Publications

rna-seq-based analysis of cold shock response in thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene.	although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. thermoanaerobacter tengcongensis mb4, a thermophile harboring only one known cold shock protein gene (ttescpc), can survive from 50° to 80 °c, but has poor natural competence under cold shock at 50 °c. we therefore examined cold shock responses ...	2014	24667527
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?	evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...	2014	24521160
the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family.	we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins.	2014	24908050
structural basis of thermal stability of the tungsten cofactor synthesis protein moab from pyrococcus furiosus.	molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. the biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (mpt) by adenylylation before the respective metal is incorporated. in the hyperthermophilic organism pyrococcus furiosus, the hexameric protein moab (pfumoab) has been shown to catalyse mpt-ad ...	2014	24465852
dna polymerases engineered by directed evolution to incorporate non-standard nucleotides.	dna polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. however, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. the focus of this review is on non-standard nucleotides that expand the genetic "alphabet." this review focuses on experiments that, by directed evolution, ha ...	2014	25400626
an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference.	crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ...	2014	25505143
an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference.	crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ...	2014	25505143
crystal structure of cas9 in complex with guide rna and target dna.	the crispr-associated endonuclease cas9 can be targeted to specific genomic loci by single guide rnas (sgrnas). here, we report the crystal structure of streptococcus pyogenes cas9 in complex with sgrna and its target dna at 2.5 å resolution. the structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgrna:dna heteroduplex in a positively charged groove at their interface. whereas the recognition lobe is essential for binding sgrna and dna, ...	2014	24529477
structures of cas9 endonucleases reveal rna-mediated conformational activation.	type ii crispr (clustered regularly interspaced short palindromic repeats)-cas (crispr-associated) systems use an rna-guided dna endonuclease, cas9, to generate double-strand breaks in invasive dna during an adaptive bacterial immune response. cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. we report 2.6 and 2.2 angstrom resolution crystal structures of two major cas9 enzyme subtypes, revealing the structural core shared by all cas9 ...	2014	24505130
phylogenetic analysis and evolutionary origins of dna polymerase x-family members.	mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ...	2014	25112931
magnesium-dependent processes are targets of bacterial manganese toxicity.	a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ...	2014	24975873
crystal structures and kinetic properties of enoyl-acyl carrier protein reductase i from candidatus liberibacter asiaticus.	huanglongbing (hlb) is a destructive citrus disease. the leading cause of hlb is candidatus liberibacter asiaticus. fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. enoyl-acyl carrier protein reductase (also called enr or fabi and a product of the fabi gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agen ...	2014	24407918
the moxr atpase rava and its cofactor viaa interact with the nadh:ubiquinone oxidoreductase i in escherichia coli.	moxr atpases are widespread throughout bacteria and archaea. the experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. in escherichia coli, the moxr atpase rava and its putative cofactor viaa are found to exist in early stationary-phase cells at 37 °c at low levels of about 350 and 90 molecules per cell, respectively. both proteins are predominantly localized to the cytopla ...	2014	24454883
conserved amino acid residues of the nuod segment important for structure and function of escherichia coli ndh-1 (complex i).	the nuod segment (homologue of mitochondrial 49 kda subunit) of the proton-translocating nadh:quinone oxidoreductase (complex i/ndh-1) from escherichia coli is in the hydrophilic domain and bears many highly conserved amino acid residues. the three-dimensional structural model of ndh-1 suggests that the nuod segment, together with the neighboring subunits, constitutes a putative quinone binding cavity. we used the homologous dna recombination technique to clarify the role of selected key amino a ...	2014	25545070
