| purification and properties of cellvibrio gilvus cellobiose phosphorylase. | the cellobiose phosphorylase (ec 2.4.1.20) of cellvibrio gilvus, which is an endocellular enzyme, has been purified 196-fold with a recovery of 11% and a specific activity of 27.4 mumol of glucose 1-phosphate formed/min per mg of protein. the purification procedure includes fractionation with protamine sulphate, and hydroxyapatite and deae-sephadex a-50 chromatography. the enzyme appears homogeneous on polyacrylamide-gel electrophoresis, and a molecular weight of 280 000 was determined by molecu ... | 1983 | 6223623 |
| construction and characterization of a chimeric beta-glucosidase. | the amino acid sequences of beta-glucosidases from cellvibrio gilvus and agrobacterium tumefaciens show significant similarity in most of the parts. however, the ph/temperature optima and stabilities of the two enzymes are quite different. c. gilvus beta-glucosidase exhibits an optimum ph of 6.2-6.4 and temperature of 35 degrees c, whereas the corresponding values for a. tumefaciens are 7.2-7.4 and 60 degrees c respectively. to analyse these properties further, a chimeric beta-glucosidase was co ... | 1995 | 7848268 |
| biodegradation of phosphonomycin by rhizobium huakuii pmy1. | the biodegradation by rhizobium huakuii pmy1 of up to 10 mm phosphonomycin as a carbon, energy, and phosphorus source with accompanying p(i) release is described. this biodegradation represents a further mechanism of resistance to this antibiotic and a novel, phosphate-deregulated route for organophosphonate metabolism by rhizobium spp. | 1998 | 9435089 |
| cloning and characterization of the glucooligosaccharide catabolic pathway beta-glucan glucohydrolase and cellobiose phosphorylase in the marine hyperthermophile thermotoga neapolitana. | characterization in thermotoga neapolitana of a catabolic gene cluster encoding two glycosyl hydrolases, 1,4-beta-d-glucan glucohydrolase (ggha) and cellobiose phosphorylase (cbpa), and the apparent absence of a cellobiohydrolase (cbh) suggest a nonconventional pathway for glucan utilization in thermotogales. ggha purified from t. neapolitana is a 52.5-kda family 1 glycosyl hydrolase with optimal activity at ph 6.5 and 95 degrees c. ggha releases glucose from soluble glucooligomers, with a prefe ... | 2000 | 10960102 |
| conserved glycines in the c terminus of minc proteins are implicated in their functionality as cell division inhibitors. | alignment of 36 minc sequences revealed four completely conserved c-terminal glycines. as minc inhibits cytokinesis in neisseria gonorrhoeae and escherichia coli, the functional importance of these glycines in n. gonorrhoeae minc (minc(ng)) and e. coli minc (minc(ec)) was investigated through amino acid substitution by using site-directed mutagenesis. each mutant was evaluated for its ability to arrest cell division and to interact with itself and mind. in contrast to overexpression of wild-type ... | 2004 | 15090526 |
| structural dissection of the reaction mechanism of cellobiose phosphorylase. | cellobiose phosphorylase, a member of the glycoside hydrolase family 94, catalyses the reversible phosphorolysis of cellobiose into alpha-d-glucose 1-phosphate and d-glucose with inversion of the anomeric configuration. the substrate specificity and reaction mechanism of cellobiose phosphorylase from cellvibrio gilvus have been investigated in detail. we have determined the crystal structure of the glucose-sulphate and glucose-phosphate complexes of this enzyme at a maximal resolution of 2.0 a ( ... | 2006 | 16646954 |
| a glycosyltransferase with a length-controlling activity as a mechanism to regulate the size of polysaccharides. | cyclic beta-1,2-glucans (cbetag) are osmolyte homopolysaccharides with a cyclic beta-1,2-backbone of 17-25 glucose residues present in the periplasmic space of several bacteria. initiation, elongation, and cyclization, the three distinctive reactions required for building the cyclic structure, are catalyzed by the same protein, the cbetag synthase. the initiation activity catalyzes the transference of the first glucose from udp-glucose to a yet-unidentified amino acid residue in the same protein ... | 2007 | 17921247 |
| characterization of three beta-galactoside phosphorylases from clostridium phytofermentans: discovery of d-galactosyl-beta1->4-l-rhamnose phosphorylase. | we characterized three d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylase (ec 2.4.1.211) homologs from clostridium phytofermentans (cphy0577, cphy1920, and cphy3030 proteins). cphy0577 and cphy3030 proteins exhibited similar activity on galacto-n-biose (gnb; d-gal-beta1-->3-d-galnac) and lacto-n-biose i (lnb; d-gal-beta1-->3-d-glcnac), thus indicating that they are d-galactosyl-beta1-->3-n-acetyl-d-hexosamine phosphorylases, subclassified as gnb/lnb phosphorylase. in contrast, cphy1920 p ... | 2009 | 19491100 |
| crystallization and x-ray diffraction studies of cellobiose phosphorylase from cellulomonas uda. | disaccharide phosphorylases are able to catalyze both the synthesis and the breakdown of disaccharides and have thus emerged as attractive platforms for tailor-made sugar synthesis. cellobiose phosphorylase from cellulomonas uda (cpcuda) is an enzyme that belongs to glycoside hydrolase family 94 and catalyzes the reversible breakdown of cellobiose [beta-d-glucopyranosyl-(1,4)-d-glucopyranose] to alpha-d-glucose-1-phosphate and d-glucose. crystals of ligand-free recombinant cpcuda and of its comp ... | 2010 | 20208178 |
