| structures of domains i and iv from ybbr are representative of a widely distributed protein family. | ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ... | 2011 | 21154411 |
| structures of domains i and iv from ybbr are representative of a widely distributed protein family. | ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ... | 2011 | 21154411 |
| functional role of ribosomal signatures. | although structure and sequence signatures in ribosomal rna and proteins are defining characteristics of the three domains of life and instrumental in constructing the modern phylogeny, little is known about their functional roles in the ribosome. in this work, the largest coevolving rna/protein signatures in the bacterial 30s ribosome are investigated both experimentally and computationally through all-atom molecular-dynamics simulations. the complex includes the n-terminal fragment of the ribo ... | 2010 | 21156135 |
| intrinsic resistance to aminoglycosides in enterococcus faecium is conferred by the 16s rrna m5c1404-specific methyltransferase efmm. | aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. here we show that aminoglycoside resistance in enterococcus faecium strain cip 54-32 is conferred by the chromosomal gene efmm, encoding the e. faecium methyltransferase, as well as by the previously characterized aac(6')-ii that encodes a 6'-n-aminoglycoside acetyltransferase. inactivation of efmm in e. faecium increases susceptibility to the aminoglycosides k ... | 2010 | 21159796 |
| biochemistry. catalyzing no to n2o in the nitrogen cycle. | | 2010 | 21164002 |
| methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. | the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ... | 2010 | 21166890 |
| methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. | the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ... | 2010 | 21166890 |
| a mechanism for single-stranded dna-binding protein (ssb) displacement from single-stranded dna upon ssb-reco interaction. | displacement of single-stranded dna (ssdna)-binding protein (ssb) from ssdna is necessary for filament formation of reca on ssdna to initiate homologous recombination. the interaction between reco and ssb is considered to be important for ssb displacement; however, the interaction has not been characterized at the atomic level. in this study, to clarify the mechanism underlying ssb displacement from ssdna upon reco binding, we examined the interaction between thermus thermophilus reco and cognat ... | 2010 | 21169364 |
| metagenomic analyses: past and future trends. | metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ... | 2010 | 21169428 |
| metagenomic analyses: past and future trends. | metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ... | 2010 | 21169428 |
| lateral transfer of the denitrification pathway genes among thermus thermophilus strains. | nitrate respiration is a common and strain-specific property in thermus thermophilus encoded by the nitrate respiration conjugative element (nce) that can be laterally transferred by conjugation. in contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. these later steps of the denitrification pathway are under the regulatory control of an nce-encoded transcription factor, but nothing is known about their coding sequences or its putative ... | 2010 | 21169443 |
| a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12. | β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ... | 2010 | 21169565 |
| a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12. | β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ... | 2010 | 21169565 |
| crystal structure of stable protein cuta1 from psychrotrophic bacterium shewanella sp. sib1. | cuta1 is widely found in bacteria, plants and animals, including humans. the functions of cuta1, however, have not been well clarified. it is known that cuta1s from pyrococcus horikoshii, thermus thermophilus and oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. in this work the crystal structure of cuta1 from the psychrotrophic bacterium shewanella sp. sib1 (sib1-cuta1) in a trimeric form was determined at 2.7 å resolution. this is the fir ... | 2010 | 21169681 |
| the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects. | rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ... | 2010 | 21177858 |
| the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects. | rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ... | 2010 | 21177858 |
| valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder. | the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro. | 2010 | 21184843 |
| valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder. | the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro. | 2010 | 21184843 |
| structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila. | fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ... | 2010 | 21185305 |
| structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila. | fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ... | 2010 | 21185305 |
| rna polymerase and transcription elongation factor spt4/5 complex structure. | spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ... | 2010 | 21187417 |
| rna polymerase and transcription elongation factor spt4/5 complex structure. | spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ... | 2010 | 21187417 |