conserved amino acid residues of the nuod segment important for structure and function of escherichia coli ndh-1 (complex i).	the nuod segment (homologue of mitochondrial 49 kda subunit) of the proton-translocating nadh:quinone oxidoreductase (complex i/ndh-1) from escherichia coli is in the hydrophilic domain and bears many highly conserved amino acid residues. the three-dimensional structural model of ndh-1 suggests that the nuod segment, together with the neighboring subunits, constitutes a putative quinone binding cavity. we used the homologous dna recombination technique to clarify the role of selected key amino a ...	2014	25545070
re-evaluation of the near infrared spectra of mitochondrial cytochrome c oxidase: implications for non invasive in vivo monitoring of tissues.	we re-determined the near infrared (nir) spectral signatures (650-980nm) of the different cytochrome c oxidase redox centres, in the process separating them into their component species. we confirm that the primary contributor to the oxidase nir spectrum between 700 and 980nm is cupric cua, which in the beef heart enzyme has a maximum at 835nm. the 655nm band characterises the fully oxidised haem a3/cub binuclear centre; it is bleached either when one or more electrons are added to the binuclear ...	2014	25175349
how periplasmic thioredoxin tlpa reduces bacterial copper chaperone scoi and cytochrome oxidase subunit ii (coxb) prior to metallation.	two critical cysteine residues in the copper-a site (cu(a)) on subunit ii (coxb) of bacterial cytochrome c oxidase lie on the periplasmic side of the cytoplasmic membrane. as the periplasm is an oxidizing environment as compared with the reducing cytoplasm, the prediction was that a disulfide bond formed between these cysteines must be eliminated by reduction prior to copper insertion. we show here that a periplasmic thioredoxin (tlpa) acts as a specific reductant not only for the cu(2+) transfe ...	2014	25274631
a third subunit in ancestral cytochrome c-dependent nitric oxide reductases.	reduction of no to n2o by denitrifiying bacteria is catalyzed either by a monomeric quinol-nitric oxide reductase (qnor) or by a heterodimeric cytochrome c-dependent nitric oxide reductase (cnor). in ancient thermophilic bacteria belonging to the thermales and aquificales phylogenetic groups, the cluster encoding the cnor includes a small third gene (norh), in addition to those encoding homologues to the subunits of a typical cnor (norc and norb). we show in thermus thermophilus that the three g ...	2014	24907324
evidence for distinct electron transfer processes in terminal oxidases from different origin by means of protein film voltammetry.	cytochrome aa3 from paracoccus denitrificans and cytochrome ba3 from thermus thermophilus, two distinct members of the heme-copper oxidase superfamily, were immobilized on electrodes modified with gold nanoparticles. this procedure allowed us to achieve direct electron transfer between the enzyme and the gold nanoparticles and to obtain evidence for different electrocatalytic properties of the two enzymes. the ph dependence and thermostability reveal that the enzymes are highly adapted to their ...	2014	25054669
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
characterisation of the active/de-active transition of mitochondrial complex i.	oxidation of nadh in the mitochondrial matrix of aerobic cells is catalysed by mitochondrial complex i. the regulation of this mitochondrial enzyme is not completely understood. an interesting characteristic of complex i from some organisms is the ability to adopt two distinct states: the so-called catalytically active (a) and the de-active, dormant state (d). the a-form in situ can undergo de-activation when the activity of the respiratory chain is limited (i.e. in the absence of oxygen). the m ...	2014	24569053
linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry dft exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.	after a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear fe-a3-cub reaction center in this enzyme. a specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. a larger family of tautomers/protonation states is generate ...	2014	24960612
conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from thermus thermophilus.	knowing how the protein environment modulates ligand pathways and redox centers in the respiratory heme-copper oxidases is fundamental for understanding the relationship between the structure and function of these enzymes. in this study, we investigated the reactions of o2 and no with the fully reduced g232v mutant of ba3 cytochrome c oxidase from thermus thermophilus (tt ba3) in which a conserved glycine residue in the o2 channel of the enzyme was replaced with a bulkier valine residue. previou ...	2014	24937405
molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.	pyridoxal-5'-phosphate or plp, the active form of vitamin b6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. plp-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. here, we structurally and functionally characterize three novel plp-dependent enzymes from bacteria in the human microbiome: ...	2014	24888348
