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deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid alvinella pompejana identifies the cvp-bias as a robust measure of eukaryotic thermostability.alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the pacific ocean. living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions, including high temperature and pressure as well as high levels of sulfide and heavy metals. a. pompejana is one of the most thermotolerant metazoans, making this animal a subject of great interest for studies of eukaryotic thermoadaptation.201323324115
a structural basis for streptomycin-induced misreading of the genetic code.during protein synthesis, the ribosome selects aminoacyl-transfer rnas with anticodons matching the messenger rna codon present in the a site of the small ribosomal subunit. the aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. here we use x-ray crystallography to define the impact of streptomycin on the decoding site of the thermus thermophilus 30s ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues ...201323322043
snapshots of a protein folding intermediate.we have investigated the folding dynamics of thermus thermophilus cytochrome c(552) by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. we have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. depending on the protein region monitored, we observed either two-state or three-state denaturation transitions. the unfolding intermediate associated with three-state folding exhibit ...201323319660
structural characterization of a mouse ortholog of human neil3 with a marked preference for single-stranded dna.endonuclease viii-like 3 (neil3) is a dna glycosylase of the base excision repair pathway that protects cells from oxidative dna damage by excising a broad spectrum of cytotoxic and mutagenic base lesions. interestingly, neil3 exhibits an unusual preference for dna with single-stranded regions. here, we report the 2.0 å crystal structure of a neil3 enzyme. although the glycosylase region of mouse neil3 (mmuneil3δ324) exhibits the same overall fold as that of other fpg/nei proteins, it presents d ...201323313161
atypical features of thermus thermophilus succinate:quinone reductase.the thermus thermophilus succinate:quinone reductase (sqr), serving as the respiratory complex ii, has been homologously produced under the control of a constitutive promoter and subsequently purified. the detailed biochemical characterization of the resulting wild type (wt-rcii) and his-tagged (rcii-his(8)-sdhb and rcii-sdhb-his(6)) complex ii variants showed the same properties as the native enzyme with respect to the subunit composition, redox cofactor content and sensitivity to the inhibitor ...201323308253
a coordinated proteomic approach for identifying proteins that interact with the e. coli ribosomal protein s12.the bacterial ribosomal protein s12 contains a universally conserved d88 residue on a loop region thought to be critically involved in translation due to its proximal location to the a site of the 30s subunit. while d88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioaspartic acid, a post-translational modification (ptm) identified in s12 orthologs from several phylogenetically distinct bacteria. in a previous report focused on characterizing thi ...201323305560
microbe-host interactions: structure and role of gram-negative bacterial porins.gram negative bacteria have evolved many mechanisms of attaching to and invading host epithelial and immune cells. in particular, many outer membrane proteins (omps) are involved in this initial interaction between the pathogen and their host. the outer membrane (om) of gram-negative bacteria performs the crucial role of providing an extra layer of protection to the organism without compromising the exchange of material required for sustaining life. the om, therefore, represents a sophisticated ...201223305369
learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications.the emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. the bacteria causing both hospital and community-acquired infections are most often multidrug resistant. in view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. the presented review focuses on the major characteristics of bacteriophages and phage-en ...201223305359
the remorin c-terminal anchor was shaped by convergent evolution among membrane binding domains.strem1.3 remorin is a well-established plant raftophilic protein, predominantly associated with sterol- and sphingolipid-rich membrane rafts. we recently identified a c-terminal domain (remca) required and sufficient for strem1.3 anchoring to the plasma membrane. here, we report a search for homologs and analogs of remca domain in publicly available protein sequence and structure databases. we could not identify remca homologous domains outside the remorin family but we identified domains sharin ...201323299327
characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium cupriavidus basilensis b-8. 201323298573
discovery of a novel class of boron-based antibacterials with activity against gram-negative bacteria.gram-negative bacteria cause approximately 70% of the infections in intensive care units. a growing number of bacterial isolates responsible for these infections are resistant to currently available antibiotics and to many in development. most agents under development are modifications of existing drug classes, which only partially overcome existing resistance mechanisms. therefore, new classes of gram-negative antibacterials with truly novel modes of action are needed to circumvent these existi ...201323295920