| asymmetric atp hydrolysis cycle of the heterodimeric multidrug abc transport complex tmrab from thermus thermophilus. | atp-binding cassette (abc) systems translocate a wide range of solutes across cellular membranes. the thermophilic gram-negative eubacterium thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 abc proteins, which are largely uncharacterized. here, we functionally analyzed the first two and only abc half-transporters of the hyperthermophilic bacterium, tmra and tmrb. the abc system mediates uptake of the drug hoechst 33342 in inside-out oriented vesic ... | 2010 | 21190941 |
| structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains. | argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ... | 2010 | 21193640 |
| structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains. | argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ... | 2010 | 21193640 |
| genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli. | escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ... | 2010 | 21195716 |
| genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli. | escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ... | 2010 | 21195716 |
| quantitative mapping of reversible mitochondrial complex i cysteine oxidation in a parkinson disease mouse model. | differential cysteine oxidation within mitochondrial complex i has been quantified in an in vivo oxidative stress model of parkinson disease. we developed a strategy that incorporates rapid and efficient immunoaffinity purification of complex i followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. this method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in murine ... | 2011 | 21196577 |
| stress-induced evolution of escherichia coli points to original concepts in respiratory cofactor selectivity. | bacterial metabolism is characterized by a remarkable capacity to rapidly adapt to environmental changes. we restructured the central metabolic network in escherichia coli to force a higher production of nadph, and then grew this strain in conditions favoring adaptive evolution. a six-fold increase in growth capacity was attained that could be attributed in multiple clones, after whole genome mutation mapping, to a specific single mutation. each clone had an evolved nuof*(e183a) enzyme in the re ... | 2011 | 21205901 |
| crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein moga from two thermophilic organisms. | molybdenum-cofactor (moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. two proteins, moga and moea, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. here, three crystal structures of the moco-biosynthesis protein moga from the two thermophilic organisms thermus thermophilus (ttmoga; 1.64 å resolution, space group p2(1)) and aquifex aeolicus (aamoga; 1.70 å resolut ... | 2010 | 21206014 |
| crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase. | quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ... | 2010 | 21206019 |
| crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase. | quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ... | 2010 | 21206019 |
| cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae. | bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ... | 2010 | 21206021 |
| cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae. | bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ... | 2010 | 21206021 |
| crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii. | type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ... | 2010 | 21206036 |
| crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii. | type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ... | 2010 | 21206036 |
| archaeal 3'-phosphate rna splicing ligase characterization identifies the missing component in trna maturation. | intron removal from trna precursors involves cleavage by a trna splicing endonuclease to yield trna 3'-halves beginning with a 5'-hydroxyl, and 5'-halves ending in a 2',3'-cyclic phosphate. a trna ligase then incorporates this phosphate into the internucleotide bond that joins the two halves. although this 3'-p rna splicing ligase activity was detected almost three decades ago in extracts from animal and later archaeal cells, the protein responsible was not yet identified. here we report the pur ... | 2011 | 21209330 |
| fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for escherichia coli threonyl-trna synthetase with toxic effects on growth. | in all living systems, the fidelity of translation is maintained in part by the editing mechanisms of aminoacyl-trna synthetases (arss). some nonproteogenic amino acids, including β-hydroxynorvaline (hnv) are nevertheless efficiently aminoacylated and become incorporated into proteins. to investigate the basis of hnv's ability to function in protein synthesis, the utilization of hnv by escherichia coli threonyl-trna synthetase (thrrs) was investigated through both in vitro functional experiments ... | 2011 | 21222438 |
| rtcb is the rna ligase component of an escherichia coli rna repair operon. | rna 2',3'-cyclic phosphate ends play important roles in rna metabolism as substrates for rna ligases during trna restriction-repair and trna splicing. diverse bacteria from multiple phyla encode a two-component rna repair cassette, comprising pnkp (polynucleotide kinase-phosphatase-ligase) and hen1 (rna 3'-terminal ribose 2'-o-methyltransferase), that heals and then seals broken trnas with 2',3'-cyclic phosphate and 5'-oh ends. the pnkp-hen1 repair operon is absent in the majority of bacterial s ... | 2011 | 21224389 |
| exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. | gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (cco) is a problem of great current interest. despite promising mechanistic proposals, so far, a physically consistent model that would reproduce all the relevant barriers needed to create a working pump has not been presented. in addition, there are major problems in elucidating the origin of key mutational effects and in understanding the nature of the apparent pk(a) values associated with th ... | 2011 | 21232525 |