parallel pathways for nitrite reduction during anaerobic growth in thermus thermophilus.	respiratory reduction of nitrate and nitrite is encoded in thermus thermophilus by the respective transferable gene clusters. nitrate is reduced by a heterotetrameric nitrate reductase (nar) encoded along transporters and regulatory signal transduction systems within the nitrate respiration conjugative element (nce). the nitrite respiration cluster (nic) encodes homologues of nitrite reductase (nir) and nitric oxide reductase (nor). the expression and role of the nirsjm genes in nitrite respirat ...	2014	24443532
a sco protein among the hypothetical proteins of bacillus lehensis g1: its 3d macromolecular structure and association with cytochrome c oxidase.	at least a quarter of any complete genome encodes for hypothetical proteins (hps) which are largely non-similar to other known, well-characterized proteins. predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. the present study highlights the primary effort to classify and cluster 1202 hps of bacillus lehensis g1 alkaliphile to serve as a platform to mine and select specific hp(s) to be studied further in ...	2014	24641837
crystal structure of an (r)-selective ω-transaminase from aspergillus terreus.	chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ...	2014	24498081
the mononuclear molybdenum enzymes.		2014	24467397
a biochemical approach to study the role of the terminal oxidases in aerobic respiration in shewanella oneidensis mr-1.	the genome of the facultative anaerobic γ-proteobacterium shewanella oneidensis mr-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a a-type cytochrome c oxidase and a cbb 3-type oxidase. in this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. our data revealed that the cbb ...	2014	24466040
transferable denitrification capability of thermus thermophilus.	laboratory-adapted strains of thermus spp. have been shown to require oxygen for growth, including the model strains t. thermophilus hb27 and hb8. in contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. the use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. in this process, nit ...	2014	24141123
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.	the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...	2014	24688489
biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics.	the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ...	2014	24688489
the dynamic nature of genomes across the tree of life.	genomes are dynamic in lineages across the tree of life. among bacteria and archaea, for example, dna content varies throughout life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. these observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. here, we synthesize information on three aspects o ...	2014	24500971
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.	the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...	2014	24931479
molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers.	highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ...	2014	26019546
evolution of mitochondria reconstructed from the energy metabolism of living bacteria.	the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ...	2014	24804722
evolution of the f0f1 atp synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.	bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. most bioenergetic pathways have a similar general ...	2014	25188293
card integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.	although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. card is an rna polymerase (rnap)-binding protein conserved in numerous bacterial species and essential in mycobacteria. despite the importance of card, its function at transcription complexes remains unclear. we have generated a panel of mutations that individually target three independent functional modules of ca ...	2014	24962732
preliminary x-ray crystallographic analysis of an engineered glutamyl-trna synthetase from escherichia coli.	the nature of interaction between glutamyl-trna synthetase (glurs) and its trna substrate is unique in bacteria in that many bacterial glurs are capable of recognizing two trna substrates: trnaglu and trnagln. to properly understand this distinctive glurs-trna interaction it is important to pursue detailed structure-function studies; however, because of the fact that trna-glurs interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation stud ...	2014	25005090
ge23077 binds to the rna polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.	using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic ge23077 (ge) binds directly to the bacterial rna polymerase (rnap) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. the target-based resistance spectrum for ge is unusually small, reflecting the fact that the ge binding site on rnap includes residues of the rnap active center that ...	2014	24755292
superoxide dismutases and superoxide reductases.		2014	24684599
carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation.	the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ...	2014	24600042
