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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 ...201021304717
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
protective role of catechin on d-galactosamine induced hepatotoxicity through a p53 dependent pathway.objective of this study was to obtain a better understanding of the mechanism responsible for the d-galactosamine (d-galn) induced hepatotoxicity and to study the effect of catechin against d-galn induced hepatotoxicity. catechin 50 and 100 mg/kg b.wt was administered for 1 week by oral route. liver damage was induced by intra-peritoneal administration of 400 mg/kg b.wt d-galactosamine on the last day of catechin treatment. at the end of treatment all animals were killed and liver enzyme levels ...201021966103
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 ...201021206014
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. ...201021206019
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. ...201021206019
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 ...201021206021
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 ...201021206021
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 ...201021206036
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 ...201021206036
superpose3d: a local structural comparison program that allows for user-defined structure representations.local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. the outcome of such analyses is critically dependent on the representation used to describe the structure. indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. we have therefore developed superpose3d, a novel structural comparison softw ...201020700534
the path to next generation biofuels: successes and challenges in the era of synthetic biology.volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for con ...201020089184
lipoic acid metabolism in microbial pathogens.lipoic acid [(r)-5-(1,2-dithiolan-3-yl)pentanoic acid] is an enzyme cofactor required for intermediate metabolism in free-living cells. lipoic acid was discovered nearly 60 years ago and was shown to be covalently attached to proteins in several multicomponent dehydrogenases. cells can acquire lipoate (the deprotonated charge form of lipoic acid that dominates at physiological ph) through either scavenging or de novo synthesis. microbial pathogens implement these basic lipoylation strategies wit ...201020508247
structure and function of enzymes in heme biosynthesis.tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. further, enzymes such as catalases, peroxidases, or cytochromes p450 rely on heme as essential cofactors. heme is synthesized in most organisms via a highly conserved biosynthetic route. in h ...201020506125
crispr interference: rna-directed adaptive immunity in bacteria and archaea.sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. the importance of such pathways is highlighted by the extensive study of rna interference (rnai) and related processes in eukaryotes. in many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (crisprs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. crisp ...201020125085
the crispr system: small rna-guided defense in bacteria and archaea.all cellular systems evolve ways to combat predators and genomic parasites. in bacteria and archaea, numerous resistance mechanisms have developed against phage. our understanding of this defensive repertoire has recently been expanded to include the crispr system of clustered, regularly interspaced short palindromic repeats. in this remarkable pathway, short sequence tags from invading genetic elements are actively incorporated into the host's crispr locus to be transcribed and processed into a ...201020129051
genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ...201020071371
two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ...201020459678
distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ...201020333228
ribonucleotide reduction - horizontal transfer of a required function spans all three domains.ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ...201021143941
prediction and analysis of the modular structure of cytochrome p450 monooxygenases.cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague.201020950472
mustang-mr structural sieving server: applications in protein structural analysis and crystallography.a central tenet of structural biology is that related proteins of common function share structural similarity. this has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. this paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program mustang.201020386610
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...201020042599
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...201020042599
bioprocessing data for the production of marine enzymes.this review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. submerged, immobilized and solid-state processes in batch mode were widely employed. the fed-batch process was also applied in several b ...201020479981
structures of membrane proteins.in reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. we group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. the first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure det ...201020667175
the nucleotide addition cycle of rna polymerase is controlled by two molecular hinges in the bridge helix domain.cellular rna polymerases (rnaps) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. previous work showed that kinking of a hinge region near the c-terminus of the bridge helix (bh-h(c)) plays a critical role in controlling the catalytic rate.201021034443
the architecture of rna polymerase fidelity.the basis for transcriptional fidelity by rna polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. a study just published in bmc biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. see research article http://www.biomedcentral.com/1741-7007/8/54.201020598112
modulation of rna polymerase activity through the trigger loop folding.folding of the trigger loop of rna polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. here, we discuss the impact of adjacent rna polymerase elements, including the f loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.201021326898
stepwise mechanism for transcription fidelity.transcription is the first step of gene expression and is characterized by a high fidelity of rna synthesis. during transcription, the rna polymerase active centre discriminates against not just non-complementary ribo ntp substrates but also against complementary 2'- and 3'-deoxy ntps. a flexible domain of the rna polymerase active centre, the trigger loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive.201020459653