crystallization and preliminary x-ray diffraction analysis of the nif3-family protein mj0927 from methanocaldococcus jannaschii.mj0927 is a member of the nif3 family and is widely distributed across living organisms. although several crystal structures of nif3 proteins have been reported, structural information on archaeal nif3 is still limited. to understand the structural differences between bacterial and archaeal nif3 proteins, mj0927 from methanocaldococcus jannaschii was purified and crystallized using the sitting-drop vapour-diffusion method. the crystals diffracted to a resolution of 2.47 å and belonged to the ort ...201223295494
crystallization and preliminary x-ray diffraction analysis of the nif3-family protein mj0927 from methanocaldococcus jannaschii.mj0927 is a member of the nif3 family and is widely distributed across living organisms. although several crystal structures of nif3 proteins have been reported, structural information on archaeal nif3 is still limited. to understand the structural differences between bacterial and archaeal nif3 proteins, mj0927 from methanocaldococcus jannaschii was purified and crystallized using the sitting-drop vapour-diffusion method. the crystals diffracted to a resolution of 2.47 å and belonged to the ort ...201223295494
the aeropath project targeting pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. a major concern is gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. in an effort to accelerate early steps in drug discovery, the eu-funded aeropath project aims to identify novel targets in the opportunistic pathogen pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization ...201223295481
the aeropath project targeting pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. a major concern is gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. in an effort to accelerate early steps in drug discovery, the eu-funded aeropath project aims to identify novel targets in the opportunistic pathogen pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization ...201223295481
characterization of the msmeg_2631 gene (mmp) encoding a multidrug and toxic compound extrusion (mate) family protein in mycobacterium smegmatis and exploration of its polyspecific nature using biolog phenotype microarray.in mycobacterium, multidrug efflux pumps can be associated with intrinsic drug resistance. comparison of putative mycobacterial transport genes revealed a single annotated open reading frame (orf) for a multidrug and toxic compound extrusion (mate) family efflux pump in all sequenced mycobacteria except mycobacterium leprae. since mate efflux pumps function as multidrug efflux pumps by conferring resistance to structurally diverse antibiotics and dna-damaging chemicals, we studied this gene (msm ...201323292779
the n termini of a-subunit isoforms are involved in signaling between vacuolar h+-atpase (v-atpase) and cytohesin-2.previously, we reported an acidification-dependent interaction of the endosomal vacuolar h(+)-atpase (v-atpase) with cytohesin-2, a gdp/gtp exchange factor (gef), suggesting that it functions as a ph-sensing receptor. here, we have studied the molecular mechanism of signaling between the v-atpase, cytohesin-2, and arf gtp-binding proteins. we found that part of the n-terminal cytosolic tail of the v-atpase a2-subunit (a2n), corresponding to its first 17 amino acids (a2n(1-17)), potently modulate ...201323288846
characterization of the alkaline laccase ssl1 from streptomyces sviceus with unusual properties discovered by genome mining.fungal laccases are well investigated enzymes with high potential in diverse applications like bleaching of waste waters and textiles, cellulose delignification, and organic synthesis. however, they are limited to acidic reaction conditions and require eukaryotic expression systems. this raises a demand for novel laccases without these constraints. we have taken advantage of the laccase engineering database lcced derived from genome mining to identify and clone the laccase ssl1 from streptomyces ...201223285009
structural and functional insights into (s)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization.nitrogen metabolism is one of essential processes in living organisms. the catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. in escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. the enzyme (s)-ureidoglycolate dehydrogenase (alld), which is a member of l-sulfolactate dehydrogenase-like family, converts (s)-ureidoglycolate, a key intermediate in the purine degra ...201223284870
dna repair by reversal of dna damage.endogenous and exogenous factors constantly challenge cellular dna, generating cytotoxic and/or mutagenic dna adducts. as a result, organisms have evolved different mechanisms to defend against the deleterious effects of dna damage. among these diverse repair pathways, direct dna-repair systems provide cells with simple yet efficient solutions to reverse covalent dna adducts. in this review, we focus on recent advances in the field of direct dna repair, namely, photolyase-, alkyltransferase-, an ...201323284047
ligand access to the active site in thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. using photolabile no and o(2) carriers, we recently found that no and o(2) binding in thermus thermophilus (tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. using x-ray crystallography, time-resolved optical absorpti ...201323282175