recent advances in in vivo applications of intein-mediated protein splicing.	intein-mediated protein splicing has become an essential tool in modern biotechnology. fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. recent work has extended these in vitro applications to the cell or to whole organisms. we review recent advances in intein-mediated protein expression and modification, post-translat ...	2014	24490831
a homolog of glyceraldehyde-3-phosphate dehydrogenase from riemerella anatipestifer is an extracellular protein and exhibits biological activity.	riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. its pathogenesis and virulence factors are still unclear. the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (gapdh), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. whether homologs of gapdh exist, and display similar characteristics in r. anatipestifer (ragapdh) has not been determined. in our research, the ...	2014	25183032
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.	targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...	2013	24062736
veillonella, firmicutes: microbes disguised as gram negatives.	the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ...	2013	24976898
biological diversity in the patent system.	biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. to address this problem we text mined 11 million patent documents for 6 million latin species names from the global names index (gni) established by the global biodiversity information facility (gbif) and encyclopedia of life (eol). we identified 76,274 full latin species names from 23,882 genera in 767,955 patent documents. 2 ...	2013	24265714
two homologous ef-g proteins from pseudomonas aeruginosa exhibit distinct functions.	genes encoding two proteins corresponding to elongation factor g (ef-g) were cloned from pseudomonas aeruginosa. the proteins encoded by these genes are both members of the efg i subfamily. the gene encoding one of the forms of ef-g is located in the str operon and the resulting protein is referred to as ef-g1a while the gene encoding the other form of ef-g is located in another part of the genome and the resulting protein is referred to as ef-g1b. these proteins were expressed and purified to 9 ...	2013	24260360
aggregate-reactivation activity of the molecular chaperone clpb from ehrlichia chaffeensis.	rickettsiale diseases, including human monocytic ehrlichiosis caused by ehrlichia chaffeensis, are the second leading cause of the tick-borne infections in the usa and a growing health concern. little is known about how e. chaffeensis survives the host-induced stress in vertebrate and tick hosts. a molecular chaperone clpb from several microorganisms has been reported to reactivate aggregated proteins in cooperation with the co-chaperones dnak/dnaj/grpe (kje). in this study, we performed the fir ...	2013	23667479
insight into centromere-binding properties of parb proteins: a secondary binding motif is essential for bacterial genome maintenance.	parb proteins are one of the three essential components of partition systems that actively segregate bacterial chromosomes and plasmids. in binding to centromere sequences, parb assembles as nucleoprotein structures called partition complexes. these assemblies are the substrates for the partitioning process that ensures dna molecules are segregated to both sides of the cell. we recently identified the sopc centromere nucleotides required for binding to the parb homologue of plasmid f, sopb. this ...	2013	23345617
type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines.	pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ...	2013	24148833
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.	full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...	2013	24084083
the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation.	full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ...	2013	24084083
type iv pili in gram-positive bacteria.	type iv pili (t4p) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, dna uptake (competence), and protein secretion and that can act as nanowires carrying electric current. t4p are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type ii secretion systems in eubacteria and the flagella of archaea. t4p are found throughout gram-negative bacterial families and have been studied most ...	2013	24006467
replacing sulfa drugs with novel dhps inhibitors.	more research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. the enzyme dhps has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. the use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. despite the large amount of structural information available for dhps, few recent publi ...	2013	23859210
angling for uniqueness in enzymatic preparation of glycosides.	in the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. this is a general bird's-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. as far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features ...	2013	24970171
molecular mechanisms of crispr-mediated microbial immunity.	bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ...	2013	23959171