non-canonical dna transcription enzymes and the conservation of two-barrel rna polymerases.dna transcription depends on multimeric rna polymerases that are exceptionally conserved in all cellular organisms, with an active site region of >500 amino acids mainly harboured by their rpb1 and rpb2 subunits. together with the distantly related eukaryotic rna-dependent polymerases involved in gene silencing, they form a monophyletic family of ribonucleotide polymerases with a similarly organized active site region based on two double-psi barrels. recent viral and phage genome sequencing have ...201020360047
the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement.the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ...201122312317
the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement.the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ...201122312317
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
the dna exonucleases of escherichia coli.dna exonucleases, enzymes that hydrolyze phosphodiester bonds in dna from a free end, play important cellular roles in dna repair, genetic recombination and mutation avoidance in all organisms. this article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium escherichia coli. these include the exonucleases associated with dna polymerases i (pola), ii (polb), and iii (dnaq/mutd); exonucleases i (xona/sbcb), iii (xtha), iv, vii ...201126442508
enzymatic synthesis of long double-stranded dna labeled with haloderivatives of nucleobases in a precisely pre-determined sequence.restriction endonucleases are widely applied in recombinant dna technology. among them, enzymes of class iis, which cleave dna beyond recognition sites, are especially useful. we use bsai enzyme for the pinpoint introduction of halogen nucleobases into dna. this has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective.201121864341
genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts.the environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. the application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. fundamental to the success of this work has been the development of reliable genetic and molecular systems. these technica ...201121310009
microbial ecology of the dark ocean above, at, and below the seafloor.the majority of life on earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. ...201121646433
mechanism of bacterial transcription initiation: rna polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of rna synthesis.initiation of rna synthesis from dna templates by rna polymerase (rnap) is a multi-step process, in which initial recognition of promoter dna by rnap triggers a series of conformational changes in both rnap and promoter dna. the bacterial rnap functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex dna in the active site cleft and then separating the nontemplate and template strands in the region surrounding ...201121371479
x-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.we have determined the x-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage n4 rna polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit rna polymerase. as observed during t7 rna polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the o-helix, but only the correct base pairing between the +2 substrate and dna b ...201121321236
seleno-detergent mad phasing of leukotriene c4 synthase in complex with dodecyl-β-d-selenomaltoside.dodecyl-β-d-selenomaltoside (seddm) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-d-maltoside. seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. crystals of a nuclear membrane-embedded enzyme, leukotriene c(4) synthase (ltc(4)s), in complex with seddm were prepared and a multiwavelength anomalous diffraction (mad) experiment was performed. the seddm in the ltc(4)s crys ...201122139193
ucsf chimera, modeller, and imp: an integrated modeling system.structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. here we present the integration of several modeling tools into ucsf chimera. these include comparative modeling by modeller, simultaneous fitting of multiple components into electron microscopy density maps by imp multifit, computing of small-angle x-ray scattering profiles and fitting of the corresponding experimental profile by imp foxs, and assessment of amino acid sidechain conformat ...201121963794
ucsf chimera, modeller, and imp: an integrated modeling system.structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. here we present the integration of several modeling tools into ucsf chimera. these include comparative modeling by modeller, simultaneous fitting of multiple components into electron microscopy density maps by imp multifit, computing of small-angle x-ray scattering profiles and fitting of the corresponding experimental profile by imp foxs, and assessment of amino acid sidechain conformat ...201121963794
a bioinformatics classifier and database for heme-copper oxygen reductases.heme-copper oxygen reductases (hcos) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). the number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of hco sequences. these enzymes were initially classified into three different types being this classificati ...201121559461
bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within bacteria. in this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and fou ...201122022440
a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ...201121673094
new target for inhibition of bacterial rna polymerase: 'switch region'.a new drug target - the 'switch region' - has been identified within bacterial rna polymerase (rnap), the enzyme that mediates bacterial rna synthesis. the new target serves as the binding site for compounds that inhibit bacterial rna synthesis and kill bacteria. since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. since the new target is different from targets of other antibacterial agents, com ...201121862392
structure-based ligand design of novel bacterial rna polymerase inhibitors.bacterial rna polymerase (rnap) is essential for transcription and is an antibacterial target for small molecule inhibitors. the binding region of myxopyronin b (myxb), a bacterial rnap inhibitor, offers the possibility of new inhibitor design. the molecular design program sprout has been used in conjunction with the x-ray cocrystal structure of thermus thermophilus rnap with myxb to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. a series of molecules, with molecular ...201124900260
defense islands in bacterial and archaeal genomes and prediction of novel defense systems.the arms race between cellular life forms and viruses is a major driving force of evolution. a substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. we analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. the defense islands are enriched ...201121908672