| the biomolecular interaction network database in psi-mi 2.5. | the biomolecular interaction network database (bind) is a major source of curated biomolecular interactions, which has been unmaintained for the last few years, a trend which will eventually result in the loss of a significant amount of unique biomolecular interaction information, mostly as database identifiers become out of date. to help reverse this trend, we converted bind to a standard format, proteomics standard initiative-molecular interaction 2.5, starting from the last curated data relea ... | 2011 | 21233089 |
| biochemical and structural characterization of wlba from bordetella pertussis and chromobacterium violaceum: enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid. | the unusual sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, or mannac3naca, has been observed in the lipopolysaccharides of both pathogenic and nonpathogenic gram-negative bacteria. it is added to the lipopolysaccharides of these organisms by glycosyltransferases that use as substrates udp-mannac3naca. five enzymes are ultimately required for the biosynthesis of udp-mannac3naca starting from udp-n-acetylglucosamine. the second enzyme in the pathway, encoded by the wlba gene and referred to ... | 2011 | 21241053 |
| crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens. | the crystal structure of the enzyme phosphoglucomutase from salmonella typhimurium (stpgm) is reported at 1.7 a resolution. this is the first high-resolution structural characterization of a bacterial protein from this large enzyme family, which has a central role in metabolism and is also important to bacterial virulence and infectivity. a comparison of the active site of stpgm with that of other phosphoglucomutases reveals conserved residues that are likely involved in catalysis and ligand bin ... | 2011 | 21246636 |
| escherichia coli class ib ribonucleotide reductase contains a dimanganese(iii)-tyrosyl radical cofactor in vivo. | escherichia coli class ib ribonucleotide reductase (rnr) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates in iron-limited and oxidative stress conditions. we have recently demonstrated in vitro that this rnr is active with both diferric-tyrosyl radical (fe(iii)(2)-y(•)) and dimanganese(iii)-y(•) (mn(iii)(2)-y(•)) cofactors in the β2 subunit, nrdf [cotruvo, j. a., jr., and stubbe, j. (2010) biochemistry 49, 1297-1309]. here we demonstrate, by purification of this protein fro ... | 2011 | 21250660 |
| superfolder gfp is fluorescent in oxidizing environments when targeted via the sec translocon. | the ability to study proteins in live cells using genetically encoded fluorescent proteins (fps) has revolutionized cell biology (1-3). researchers have created numerous fp biosensors and optimized fps for specific organisms and subcellular environments in a rainbow of colors (4,5). however, expressing fps in oxidizing environments such as the eukaryotic endoplasmic reticulum (er) or the bacterial periplasm can impair folding, thereby preventing fluorescence (6,7). a substantial fraction of enha ... | 2011 | 21255213 |
| identification of macrodomain proteins as novel o-acetyl-adp-ribose deacetylases. | sirtuins are a family of protein lysine deacetylases, which regulate gene silencing, metabolism, life span, and chromatin structure. sirtuins utilize nad(+) to deacetylate proteins, yielding o-acetyl-adp-ribose (oaadpr) as a reaction product. the macrodomain is a ubiquitous protein module known to bind adp-ribose derivatives, which diverged through evolution to support many different protein functions and pathways. the observation that some sirtuins and macrodomains are physically linked as fusi ... | 2011 | 21257746 |
| manipulations in the peripheral stalk of the saccharomyces cerevisiae f1f0-atp synthase. | the saccharomyces cerevisiae f(1)f(0)-atp synthase peripheral stalk is composed of the oscp, h, d, and b subunits. the b subunit has two membrane-spanning domains and a large hydrophilic domain that extends along one side of the enzyme to the top of f(1). in contrast, the escherichia coli peripheral stalk has two identical b subunits, and subunits with substantially altered lengths can be incorporated into a functional f(1)f(0)-atp synthase. the differences in subunit structure between the eukar ... | 2011 | 21257750 |
| identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis. | dephosphocoenzyme a kinase performs the transfer of the ?-phosphate of atp to dephosphocoenzyme a, catalyzing the last step of coenzyme a biosynthesis. this enzyme belongs to the p-loop-containing ntp hydrolase superfamily, all members of which posses a three domain topology consisting of a coa domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have ... | 2011 | 21264299 |
| bacillus pumilus laccase: a heat stable enzyme with a wide substrate spectrum. | laccases are multi-copper oxidases that catalyze the one electron oxidation of a broad range of compounds. laccase substrates include substituted phenols, arylamines and aromatic thiols. such compounds are activated by the enzyme to the corresponding radicals. owing to their broad substrate range laccases are considered to be versatile biocatalysts which are capable of oxidizing natural and non-natural industrial compounds, with water as sole by-product. | 2011 | 21266052 |