molecular mechanisms of crispr-mediated microbial immunity.	bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ...	2013	23959171
density functional study for the bridged dinuclear center based on a high-resolution x-ray crystal structure of ba3 cytochrome c oxidase from thermus thermophilus.	strong electron density for a peroxide type dioxygen species bridging the fea3 and cub dinuclear center (dnc) was observed in the high-resolution (1.8 å) x-ray crystal structures (pdb entries 3s8g and 3s8f) of ba3 cytochrome c oxidase (cco) from thermus thermophilus. the crystals represent the as-isolated x-ray photoreduced cco structures. the bridging peroxide was proposed to arise from the recombination of two radiation-produced ho(•) radicals formed either very near to or even in the space be ...	2013	24262070
investigating the function of [2fe-2s] cluster n1a, the off-pathway cluster in complex i, by manipulating its reduction potential.	nadh:quinone oxidoreductase (complex i) couples nadh oxidation and quinone reduction to proton translocation across an energy-transducing membrane. all complexes i contain a flavin to oxidize nadh, seven iron-sulfur clusters to transfer electrons from the flavin to quinone and an eighth cluster (n1a) on the opposite side of the flavin. the role of cluster n1a is unknown, but escherichia coli complex i has an unusually high-potential cluster n1a and its reduced flavin produces h2o2, not superoxid ...	2013	23980528
molecular mechanism and physiological role of active-deactive transition of mitochondrial complex i.	the unique feature of mitochondrial complex i is the so-called a/d transition (active-deactive transition). the a-form catalyses rapid oxidation of nadh by ubiquinone (k ~104 min-1) and spontaneously converts into the d-form if the enzyme is idle at physiological temperatures. such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. the d-form can undergo reactivation given both nadh and ubiquinone availability during slow ( ...	2013	24059527
the nitric-oxide reductase from paracoccus denitrificans uses a single specific proton pathway.	the no reductase from paracoccus denitrificans reduces no to n2o (2no + 2h(+) + 2e(-) → n2o + h2o) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent no reductase; cnor). cnors are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the o2-reducing, proton-pumping respiratory enzymes. in contrast, although no reduction is as exergonic as o2 reduction, there are no protons pumped in cnor, and in addition, protons needed for no reduction ...	2013	24014024
axial interactions in the mixed-valent cua active site and role of the axial methionine in electron transfer.	within cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent cua sites is less clear. recently, the mutation of the axial met to leu in a cua site engineered into azurin (cua az) was found to have a limited effect on e(0) relative to this mutation in blue copper (bc). detailed low-temperature absorption and magnetic circular dichroism, resonance raman, and electron paramagnetic resonance studies on c ...	2013	23964128
comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.	metal sulfide mineral dissolution during bioleaching and acid mine drainage (amd) formation creates an environment that is inhospitable to most life. despite dominance by a small number of bacteria, amd microbial biofilm communities contain a notable variety of coexisting and closely related euryarchaea, most of which have defied cultivation efforts. for this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring amd arch ...	2013	23865623
characterization of the nitric oxide reductase from thermus thermophilus.	nitrous oxide (n2o) is a powerful greenhouse gas implicated in climate change. the dominant source of atmospheric n2o is incomplete biological dentrification, and the enzymes responsible for the release of n2o are no reductases. it was recently reported that ambient emissions of n2o from the great boiling spring in the united states great basin are high, and attributed to incomplete denitrification by thermus thermophilus and related bacterial species [hedlund bp, et al. (2011) geobiology 9(6)47 ...	2013	23858452
post-translational modifications near the quinone binding site of mammalian complex i.	complex i (nadh:ubiquinone oxidoreductase) in mammalian mitochondria is an l-shaped assembly of 44 protein subunits with one arm buried in the inner membrane of the mitochondrion and the orthogonal arm protruding about 100 å into the matrix. the protruding arm contains the binding sites for nadh, the primary acceptor of electrons flavin mononucleotide (fmn), and a chain of seven iron-sulfur clusters that carries the electrons one at a time from fmn to a coenzyme q molecule bound in the vicinity ...	2013	23836892
combined effect of loss of the caa3 oxidase and crp regulation drives shewanella to thrive in redox-stratified environments.	shewanella species are a group of facultative gram-negative microorganisms with remarkable respiration abilities that allow the use of a diverse array of terminal electron acceptors (ea). like most bacteria, s. oneidensis possesses multiple terminal oxidases, including two heme-copper oxidases (caa3- and cbb3-type) and a bd-type quinol oxidase. as aerobic respiration is energetically favored, mechanisms underlying the fact that these microorganisms thrive in redox-stratified environments remain ...	2013	23575370