the universally conserved prokaryotic gtpases.members of the large superclass of p-loop gtpases share a core domain with a conserved three-dimensional structure. in eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. as targets of mutation and toxins, gtpases are involved in the pathogenesis of cancer and infectious diseases. in prokaryotes also, it is hard to overestimate the importance of gtpases in cell physiology. nu ...201121885683
the fggy carbohydrate kinase family: insights into the evolution of functional specificities.function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. however, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. here, using the fggy carbohydrate kinase family as an example, we bu ...201122215998
the origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.the tree of life is usually rooted between archaea and bacteria. we have previously presented three arguments that support placing the root of the tree of life in bacteria. the data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.201121356104
heme ligand identification and redox properties of the cytochrome c synthetase, ccmf.cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein ccmf, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. we previously reported that the e. coli ccmf protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. here, we show that mutation of either of two conserved ...201122066495
eukaryote-like serine/threonine kinases and phosphatases in bacteria.genomic studies have revealed the presence of ser/thr kinases and phosphatases in many bacterial species, although their physiological roles have largely been unclear. here we review bacterial ser/thr kinases (estks) that show homology in their catalytic domains to eukaryotic ser/thr kinases and their partner phosphatases (estps) that are homologous to eukaryotic phosphatases. we first discuss insights into the enzymatic mechanism of estk activation derived from structural studies on both the li ...201121372323
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 ...201121209330
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 ...201121222438
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 ...201121224389
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 ...201121232525
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 ...201121233089
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 ...201121241053
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 ...201121246636
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 ...201121250660
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 ...201121255213
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 ...201121257746
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 ...201121257750
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 ...201121264299
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.201121266052
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 ...201121278279
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 ...201121282428
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. ...201121282615
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 ...201121285351
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 ...201121296881
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 ...201121297114
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 ...201121301086
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 ...201121301093
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 ...201121303937
pseudomonas aeruginosa 4-amino-4-deoxychorismate lyase: spatial conservation of an active site tyrosine and classification of two types of enzyme.4-amino-4-deoxychorismate lyase (pabc) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. this is an essential activity for the growth of gram-negative bacteria, including important pathogens such as pseudomonas aeruginosa. a high-resolution (1.75 å) crystal structure of pabc from p. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. residues around the pyridoxal 5'-phosphate cofactor are high ...201121935381
Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA.Class II photolyases ubiquitously occur in plants, animals, prokaryotes and some viruses. Like the distantly related microbial class I photolyases, these enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light. Methanosarcina mazei Mm0852 is a class II photolyase of the archaeal order of Methanosarcinales, and is closely related to plant and metazoan counterparts. Mm0852 catalyses light-driven DNA repair and photoreduction, but in contrast ...201121892138
structures of phosphopantetheine adenylyltransferase from burkholderia pseudomallei.phosphopantetheine adenylyltransferase (ppat) catalyzes the fourth of five steps in the coenzyme a biosynthetic pathway, reversibly transferring an adenylyl group from atp onto 4'-phosphopantetheine to yield dephospho-coenzyme a and pyrophosphate. burkholderia pseudomallei is a soil- and water-borne pathogenic bacterium and the etiologic agent of melioidosis, a potentially fatal systemic disease present in southeast asia. two crystal structures are presented of the ppat from b. pseudomallei with ...201121904046
Overexpression, crystallization and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Archaeoglobus fulgidus.Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies have shown that SDH exists in two conformations, an open and a closed form, and it is believed that the conformational state is crucial to understanding its catalytic mechanism. In order to facilitate further structural comparisons among SDHs, includ ...201122139165
Systematic chromosomal deletion of bacterial ribosomal protein genes.Detailed studies of ribosomal proteins (RPs), essential components of the protein biosynthetic machinery, have been hampered by the lack of readily accessible chromosomal deletions of the corresponding genes. Here, we report the systematic genomic deletion of 41 individual RP genes in Escherichia coli, which are not included in the Keio collection. Chromosomal copies of these genes were replaced by an antibiotic resistance gene in the presence of an inducible, easy-to-exchange plasmid-born allel ...201121945294
antimutator variants of dna polymerases.evolution balances dna replication speed and accuracy to optimize replicative fitness and genetic stability. there is no selective pressure to improve dna replication fidelity beyond the background mutation rate from other sources, such as dna damage. however, dna polymerases remain amenable to amino acid substitutions that lower intrinsic error rates. here, we review these 'antimutagenic' changes in dna polymerases and discuss what they reveal about mechanisms of replication fidelity. pioneerin ...201121977975
Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage.Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ...201122167184
Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage.Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ...201122167184
The role of E. coli Nus-factors in transcription regulation and transcription:translation coupling: From structure to mechanism.Bacterial transcription mediated by RNA polymerase (RNAP) is a highly regulated process and RNAP action is modulated during the different phases of initiation, elongation and termination by proteins such as the Escherichia coli Nus transcription-factors. Here we discuss the structural interplay and the mechanistic role of the Nus-factors that are directly involved in the processivity of elongation, transcription:translation coupling and termination, as well as the varying effects of these protei ...201121922055
neutrons, magnets, and photons: a career in structural biology.the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ...201122086921
neutrons, magnets, and photons: a career in structural biology.the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ...201122086921
a photolyase-like protein from agrobacterium tumefaciens with an iron-sulfur cluster.photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. while photolyases can repair uv-induced dna lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. here we report about two photolyase-related proteins, named phra and phrb, found in the phytopathogen agrobacterium tumefaciens. phra belongs to the class iii cyclobutane pyrimidine dimer (cpd) photolyases, the sister class of plant ...201122066008
Functional characterization of the RuvB homologs from Mycoplasma pneumoniae and Mycoplasma genitalium.Homologous recombination between repeated DNA elements in the genomes of Mycoplasma species has been hypothesized to be a crucial causal factor in sequence variation of antigenic proteins at the bacterial surface. To investigate this notion, studies were initiated to identify and characterize the proteins that form part of the homologous DNA recombination machinery in Mycoplasma pneumoniae as well as Mycoplasma genitalium. Among the most likely participants of this machinery are homologs of the ...201121949077
Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl.Pseudomonas aeruginosa thrives in many aqueous environments and is an opportunistic pathogen that can cause both acute and chronic infections. Environmental conditions and host defenses cause differing stresses on the bacteria, and to survive in vastly different environments, P. aeruginosa must be able to adapt to its surroundings. One strategy for bacterial adaptation is to self-encapsulate with matrix material, primarily composed of secreted extracellular polysaccharides. P. aeruginosa has the ...201121991261
Probing the mechanistic role of the long a-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis.The C-terminus of the NuoL subunit of Complex I includes a long amphipathic a-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the ...201122060017
Identification, tissue distribution, and molecular modeling of novel human isoforms of the key enzyme in sialic acid synthesis, UDP-GlcNAc 2-epimerase/ManNAc kinase.UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) catalyzes the first two committed steps in sialic acid synthesis. In addition to the three previously described human GNE isoforms (hGNE1-hGNE3), our database and polymerase chain reaction analysis yielded five additional human isoforms (hGNE4-hGNE8). hGNE1 is the ubiquitously expressed major isoform, while the hGNE2-hGNE8 isoforms are differentially expressed and may act as tissue-specific regulators of sialylation. hGNE2 and hGNE7 display a 31-residue ...201121910480
Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria?Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ...201121893586
insights into folate/fad-dependent trna methyltransferase mechanism: role of two highly conserved cysteines in catalysis.the flavoprotein trmfo methylates specifically the c5 carbon of the highly conserved uridine 54 in trnas. contrary to most methyltransferases, the 1-carbon unit transferred by trmfo derives from 5,10-methylenetetrahydrofolate and not from s-adenosyl-l-methionine. the enzyme also employs the fad hydroquinone as a reducing agent of the c5 methylene u54-trna intermediate in vitro. by analogy with the catalytic mechanism of thymidylate synthase thya, a conserved cysteine located near the fad isoallo ...201121846722
crystallization and preliminary x-ray diffraction of the first periplasmic domain of secdf, a translocon-associated membrane protein, from thermus thermophilus.a membrane-integrated sec component, secdf, associates with the secyeg protein-conducting channel and facilitates protein secretion and membrane-protein integration. secdf contains 12 transmembrane helices and two periplasmic domains. the first periplasmic domain (p1) plays an important role in protein translocation. here, the overexpression, purification and crystallization of the p1 domain of thermus thermophilus secdf are reported. the crystals diffracted x-rays to 2.3 å resolution and belong ...201122102233
initiation factor eif2γ promotes eif2-gtp-met-trnai(met) ternary complex binding to the 40s ribosome.in contrast to prokaryotic elongation factor ef-tu, which delivers aminoacyl-trnas to the ribosomal a-site, eukaryotic initiation factor eif2 binds methionyl initiator transfer rna (met-trna(i)(met)) to the p-site of the 40s ribosomal subunit. the results of directed hydroxyl radical probing experiments to map binding of saccharomyces cerevisiae eif2 on the ribosome and on met-trna(i)(met) revealed that eif2γ primarily contacts the acceptor stem of met-trna(i)(met) and identified a key binding i ...201122002225
transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor rex.redox-sensing repressor rex was previously implicated in the control of anaerobic respiration in response to the cellular nadh/nad(+) levels in gram-positive bacteria. we utilized the comparative genomics approach to infer candidate rex-binding dna motifs and assess the rex regulon content in 119 genomes from 11 taxonomic groups. both dna-binding and nad-sensing domains are broadly conserved in rex orthologs identified in the phyla firmicutes, thermotogales, actinobacteria, chloroflexi, deinococ ...201122210771
Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.201121899737
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