| poly-alpha-glutamic acid synthesis using a novel catalytic activity of rimk from escherichia coli k-12. | poly-l-a-amino acids have various applications because of their biodegradable properties and biocompatibility. microorganisms contain several enzymes that catalyze the polymerization of l-amino acids in an atp-dependent manner, but the products from these reactions contain amide linkages at the side residues of amino acids: e.g., poly-?-glutamic acid, poly-e-lysine, and cyanophycin. in this study, we found a novel catalytic activity of rimk, a ribosomal protein s6-modifying enzyme derived from e ... | 2011 | 21278279 |
| selective inhibitors of methionyl-trna synthetase have potent activity against trypanosoma brucei infection in mice. | human african trypanosomiasis continues to be an important public health threat in extensive regions of sub-saharan africa. treatment options for infected patients are unsatisfactory due to toxicity, difficult administration regimes, and poor efficacy of available drugs. the aminoacyl-trna synthetases were selected as attractive drug targets due to their essential roles in protein synthesis and cell survival. comparative sequence analysis disclosed differences between the trypanosome and mammali ... | 2011 | 21282428 |
| crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. | the structures of the large ribosomal subunit of deinococcus radiodurans (d50s) in complex with the antibiotic lankamycin (3.2 å) and a double antibiotic complex of lankamycin and lankacidin c (3.45 å) have been determined, in continuation of previous crystallographic studies on lankacidin-d50s complex. these two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. ... | 2011 | 21282615 |
| structure and function of pilq, a secretin of the dna transporter from the thermophilic bacterium thermus thermophilus hb27. | secretins are a family of large bacterial outer membrane protein complexes mediating the transport of complex structures, such as type iv pili, dna and filamentous phage, or various proteins, such as extracellular enzymes and pathogenicity determinants. pilq of the thermophilic bacterium thermus thermophilus hb27 is a member of the secretin family required for natural transformation. here we report the isolation, structural, and functional analyses of a unique pilq from t. thermophilus. native p ... | 2011 | 21285351 |
| two novel classes of enzymes are required for the biosynthesis of aurofusarin in fusarium graminearum. | previous studies have reported the functional characterization of 9 out of 11 genes found in the gene cluster responsible for biosynthesis of the polyketide pigment aurofusarin in fusarium graminearum. here we reanalyze the function of a putative aurofusarin pump (aurt) and the two remaining orphan genes, aurz and aurs. targeted gene replacement of aurz resulted in the discovery that the compound ywa1, rather than nor-rubrofusarin, is the primary product of f. graminearum polyketide synthase 12 ... | 2011 | 21296881 |
| molecular breeding of polymerases for resistance to environmental inhibitors. | potent inhibitors limit the use of pcr assays in a wide spectrum of specimens. here, we describe the engineering of polymerases with a broad resistance to complex environmental inhibitors using molecular breeding of eight different polymerase orthologues from the genus thermus and directed evolution by csr in the presence of inhibitors. selecting for resistance to the inhibitory effects of neomylodon bone powder, we isolated 2d9, a chimeric polymerase comprising sequence elements derived from dn ... | 2011 | 21297114 |
| structure of the dimeric form of ctp synthase from sulfolobus solfataricus. | ctp synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. active ctp synthase is a tetrameric enzyme composed of a dimer of dimers. the tetramer is favoured in the presence of the substrate nucleotides atp and utp; when saturated with nucleotide, the tetramer completely dominates the oligomeric state of the enzyme. furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. the crystal structure of a dimer ... | 2011 | 21301086 |
| crystallization and preliminary x-ray crystallographic studies of ß-transaminase from mesorhizobium sp. strain luk. | ß-transaminase (ß-ta) catalyzes the transamination reaction between ß-aminocarboxylic acids and keto acids. this enzyme is a particularly suitable candidate for use as a biocatalyst for the asymmetric synthesis of enantiochemically pure ß-amino acids for pharmaceutical purposes. the ß-ta from mesorhizobium sp. strain luk (ß-tams) belongs to a novel class in that it shows ß-transaminase activity with a broad and unique substrate specificity. in this study, ß-tams was overexpressed in escherichia ... | 2011 | 21301093 |
| understanding ribosome assembly: the structure of in vivo assembled immature 30s subunits revealed by cryo-electron microscopy. | four decades after early in vitro assembly studies demonstrated that ribosome assembly is a controlled process, our understanding of ribosome assembly is still incomplete. just as structure determination has been so important to understanding ribosome function, so too will it be critical to sorting out the assembly process. here, we used a viable deletion in the yjeq gene, a recognized ribosome assembly factor, to isolate and structurally characterize immature 30s subunits assembled in vivo. the ... | 2011 | 21303937 |
| complete genome sequence of meiothermus ruber type strain (21). | meiothermus ruber (loginova et al. 1984) nobre et al. 1996 is the type species of the genus meiothermus. this thermophilic genus is of special interest, as its members share relatively low degrees of 16s rrna gene sequence similarity and constitute a separate evolutionary lineage from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. the temperature related split is in accordance with the chemotaxonomic feature of the polar l ... | 2010 | 21304689 |