semiquinone and cluster n6 signals in his-tagged proton-translocating nadh:ubiquinone oxidoreductase (complex i) from escherichia coli.	nadh:ubiquinone oxidoreductase (complex i) pumps protons across the membrane using downhill redox energy. the escherichia coli complex i consists of 13 different subunits named nuoa-n coded by the nuo operon. due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ~15-kb operon, purification of e. coli complex i has been technically challenging. here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoe in the op ...	2013	23543743
the mechanism of ubihydroquinone oxidation at the qo-site of the cytochrome bc1 complex.	1. recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. the bifurcated reaction at the qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (sq) intermediate, and a rapid second electron transfer in which the sq is oxidized by the low potential chain. 3. the rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a ma ...	2013	23396004
etmb-rbf: discrimination of metal-binding sites in electron transporters based on rbf networks with pssm profiles and significant amino acid pairs.	cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. as cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. the function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. in these oxidation-reduction reactions in electron transport chains, metal ions play very i ...	2013	23405059
ligand access to the active site in thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.	knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. using photolabile no and o(2) carriers, we recently found that no and o(2) binding in thermus thermophilus (tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. using x-ray crystallography, time-resolved optical absorpti ...	2013	23282175
atypical features of thermus thermophilus succinate:quinone reductase.	the thermus thermophilus succinate:quinone reductase (sqr), serving as the respiratory complex ii, has been homologously produced under the control of a constitutive promoter and subsequently purified. the detailed biochemical characterization of the resulting wild type (wt-rcii) and his-tagged (rcii-his(8)-sdhb and rcii-sdhb-his(6)) complex ii variants showed the same properties as the native enzyme with respect to the subunit composition, redox cofactor content and sensitivity to the inhibitor ...	2013	23308253
systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.	we present a novel analysis of compositional order (co) based on the occurrence of frequent amino-acid triplets (fts) that appear much more than random in protein sequences. the method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. we introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and t ...	2013	24278003
initiation of mrna decay in bacteria.	the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ...	2013	24064983
initiation of mrna decay in bacteria.	the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ...	2013	24064983
detection, distribution and characterization of novel superoxide dismutases from yersinia enterocolitica biovar 1a.	superoxide dismutases (sods) cause dismutation of superoxide radicals to hydrogen peroxide and oxygen. besides protecting the cells against oxidative damage by endogenously generated oxygen radicals, sods play an important role in intraphagocytic survival of pathogenic bacteria. the complete genome sequences of yersinia enterocolitica strains show presence of three different sod genes. however, not much is known about the types of sods present in y. enterocolitica, their characteristics and role ...	2013	23704955
psychrophily and catalysis.	polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. ...	2013	24832805
structures of protein-protein complexes involved in electron transfer.	electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of atp, and are involved in many reactions of intermediary metabolism. key to these roles is the formation of transient inter-protein electron transfer complexes. the structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic ...	2013	23535590
integron gene cassettes: a repository of novel protein folds with distinct interaction sites.	mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. in most cases, functional annotation of gene cassettes directly recovered by cassette-pcr is obscured by their characteristically high sequence novelty. this inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. a structural genomics approach incorporating x-ray crystallograph ...	2013	23349695