space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.to discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). in general, the polypharmacological proteins often share similar local binding environments and motifs. as the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions.201223281852
functional relevance of dynamic properties of dimeric nadp-dependent isocitrate dehydrogenases.isocitrate dehydrogenases (idhs) are important enzymes present in all living cells. three subfamilies of functionally dimeric idhs (subfamilies i, ii, iii) are known. subfamily i are well-studied bacterial idhs, like that of escherischia coli. subfamily ii has predominantly eukaryotic members, but it also has several bacterial members, many being pathogens or endosymbionts. subfamily iii idhs are nad-dependent. the eukaryotic-like subfamily ii idh from pathogenic bacteria such as mycobacterium t ...201223281650
capture and quality control mechanisms for adenosine-5'-triphosphate binding.the catalytic events in members of the nucleotidylyl transferase superfamily are initiated by a millisecond binding of atp in the active site. through metadynamics simulations on a class i aminoacyl-trna synthetase (aarss), the largest group in the superfamily, we calculate the free energy landscape of atp selection and binding. mutagenesis studies and fluorescence spectroscopy validated the identification of the most populated intermediate states. the rapid first binding step involves formation ...201323276298
thermodynamic properties distinguish human mitochondrial aspartyl-trna synthetase from bacterial homolog with same 3d architecture.in the mammalian mitochondrial translation apparatus, the proteins and their partner rnas are coded by two genomes. the proteins are nuclear-encoded and resemble their homologs, whereas the rnas coming from the rapidly evolving mitochondrial genome have lost critical structural information. this raises the question of molecular adaptation of these proteins to their peculiar partner rnas. the crystal structure of the homodimeric bacterial-type human mitochondrial aspartyl-trna synthetase (drs) co ...201223275545
thermodynamic properties distinguish human mitochondrial aspartyl-trna synthetase from bacterial homolog with same 3d architecture.in the mammalian mitochondrial translation apparatus, the proteins and their partner rnas are coded by two genomes. the proteins are nuclear-encoded and resemble their homologs, whereas the rnas coming from the rapidly evolving mitochondrial genome have lost critical structural information. this raises the question of molecular adaptation of these proteins to their peculiar partner rnas. the crystal structure of the homodimeric bacterial-type human mitochondrial aspartyl-trna synthetase (drs) co ...201223275545
crucial role of the c-terminal domain of mycobacterium tuberculosis leucyl-trna synthetase in aminoacylation and editing.the c-terminal extension of prokaryotic leucyl-trna synthetase (leurs) has been shown to make contacts with the tertiary structure base pairs of trna(leu) as well as its long variable arm. however, the precise role of the flexibly linked leurs c-terminal domain (ctd) in aminoacylation and editing processes has not been clarified. in this study, we carried out aspartic acid scanning within the ctd of mycobacterium tuberculosis leurs (mtbleurs) and studied the effects on trna(leu)-binding capacity ...201223268443
crucial role of the c-terminal domain of mycobacterium tuberculosis leucyl-trna synthetase in aminoacylation and editing.the c-terminal extension of prokaryotic leucyl-trna synthetase (leurs) has been shown to make contacts with the tertiary structure base pairs of trna(leu) as well as its long variable arm. however, the precise role of the flexibly linked leurs c-terminal domain (ctd) in aminoacylation and editing processes has not been clarified. in this study, we carried out aspartic acid scanning within the ctd of mycobacterium tuberculosis leurs (mtbleurs) and studied the effects on trna(leu)-binding capacity ...201223268443
twisting and subunit rotation in single f(o)(f1)-atp synthase.f(o)f(1)-atp synthases are ubiquitous proton- or ion-powered membrane enzymes providing atp for all kinds of cellular processes. the mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule förster resonance energy transfer. here we review recent developments of approaches to monitor the st ...201323267178
anticodon g recognition by trna synthetases mimics the trna core.ancient mechanisms for nucleotide base recognition in the rna world are candidates for mimicking by early proteins like trna synthetases. in the core of the trna, conserved g22 interacts with two internal bases in a complex further stabilized by stacking interactions. this particular trna format for g recognition is shown here to be adapted by nine different and even nonhomologous anticodon binding domains (abds) of trna synthetases, in which amino acid side chains mimic all of the trna g22 base ...201223266103
anticodon g recognition by trna synthetases mimics the trna core.ancient mechanisms for nucleotide base recognition in the rna world are candidates for mimicking by early proteins like trna synthetases. in the core of the trna, conserved g22 interacts with two internal bases in a complex further stabilized by stacking interactions. this particular trna format for g recognition is shown here to be adapted by nine different and even nonhomologous anticodon binding domains (abds) of trna synthetases, in which amino acid side chains mimic all of the trna g22 base ...201223266103