| complete genome sequence of meiothermus silvanus type strain (vi-r2). | meiothermus silvanus (tenreiro et al. 1995) nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16s rrna gene sequence similarity. meiothermus constitutes an evolutionary lineage separate from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. m. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biof ... | 2010 | 21304690 |
| complete genome sequence of archaeoglobus profundus type strain (av18). | archaeoglobus profundus (burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class archaeoglobi, which is currently represented by the single family archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. all members were isolated from marine hydrothermal habitats and are obligate anaerobes. here we describe the features of the ... | 2010 | 21304717 |
| proline dehydrogenase contributes to pathogen defense in arabidopsis. | l-proline (pro) catabolism is activated in plants recovering from abiotic stresses associated with water deprivation. in this catabolic pathway, pro is converted to glutamate by two reactions catalyzed by proline dehydrogenase (prodh) and ?(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh), with ?(1)-pyrroline-5-carboxylate (p5c) as the intermediate. alternatively, under certain conditions, the p5c derived from pro is converted back to pro by p5c reductase, thus stimulating the pro-p5c cycle, whi ... | 2011 | 21311034 |
| energetics of seca dimerization. | transport of many proteins to extracytoplasmic locations occurs via the general secretion (sec) pathway. in escherichia coli, this pathway is composed of the secyeg protein-conducting channel and the seca atpase. seca plays a central role in binding the signal peptide region of preproteins, directing preproteins to membrane-bound secyeg and promoting translocation coupled with atp hydrolysis. although it is well established that seca is crucial for preprotein transport and thus cell viability, i ... | 2011 | 21315086 |
| natural competence in the hyperthermophilic archaeon pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. | in attempts to develop a method of introducing dna into pyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for dna uptake. a pyrf gene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear dna. we have demonstrated the use of this strain, designated com1, for genetic manipulation. using genetic sele ... | 2011 | 21317259 |
| il-10 expression by primary tumor cells correlates with melanoma progression from radial to vertical growth phase and development of metastatic competence. | downregulation of the immune system facilitates tumor progression at different stages of cutaneous melanoma. sentinel nodes, the first lymph nodes on lymphatics draining directly from a primary melanoma, are immune downregulated by tumor-generated immunosuppressive cytokines, including interleukin-10 (il-10). to better understand the kinetics of sentinel node suppression, we investigated il-10 expression by melanoma cells and tumor-associated macrophages and lymphocytes at different stages of pr ... | 2011 | 21317876 |
| unusual outer membrane lipid composition of the gram-negative, lipopolysaccharide-lacking myxobacterium sorangium cellulosum so ce56. | the gram-negative myxobacterium sorangium cellulosum so ce56 bears the largest bacterial genome published so far, coding for nearly 10,000 genes. careful analysis of this genome data revealed that part of the genes coding for the very well conserved biosynthesis of lipopolysaccharides (lps) are missing in this microbe. biochemical analysis gave no evidence for the presence of lps in the membranes of so ce56. by analyzing the lipid composition of its outer membrane sphingolipids were identified a ... | 2011 | 21321121 |
| activity of and development of resistance to corallopyronin a, an inhibitor of rna polymerase. | we explored the properties of corallopyronin a (cora), a poorly characterized inhibitor of bacterial rna polymerase (rnap). it displayed a 50% inhibitory concentration of 0.73 µm against rnap, compared with 11.5 nm for rifampin. the antibacterial activity of cora was also inferior to rifampin, and resistant mutants of staphylococcus aureus were easily selected. the mutations conferring resistance resided in the rpob and rpoc subunits of rnap. we conclude that cora is not a promising antibacteria ... | 2011 | 21321139 |
| bacterial toxin rele mediates frequent codon-independent mrna cleavage from the 5' end of coding regions in vivo. | the enzymatic activity of the rele bacterial toxin component of the escherichia coli relbe toxin-antitoxin system has been extensively studied in vitro and to a lesser extent in vivo. these earlier reports revealed that 1) rele alone does not exhibit mrna cleavage activity, 2) rele mediates mrna cleavage through its association with the ribosome, 3) rele-mediated mrna cleavage occurs at the ribosomal a site and, 4) cleavage of mrna by rele exhibits high codon specificity. more specifically, rele ... | 2011 | 21324908 |
| a highly conserved protein of unknown function in sinorhizobium meliloti affects srna regulation similar to hfq. | the smc01113/ybey protein, belonging to the upf0054 family, is highly conserved in nearly every bacterium. however, the function of these proteins still remains elusive. our results show that smc01113/ybey proteins share structural similarities with the mid domain of the argonaute (ago) proteins, and might similarly bind to a small-rna (srna) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial srna pathway. indee ... | 2011 | 21325267 |