| structure of cellobiose phosphorylase from clostridium thermocellum in complex with phosphate. | clostridium thermocellum is a cellulosome-producing bacterium that is able to efficiently degrade and utilize cellulose as a sole carbon source. cellobiose phosphorylase (cbp) plays a critical role in cellulose degradation by catalyzing the reversible phosphate-dependent hydrolysis of cellobiose, the major product of cellulose degradation, into α-d-glucose 1-phosphate and d-glucose. cbp from c. thermocellum is a modular enzyme composed of four domains [n-terminal domain, helical linker, (α/α)(6) ... | 2011 | 22102229 |
| microbial cellulases and their industrial applications. | microbial cellulases have shown their potential application in various industries including pulp and paper, textile, laundry, biofuel production, food and feed industry, brewing, and agriculture. due to the complexity of enzyme system and immense industrial potential, cellulases have been a potential candidate for research by both the academic and industrial research groups. nowadays, significant attentions have been devoted to the current knowledge of cellulase production and the challenges in ... | 2011 | 21912738 |
| variable stoichiometry and homeostatic regulation of bacterial biomass elemental composition. | prokaryotic heterotrophs (hereafter, bacteria) represent a large proportion of global biomass, and therefore bacterial biomass stoichiometry likely exerts control on global phosphorus (p), carbon (c), and nitrogen cycling and primary productivity. in this study we grew recently isolated freshwater heterotrophic bacteria across an ecologically relevant range of resource c:p ratios (organic c to p ratio in available resources) to quantify the p requirements of these organisms and examine the degre ... | 2012 | 22371708 |
| the genome sequences of cellulomonas fimi and "cellvibrio gilvus" reveal the cellulolytic strategies of two facultative anaerobes, transfer of "cellvibrio gilvus" to the genus cellulomonas, and proposal of cellulomonas gilvus sp. nov. | actinobacteria in the genus cellulomonas are the only known and reported cellulolytic facultative anaerobes. to better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the cellulomonas fimi atcc 484(t). for comparative purposes, we also sequenced the genome of the aerobic cellulolytic "cellvibrio gilvus" atcc 13127(t). an initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that "cellvibrio gilvus" belongs to the gen ... | 2013 | 23342046 |
| unique aspects of fiber degradation by the ruminal ethanologen ruminococcus albus 7 revealed by physiological and transcriptomic analysis. | bacteria in the genus ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. in particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. for example, ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. the mechanism of cellulose degradation by r. albus 7 i ... | 2014 | 25477200 |
| overcoming inefficient cellobiose fermentation by cellobiose phosphorylase in the presence of xylose. | cellobiose and xylose co-fermentation holds promise for efficiently producing biofuels from plant biomass. cellobiose phosphorylase (cbp), an intracellular enzyme generally found in anaerobic bacteria, cleaves cellobiose to glucose and glucose-1-phosphate, providing energetic advantages under the anaerobic conditions required for large-scale biofuel production. however, the efficiency of cbp to cleave cellobiose in the presence of xylose is unknown. this study investigated the effect of xylose o ... | 2014 | 24944578 |
| intrastrand triplex dna repeats in bacteria: a source of genomic instability. | repetitive nucleic acid sequences are often prone to form secondary structures distinct from b-dna. prominent examples of such structures are dna triplexes. we observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. a systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the itxf database available online at http://bioinformatics.uni-konstanz.de/utils/itxf/ ... | 2015 | 26450966 |
| crystal structure and substrate recognition of cellobionic acid phosphorylase, which plays a key role in oxidative cellulose degradation by microbes. | the microbial oxidative cellulose degradation system is attracting significant research attention after the recent discovery of lytic polysaccharide mono-oxygenases. a primary product of the oxidative and hydrolytic cellulose degradation system is cellobionic acid (cba), the aldonic acid form of cellobiose. we previously demonstrated that the intracellular enzyme belonging to glycoside hydrolase family 94 from cellulolytic fungus and bacterium is cellobionic acid phosphorylase (cbap), which cata ... | 2015 | 26041776 |
| genomic analysis of six new geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. | in this work we report the whole genome sequences of six new geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. the six sequenced geobacillus strains described here have a range of gc contents from 43.9% to 52.5% and clade with named geobacillus species throughout the entire genus. we have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic ... | 2015 | 26029180 |
| c/n ratio drives soil actinobacterial cellobiohydrolase gene diversity. | cellulose accounts for approximately half of photosynthesis-fixed carbon; however, the ecology of its degradation in soil is still relatively poorly understood. the role of actinobacteria in cellulose degradation has not been extensively investigated despite their abundance in soil and known cellulose degradation capability. here, the diversity and abundance of the actinobacterial glycoside hydrolase family 48 (cellobiohydrolase) gene in soils from three paired pasture-woodland sites were determ ... | 2015 | 25710367 |
