enhance sensitivity in magic-angle spinning nmr spectra of cryo-trapped photocycle intermediates of bacteriorhodopsin (br) by a factor of approximately 90. multidimensio ... | 2009 | 19474298 |
| analysis of the electrochemistry of hemes with e(m)s spanning 800 mv. | the free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. it is a challenge to determine how proteins manage to achieve this enormous range of e(m)s with a single type of redox cofactor. proteins containing 141 unique hemes of a-, b-, and c-type, with bis-his, his-met, and aquo-his ligation were calculated using multi-conformation continuum electrostatics (mcce). the experimental e(m)s range over 800 mv from -350 mv in cytochrome c(3) to 450 mv in cytoc ... | 2009 | 19003997 |
| studies on the mechanism of electron bifurcation catalyzed by electron transferring flavoprotein (etf) and butyryl-coa dehydrogenase (bcd) of acidaminococcus fermentans. | electron bifurcation is a fundamental strategy of energy coupling originally discovered in the q-cycle of many organisms. recently a flavin-based electron bifurcation has been detected in anaerobes, first in clostridia and later in acetogens and methanogens. it enables anaerobic bacteria and archaea to reduce the low-potential [4fe-4s] clusters of ferredoxin, which increases the efficiency of the substrate level and electron transport phosphorylations. here we characterize the bifurcating electr ... | 2014 | 24379410 |
| superpose3d: a local structural comparison program that allows for user-defined structure representations. | local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. the outcome of such analyses is critically dependent on the representation used to describe the structure. indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. we have therefore developed superpose3d, a novel structural comparison softw ... | 2010 | 20700534 |
| modular architecture of nucleotide-binding pockets. | recently, modularity has emerged as a general attribute of complex biological systems. this is probably because modular systems lend themselves readily to optimization via random mutation followed by natural selection. although they are not traditionally considered to evolve by this process, biological ligands are also modular, being composed of recurring chemical fragments, and moreover they exhibit similarities reminiscent of mutations (e.g. the few atoms differentiating adenine and guanine). ... | 2010 | 20185567 |
| a conserved active-site threonine is important for both sugar and flavin oxidations of pyranose 2-oxidase. | pyranose 2-oxidase (p2o) catalyzes the oxidation by o(2) of d-glucose and several aldopyranoses to yield the 2-ketoaldoses and h(2)o(2). based on crystal structures, in one rotamer conformation, the threonine hydroxyl of thr(169) forms h-bonds to the flavin-n5/o4 locus, whereas, in a different rotamer, it may interact with either sugar or other parts of the p2o.sugar complex. transient kinetics of wild-type (wt) and thr(169) --> s/n/g/a replacement variants show that d-glc binds to t169s, t169n, ... | 2010 | 20089849 |
| analysis of bacterial core communities in the central baltic by comparative rna-dna-based fingerprinting provides links to structure-function relationships. | understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. to this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central baltic sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (gotland deep, 235 m). bacterial community structure was followed by 16s ribosomal rna (rrna)- and 16s rrna gene-based fingerprint ... | 2011 | 21697960 |
| analysis of bacterial core communities in the central baltic by comparative rna-dna-based fingerprinting provides links to structure-function relationships. | understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. to this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central baltic sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (gotland deep, 235 m). bacterial community structure was followed by 16s ribosomal rna (rrna)- and 16s rrna gene-based fingerprint ... | 2011 | 21697960 |
| endonuclease specificity and sequence dependence of type iis restriction enzymes. | restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. despite this, systematic functional categorization of cleavage performance has largely been lacking. we established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. we coupled this to massively parallel sequencing in order to provide sensitive and accurat ... | 2015 | 25629514 |
| phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches. | group-wise diversity of sediment methylotrophs of chilika lake (lat. 19°28'-19°54'n; long. 85°06'-85°35'e) odisha, india at various identified sites was studied. both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaf and 16s rrna genes as markers. ardra profiling, 16s rrna gene sequencing, page profiling of haeiii, ecori restricted mxaf gene and the mxaf gene sequences using culture-dependent approach revealed the relatedness o ... | 2015 | 25805901 |
| bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria. | autoclaving of crude oil is often used to evaluate the hydrocarbon-degrading abilities of bacteria. this may be potentially useful for bioaugmentation and microbial enhanced oil recovery (meor). however, it is not entirely clear if "endogenous" bacteria (e.g., spores) in/on crude oil survive the autoclaving process, or influence subsequent evaluation of the hydrocarbon-degradation abilities of the "exogenous" bacterial strains. to test this, we inoculated autoclaved crude oil medium with six exo ... | 2012 | 23028421 |