| avoiding premature oxidation during the binding of cu(ii) to a dithiolate site in bssco. a rapid freeze-quench epr study. | the bacillus subtilis version of sco1 (bssco) is required for assembly of cu(a) in cytochrome c oxidase and may function in thiol-disulfide exchange and/or copper delivery. bssco binds cu(ii) with ligation by two cysteines, one histidine and one water. however, copper is a catalyst of cysteine oxidation and bssco must avoid this reaction to remain functional. time resolved, rapid freeze-quench (rfq) electron paramagnetic resonance of apo-bssco reacting with cu(ii) reveals an initial cu(ii) speci ... | 2011 | 21333651 |
| organic hydroperoxide resistance protein and ergothioneine compensate for loss of mycothiol in mycobacterium smegmatis mutants. | the msha::tn5 mutant of mycobacterium smegmatis does not produce mycothiol (msh) and was found to markedly overproduce both ergothioneine and an ~15-kda protein determined to be organic hydroperoxide resistance protein (ohr). an msha(g32d) mutant lacking msh overproduced ergothioneine but not ohr. comparison of the mutant phenotypes with those of the wild-type strain indicated the following: ohr protects against organic hydroperoxide toxicity, whereas ergothioneine does not; an additional msh-de ... | 2011 | 21335456 |
| chlorite dismutases, dyps, and efeb: 3 microbial heme enzyme families comprise the cde structural superfamily. | heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. the chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic clo(2)(-), a function believed to have evolved only in the last few decades. family members have since been found in 15 bacterial and archaeal genera, suggesting ancient roots. a structure- and sequence-based examination of the family is presented ... | 2011 | 21354424 |
| activity map of the escherichia coli rna polymerase bridge helix. | transcription, the synthesis of rna from a dna template, is performed by multisubunit rna polymerases (rnaps) in all cellular organisms. the bridge helix (bh) is a distinct feature of all multisubunit rnaps and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and rna and dna binding. because the bh has been captured in both kinked and straight conformations in different crystals structures of rnap, recently supported by mol ... | 2011 | 21357417 |
| correct assembly of iron-sulfur cluster fs0 into escherichia coli dimethyl sulfoxide reductase (dmsabc) is a prerequisite for molybdenum cofactor insertion. | the fs0 [4fe-4s] cluster of the catalytic subunit (dmsa) of escherichia coli dimethyl sulfoxide reductase (dmsabc) plays a key role in the electron transfer relay. we have now established an additional role for the cluster in directing molybdenum cofactor assembly during enzyme maturation. epr spectroscopy indicates that fs0 has a high spin ground state (s = 3/2) in its reduced form, resulting in an epr spectrum with a peak at g ~ 5.0. the cluster is predicted to be in close proximity to the mol ... | 2011 | 21357619 |
| an expanded collection and refined consensus model of glms ribozymes. | self-cleaving glms ribozymes selectively bind glucosamine-6-phosphate (glcn6p) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. representatives of the glms ribozyme class are found in gram-positive bacteria where they reside in the 5' untranslated regions (utrs) of glms messenger rnas that code for the essential enzyme l-glutamine:d-fructose-6-phosphate aminotransferase. by using comparative sequence analyses, we have expanded the number of glms r ... | 2011 | 21367971 |
| insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. | mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or atp generation). translation initiation in mammalian mitochondria requires two initiation factors, if2(mt) and if3(mt), instead of the three that are present in eubacteria. the mammalian if2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation ... | 2011 | 21368145 |
| two rotary motors in f-atp synthase are elastically coupled by a flexible rotor and a stiff stator stalk. | atp is synthesized by atp synthase (f(o)f(1)-atpase). its rotary electromotor (f(o)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (f(1)). elastic power transmission between f(o) and f(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. a particularly compliant elastic domain is located on the central rotor (c(10-15)/e/?), right between the two sites of torque ge ... | 2011 | 21368147 |
| e1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. | based on our recent work with haloferax volcanii, ubiquitin-like (ubl) proteins (samp1 and samp2) are known to be covalently attached to proteins in archaea. here, we investigated the enzymes required for the formation of these ubl-protein conjugates (sampylation) and whether this system is linked to sulfur transfer. markerless in-frame deletions were generated in h. volcanii target genes. the mutants were examined for: (i) the formation of ubl protein conjugates, (ii) growth under various condi ... | 2011 | 21368171 |
| oxidative stress resistance in deinococcus radiodurans. | deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive dna damage efficiently and accurately. it is extremely resistant to many dna-damaging agents, including ionizing radiation and uv radiation (100 to 295 nm), desiccation, and mitomycin c, which induce oxidative damage not only to dna but also to all cellular macromolecules via the production of reactive oxygen species. the extreme resilience of d. radiodurans to oxidative stress is imparted synergistically ... | 2011 | 21372322 |