| enzymatic synthesis using glycoside phosphorylases. | carbohydrate phosphorylases are readily accessible but under-explored catalysts for glycoside synthesis. their use of accessible and relatively stable sugar phosphates as donor substrates underlies their potential. a wide range of these enzymes has been reported of late, displaying a range of preferences for sugar donors, acceptors and glycosidic linkages. this has allowed this class of enzymes to be used in the synthesis of diverse carbohydrate structures, including at the industrial scale. as ... | 2015 | 25060838 |
| molecular mechanism and evolution of guanylate kinase regulation by (p)ppgpp. | the nucleotide (p)ppgpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. here, we characterize the molecular interaction between (p)ppgpp and guanylate kinase (gmk), revealing the importance of this interaction in adaptation to starvation. combining structural and kinetic analyses, we show that (p)ppgpp binds the gmk active site and competitively inhibits the enzyme. the (p)ppgpp-gmk interact ... | 2015 | 25661490 |
| comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales. | production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ... | 2015 | 25607991 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| genome-wide gene order distances support clustering the gram-positive bacteria. | initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ... | 2015 | 25653643 |
| highly diverse nirk genes comprise two major clades that harbour ammonium-producing denitrifiers. | copper dependent nitrite reductase, nirk, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. distinct structural nirk classes and phylogenetic clades of nirk-type denitrifiers have previously been observed based on a limited set of nirk sequences, however, their environmental distribution or ecological strategies are currently unknown. in addition, environmental nirk-type denitrifiers are currently underestimated in pcr-dependent surveys due to primer coverage lim ... | 2016 | 26923558 |
| bactquant: an enhanced broad-coverage bacterial quantitative real-time pcr assay. | bacterial load quantification is a critical component of bacterial community analysis, but a culture-independent method capable of detecting and quantifying diverse bacteria is needed. based on our analysis of a diverse collection of 16 s rrna gene sequences, we designed a broad-coverage quantitative real-time pcr (qpcr) assay--bactquant--for quantifying 16 s rrna gene copy number and estimating bacterial load. we further utilized in silico evaluation to complement laboratory-based qpcr characte ... | 2012 | 22510143 |
| microbial cellulose utilization: fundamentals and biotechnology. | fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. the methodological basis for studying microbial cellulose utilization is considered relative to qu ... | 2002 | 12209002 |
| freshwater bacteria are stoichiometrically flexible with a nutrient composition similar to seston. | although aquatic bacteria are assumed to be nutrient-rich, they out-compete other foodweb osmotrophs for nitrogen (n) and phosphorus (p) an apparent contradiction to resource ratio theory. this paradox could be resolved if aquatic bacteria were demonstrated to be nutrient-poor relative other portions of the planktonic food web. in a survey of >120 lakes in the upper midwest of the usa, the nutrient content of bacteria was lower than previously reported and very similar to the redfield ratio, wit ... | 2010 | 21687767 |
| structures of streptococcus pneumoniae piaa and its complex with ferrichrome reveal insights into the substrate binding and release of high affinity iron transporters. | iron scarcity is one of the nutrition limitations that the gram-positive infectious pathogens streptococcus pneumoniae encounter in the human host. to guarantee sufficient iron supply, the atp binding cassette (abc) transporter pia is employed to uptake iron chelated by hydroxamate siderophore, via the membrane-anchored substrate-binding protein piaa. the high affinity towards ferrichrome enables piaa to capture iron at a very low concentration in the host. we presented here the crystal structur ... | 2013 | 23951167 |
| draft genome sequence of cellulomonas carbonis t26(t) and comparative analysis of six cellulomonas genomes. | most cellulomonas strains are cellulolytic and this feature may be applied in straw degradation and bioremediation. in this study, cellulomonas carbonis t26(t), cellulomonas bogoriensis dsm 16987(t) and cellulomonas cellasea 20108(t) were sequenced. here we described the draft genomic information of c. carbonis t26(t) and compared it to the related cellulomonas genomes. strain t26(t) has a 3,990,666 bp genome size with a g + c content of 73.4 %, containing 3418 protein-coding genes and 59 rna ge ... | 2015 | 26587181 |
| whole genome comparison of thermus sp. nmx2.a1 reveals principle carbon metabolism differences with closest relation thermus scotoductus sa-01. | genome sequencing of the yellow-pigmented, thermophilic bacterium thermus sp. nmx2.a1 resulted in a 2.29 mb draft genome that encodes for 2312 proteins. the genetic relationship between various strains from the genus thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. the resulting phylogenetic tree illustrated that thermus sp. nmx2 a.1 clusters together with thermus scotoductus sa-01, despite being isolated from vastly different geographical locat ... | 2016 | 27412985 |