phosphoproteomic analysis reveals the effects of pilf phosphorylation on type iv pilus and biofilm formation in thermus thermophilus hb27.	thermus thermophilus hb27 is an extremely thermophilic eubacteria with a high frequency of natural competence. this organism is therefore often used as a thermophilic model to investigate the molecular basis of type iv pili-mediated functions, such as the uptake of free dna, adhesion, twitching motility, and biofilm formation, in hot environments. in this study, the phosphoproteome of t. thermophilus hb27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. ninety-three uniqu ...	2013	23828892
structure of the mtb card/rnap β-lobes complex reveals the molecular basis of interaction and presents a distinct dna-binding domain for mtb card.	card from mycobacterium tuberculosis (mtb) is an essential protein shown to be involved in stringent response through downregulation of rrna and ribosomal protein genes. card interacts with the β-subunit of rnap and this interaction is vital for mtb's survival during the persistent infection state. we have determined the crystal structure of card in complex with the rnap β-subunit β1 and β2 domains at 2.1 å resolution. the structure reveals the molecular basis of card/rnap interaction, providing ...	2013	24055315
crystallization and preliminary x-ray analysis of an alanine dehydrogenase from bacillus megaterium wsh-002.	alanine dehydrogenase (l-aladh) from bacillus megaterium wsh-002 catalyses the nad⁺-dependent interconversion of l-alanine and pyruvate. the enzyme was expressed in escherichia coli bl21 (de3) cells and purified with a his6 tag by ni²⁺-chelating affinity chromatography for x-ray crystallographic analysis. crystals were grown in a solution consisting of 0.1 m hepes ph 8.0, 12%(w/v) polyethylene glycol 8000, 8%(v/v) ethylene glycol at a concentration of 15 mg ml⁻¹ purified protein. the crystal dif ...	2013	23908047
type iv pilus proteins form an integrated structure extending from the cytoplasm to the outer membrane.	the bacterial type iv pilus (t4p) is the strongest biological motor known to date as its retraction can generate forces well over 100 pn. myxococcus xanthus, a δ-proteobacterium, provides a good model for t4p investigations because its social (s) gliding motility is powered by t4p. in this study, the interactions among m. xanthus t4p proteins were investigated using genetics and the yeast two-hybrid (y2h) system. our genetic analysis suggests that there is an integrated t4p structure that crosse ...	2013	23922942
structure and function of card, an essential mycobacterial transcription factor.	card, an essential transcription regulator in mycobacterium tuberculosis, directly interacts with the rna polymerase (rnap). we used a combination of in vivo and in vitro approaches to establish that card is a global regulator that stimulates the formation of rnap-holoenzyme open promoter (rpo) complexes. we determined the x-ray crystal structure of thermus thermophilus card, allowing us to generate a structural model of the card/rpo complex. on the basis of our structural and functional analyse ...	2013	23858468
activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpob) mutations in actinomycetes.	a subset of rifampin resistance (rpob) mutations result in the overproduction of antibiotics in various actinomycetes, including streptomyces, saccharopolyspora, and amycolatopsis, with h437y and h437r rpob mutations effective most frequently. moreover, the rpob mutations markedly activate (up to 70-fold at the transcriptional level) the cryptic/silent secondary metabolite biosynthetic gene clusters of these actinomycetes, which are not activated under general stressful conditions, with the exce ...	2013	23603745
peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly.	the peptidoglycan (pg) cell wall is a unique macromolecule responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria. a quantitative understanding of the relationships between pg architecture, morphogenesis, immune system activation and pathogenesis can provide molecular-scale insights into the function of proteins involved in cell wall synthesis and cell growth. high-performance liquid chromatography (hplc) has played an important role in our ...	2013	23679048
nusg-spt5 proteins-universal tools for transcription modification and communication.		2013	23638618
pilmnopq from the pseudomonas aeruginosa type iv pilus system form a transenvelope protein interaction network that interacts with pila.	pseudomonas aeruginosa type iv pili (t4p) are virulence factors that promote infection of cystic fibrosis and immunosuppressed patients. as the absence of t4p impairs colonization, they are attractive targets for the development of novel therapeutics. genes in the pilmnopq operon are important for both t4p assembly and a form of bacterial movement, called twitching motility, that is required for pathogenicity. the type ii membrane proteins, piln and pilo, dimerize via their periplasmic domains a ...	2013	23457250