| partial functional replacement of cyma by sircd in shewanella oneidensis mr-1. | the gammaproteobacterium shewanella oneidensis mr-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (dmso), in addition to the minerals fe(iii) and mn(iv). central to several respiratory pathways is cyma, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. to investigate functional redunda ... | 2011 | 21378180 |
| structural insights into cognate versus near-cognate discrimination during decoding. | the structural basis of the trna selection process is investigated by cryo-electron microscopy of ribosomes programmed with uga codons and incubated with ternary complex (tc) containing the near-cognate trp-trna(trp) in the presence of kirromycin. going through more than 350 000 images and employing image classification procedures, we find ~8% in which the tc is bound to the ribosome. the reconstructed 3d map provides a means to characterize the arrangement of the near-cognate aa-trna with respe ... | 2011 | 21378755 |
| architecture of the rna polymerase-spt4/5 complex and basis of universal transcription processivity. | related rna polymerases (rnaps) carry out cellular gene transcription in all three kingdoms of life. the universal conservation of the transcription machinery extends to a single rnap-associated factor, spt5 (or nusg in bacteria), which renders rnap processive and may have arisen early to permit evolution of long genes. spt5 associates with spt4 to form the spt4/5 heterodimer. here, we present the crystal structure of archaeal spt4/5 bound to the rnap clamp domain, which forms one side of the rn ... | 2011 | 21386817 |
| mutagenesis of the l, m, and n subunits of complex i from escherichia coli indicates a common role in function. | the membrane arm of complex i (nadh:ubiquinone oxidoreductase) contains three large, and closely related subunits, which are called l, m, and n in e. coli. these subunits are homologous to components of multi-subunit na(+)/h(+) antiporters, and so are implicated in proton translocation. | 2011 | 21387012 |
| susceptibility and mode of binding of the mycobacterium tuberculosis cysteinyl transferase mycothiol ligase to trna synthetase inhibitors. | the cysteinyl transferase mycothiol ligase, or mshc, catalyzes the fourth step in the biosynthesis of the small molecular weight thiol mycothiol. mshc is essential for growth of mycobacterium tuberculosis. two groups of known aminoacyl trna synthetase inhibitors were evaluated for inhibition of m. tuberculosis mshc including aminoacyl adenosine analogs and natural products. using enzyme assays, isothermal titration calorimetry and nmr, we show that mshc is selectively inhibited by cysteinyl sulf ... | 2011 | 21392992 |
| cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of the regulatory domain of aspartokinase (rv3709c) from mycobacterium tuberculosis. | the regulatory domain of mycobacterium tuberculosis aspartokinase (mtb-ak, mtb-ask, rv3709c) has been cloned, heterologously expressed in escherichia coli and purified using standard chromatographic techniques. screening for initial crystallization conditions using the regulatory domain (ak-+¦) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for x-ray diffraction analysis. from these four conditions five different crystal f ... | 2011 | 21393848 |
| crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate phosphatase from thermus thermophilus hb27. | mannosylglycerate (mg) is primarily known as an osmolyte and is widely distributed among (hyper)thermophilic marine microorganisms. the synthesis of mg via mannosyl-3-phosphoglycerate synthase (mpgs) and mannosyl-3-phosphoglycerate phosphatase (mpgp), the so-called two-step pathway, is the most prevalent route among these organisms. the phosphorylated intermediate mannosyl-3-phosphoglycerate is synthesized by the first enzyme and is subsequently dephosphorylated by the second. the structure of m ... | 2011 | 21393850 |
| purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon aeropyrum pernix. | the bioenergetics of archaea with respect to the evolution of electron transfer systems is very interesting. in contrast to terminal oxidases, a canonical bc1 complex has not yet been isolated from archaea. in particular, c-type cytochromes have been reported only for a limited number of species. | 2011 | 21396131 |
| the antibacterial threaded-lasso peptide capistruin inhibits bacterial rna polymerase. | capistruin, a ribosomally synthesized, post-translationally modified peptide produced by burkholderia thailandensis e264, efficiently inhibits growth of burkholderia and closely related pseudomonas strains. the functional target of capistruin is not known. capistruin is a threaded-lasso peptide (lariat peptide) consisting of an n-terminal ring of nine amino acids and a c-terminal tail of 10 amino acids threaded through the ring. the structure of capistruin is similar to that of microcin j25 (mcc ... | 2011 | 21396375 |
| biosynthesis of the rna polymerase inhibitor streptolydigin in streptomyces lydicus: tailoring modification of 3-methyl-aspartate. | the asparaginyl-trna synthetase-like slgz and methyltransferase slgm enzymes are involved in the biosynthesis of the tetramic acid streptolydigin in streptomyces lydicus. inactivation of slgz led to a novel streptolydigin derivative. overexpression of slgz, slgm, or both in s. lydicus led to a considerable increase in streptolydigin production. | 2011 | 21398531 |
| resolving stepping rotation in thermus thermophilus h(+)-atpase/synthase with an essentially drag-free probe. | vacuole-type atpases (v(o)v1) and f(o)f1 atp synthases couple atp hydrolysis/synthesis in the soluble v(1) or f1 portion with proton (or na(+)) flow in the membrane-embedded v(o) or f(o) portion through rotation of one common shaft. here we show at submillisecond resolutions the atp-driven rotation of isolated v1 and the whole v(o)v1 from thermus thermophilus, by attaching a 40-nm gold bead for which viscous drag is almost negligible. v1 made 120° steps, commensurate with the presence of three c ... | 2011 | 21407199 |
| genetic components of stringent response in vibrio cholerae. | nutritional stress elicits stringent response in bacteria involving modulation of expression of several genes. this is mainly triggered by the intracellular accumulation of two small molecules, namely, guanosine 3'-diphosphate 5'-triphosphate and guanosine 3',5'-bis(diphosphate), collectively called (p)ppgpp. like in other gram-negative bacteria, the cellular level of (p)ppgpp is maintained in vibrio cholerae, the causative bacterial pathogen of the disease cholera, by the products of two genes ... | 2011 | 21415497 |
| involvement of cara/litr and crp/fnr family transcriptional regulators in light-induced carotenoid production in thermus thermophilus. | members of the cara/litr family are merr-type transcriptional regulators that contain a c-terminal cobalamin-binding domain. they are thought to be involved in light-induced transcriptional regulation in a wide variety of nonphototrophic bacteria. based on the distribution of this kind of regulator, the current study examined carotenoid production in thermus thermophilus, and it was found to occur in a light-induced manner. litr and carotenoid and cobalamin biosynthesis genes were all located on ... | 2011 | 21421762 |
| substrate specificity of the bacillus licheniformis lyxose isomerase ydae and its application in in vitro catalysis for bioproduction of lyxose and glucose by two-step isomerization. | enzymatic processes are useful for industrially important sugar production, and in vitro two-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. a hypothetical uncharacterized protein encoded by ydae of bacillus licheniformis was found to have broad substrate specificities and has shown high catalytic efficiency on d-lyxose, suggesting that the enzyme is d-lyxose isomerase. escherichia coli bl21 expressing the recombinant protein, of 19.5 kda, s ... | 2011 | 21421786 |
| insights into physiological and genetic mupirocin susceptibility in bifidobacteria. | mupirocin is an antibiotic commonly used in selective media for the isolation of bifidobacteria. however, little is known about the genetic traits responsible for bifidobacterial resistance to mupirocin. our investigation demonstrates that all of the bifidobacteria tested exhibit a phenotype of generally high resistance to this antibiotic. the genotypic reason for bifidobacterial mupirocin resistance was further characterized by sequencing of the isoleucyl-trna synthetase gene (iles) coupled wit ... | 2011 | 21421794 |
| a rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity. | thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. one hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. here we employed a thermophilic acylphosphatase from pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. | 2011 | 21423654 |
| phylogenetic distribution and evolutionary history of bacterial dead-box proteins. | dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ... | 2011 | 21437710 |
| nmr structure of the c-terminal domain of a tyrosyl-trna synthetase that functions in group i intron splicing. | the mitochondrial tyrosyl-trna synthetases (mt tyrrss) of pezizomycotina fungi are bifunctional proteins that aminoacylate mitochondrial trna(tyr) and are structure-stabilizing splicing cofactors for group i introns. studies with the neurospora crassa synthetase (cyt-18 protein) showed that splicing activity is dependent upon pezizomycotina-specific structural adaptations that form a distinct group i intron-binding site in the n-terminal catalytic domain. although cyt-18's c-terminal domain also ... | 2011 | 21438536 |
| unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from nitrobacter winogradskyi. | chlorite dismutase (cld) is a unique heme enzyme catalyzing the conversion of clo(2)(-) to cl(-) and o(2). cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus nitrospira. here we characterized a novel cld-like protein from the chemolithoautotrophic nitrite oxidizer nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. its three-dimensional (3d) crystal st ... | 2011 | 21441524 |
| solution structure of an alternate conformation of helix27 from escherichia coli16s rrna. | helix (h)27 of 16s ribosomal (r)rna from escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. although more recent genetic analyses suggest that h27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated e. coli h27 can dynamically convert between the 885 and 888 conformations. here, we have solved the nuclear magn ... | 2011 | 21442607 |
| a model of the proton translocation mechanism of complex i. | despite decades of speculation, the proton pumping mechanism of complex i (nadh-ubiquinone oxidoreductase) is unknown and continues to be controversial. recent descriptions of the architecture of the hydrophobic region of complex i have resolved one vital issue: this region appears to have multiple proton transporters that are mechanically interlinked. thus, transduction of conformational changes to drive the transmembrane transporters linked by a "connecting rod" during the reduction of ubiquin ... | 2011 | 21454533 |