the crispr-associated gene cas2 of legionella pneumophila is required for intracellular infection of amoebae.	recent studies have shown that the clustered regularly interspaced palindromic repeats (crispr) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. upon analysis of the legionella pneumophila strain 130b chromosome, we detected a subtype ii-b crispr-cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. reverse transcription (rt)-pcr analysis demonstrated that the entire crispr-cas locus is expres ...	2013	23481601
bacterial cell-envelope glycoconjugates.	prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. the scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. this article a ...	2013	24274370
in planta mutagenesis of src homology 3 domain-like fold of ndhs, a ferredoxin-binding subunit of the chloroplast nadh dehydrogenase-like complex in arabidopsis: a conserved arg-193 plays a critical role in ferredoxin binding.	chloroplast nadh dehydrogenase-like (ndh) complex mediates cyclic electron transport around photosystem i and chlororespiration in angiosperms. the src homology 3 domain (sh3)-like fold protein ndhs/crr31 is an ndh subunit that is necessary for high affinity binding of ferredoxin, indicating that chloroplast ndh functions as a ferredoxin:plastoquinone oxidoreductase. however, the mechanism of the interaction between ndhs and ferredoxin is unclear. in this study, we analyzed their interaction in ...	2013	24225949
a novel type of n-acetylglutamate synthase is involved in the first step of arginine biosynthesis in corynebacterium glutamicum.	arginine biosynthesis in corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by n-acetylglutamate synthase (nags). there are different kinds of known nagss, for example, "classical" arga, bifunctional argj, argo, and s-nags. however, since c. glutamicum possesses a monofunctional argj, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown nags gene.	2013	24138314
archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in sulfolobus acidocaldarius.	in this study, the in vitro and in vivo functions of the only two identified protein phosphatases, saci-ptp and saci-pp2a, in the crenarchaeal model organism sulfolobus acidocaldarius were investigated. biochemical characterization revealed that saci-ptp is a dual-specific phosphatase (against pser/pthr and ptyr), whereas saci-pp2a exhibited specific pser/pthr activity and inhibition by okadaic acid. deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, wh ...	2013	24078887
the tetr family of regulators.	the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ...	2013	24006471
cloning and characterization of ef-tu and ef-ts from pseudomonas aeruginosa.	we have cloned genes encoding elongation factors ef-tu and ef-ts from pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. sequence analysis indicated that p. aeruginosa ef-tu and ef-ts are 84% and 55% identical to e. coli counterparts, respectively. p. aeruginosa ef-tu was active when assayed in gdp exchange assays. kinetic parameters for the interaction of ef-tu with gdp in the absence of ef-ts were observed to be k m = 33 μm, k cat (obs) = 0.003 s(-1 ...	2013	23984384
the glove-like structure of the conserved membrane protein tatc provides insight into signal sequence recognition in twin-arginine translocation.	in bacteria, two signal-sequence-dependent secretion pathways translocate proteins across the cytoplasmic membrane. although the mechanism of the ubiquitous general secretory pathway is becoming well understood, that of the twin-arginine translocation pathway, responsible for translocation of folded proteins across the bilayer, is more mysterious. tatc, the largest and most conserved of three integral membrane components, provides the initial binding site of the signal sequence prior to pore ass ...	2013	23583035
determination of the structure of the catabolic n-succinylornithine transaminase (astc) from escherichia coli.	escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (astc) and the other anabolic (argd), that participate in l-arginine metabolism. although only 58% identical, the enzymes have been shown to be functionally interchangeable. here we have purified astc and have obtained x-ray crystal structures of apo and holo-astc and of the enzyme complexed with its physiological substrate, succinylornithine. we compare the structures obtained in this study with those of argd from sa ...	2013	23484010
shallow breathing: bacterial life at low o(2).	competition for molecular oxygen (o(2)) among respiratory microorganisms is intense because o(2) is a potent electron acceptor. this competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. bacteria can harvest o(2) present at low, even nanomolar, concentrations using high-affinity terminal oxidases. here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced ...	2013	23411864
the variability of the 16s rrna gene in bacterial genomes and its consequences for bacterial community analyses.	16s ribosomal rna currently represents the most important target of study in bacterial ecology. its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. here we use the information from sequenced bacterial genomes to explore the variability of 16s rrna sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome an ...	2013	23460914