take home lessons from studies of related proteins.the 'fold approach' involves a detailed analysis of the folding of several topologically, structurally and/or evolutionarily related proteins. such studies can reveal determinants of the folding mechanism beyond the gross topology, and can dissect the residues required for folding from those required for stability or function. while this approach has not yet matured to the point where we can predict the native conformation of any polypeptide chain in silico, it has been able to highlight, amongs ...201323265640
engineering the substrate specificity of a thermophilic penicillin acylase from thermus thermophilus.a homologue of the escherichia coli penicillin acylase is encoded in the genomes of several thermophiles, including in different thermus thermophilus strains. although the natural substrate of this enzyme is not known, this acylase shows a marked preference for penicillin k over penicillin g. three-dimensional models were created in which the catalytic residues and the substrate binding pocket were identified. through rational redesign, residues were replaced to mimic the aromatic binding site o ...201223263966
role of nonspecific interactions in molecular chaperones through model-based bioinformatics.molecular chaperones are large proteins or protein complexes from which many proteins require assistance in order to fold. one unique property of molecular chaperones is the cavity they provide in which proteins fold. the interior surface residues which make up the cavities of molecular chaperone complexes from different organisms has recently been identified, including the well-studied groel-groes chaperonin complex found in escherichia coli. it was found that the interior of these protein comp ...201223260050
genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer thermacetogenium phaeum.thermacetogenium phaeum is a thermophilic strictly anaerobic bacterium oxidizing acetate to co(2) in syntrophic association with a methanogenic partner. it can also grow in pure culture, e.g., by fermentation of methanol to acetate. the key enzymes of homoacetate fermentation (wood-ljungdahl pathway) are used both in acetate oxidation and acetate formation. the obvious reversibility of this pathway in this organism is of specific interest since syntrophic acetate oxidation operates close to the ...201223259483
a trna-independent mechanism for transamidosome assembly promotes aminoacyl-trna transamidation.many bacteria lack genes encoding asparaginyl- and/or glutaminyl-trna synthetase and consequently rely on an indirect path for the synthesis of both asn-trna(asn) and gln-trna(gln). in some bacteria such as thermus thermophilus, efficient delivery of misacylated trna to the downstream amidotransferase (adt) is ensured by formation of a stable, trna-dependent macromolecular complex called the asn-transamidosome. this complex enables direct delivery of asp-trna(asn) from the non-discriminating asp ...201223258533
a trna-independent mechanism for transamidosome assembly promotes aminoacyl-trna transamidation.many bacteria lack genes encoding asparaginyl- and/or glutaminyl-trna synthetase and consequently rely on an indirect path for the synthesis of both asn-trna(asn) and gln-trna(gln). in some bacteria such as thermus thermophilus, efficient delivery of misacylated trna to the downstream amidotransferase (adt) is ensured by formation of a stable, trna-dependent macromolecular complex called the asn-transamidosome. this complex enables direct delivery of asp-trna(asn) from the non-discriminating asp ...201223258533
structure and mechanism of the pilf dna transformation atpase from thermus thermophilus.many gram-negative bacteria contain specific systems for uptake of foreign dna, which play a critical role in the acquisition of antibiotic resistance. the ttpilf (pilf atpase from thermus thermophilus) is required for high transformation efficiency, but its mechanism of action is unknown. in the present study, we show that ttpilf is able to bind to both dna and rna. the structure of ttpilf was determined by cryoelectron microscopy in the presence and absence of the atp analogue p[nh]ppa (adenos ...201323252471
protein translocation across the rough endoplasmic reticulum.the rough endoplasmic reticulum is a major site of protein biosynthesis in all eukaryotic cells, serving as the entry point for the secretory pathway and as the initial integration site for the majority of cellular integral membrane proteins. the core components of the protein translocation machinery have been identified, and high-resolution structures of the targeting components and the transport channel have been obtained. research in this area is now focused on obtaining a better understandin ...201323251026
trnahis 5-methylcytidine levels increase in response to several growth arrest conditions in saccharomyces cerevisiae.trnas are highly modified, each with a unique set of modifications. several reports suggest that trnas are hypomodified or, in some cases, hypermodified under different growth conditions and in certain cancers. we previously demonstrated that yeast strains depleted of trna(his) guanylyltransferase accumulate uncharged trna(his) lacking the g(-1) residue and subsequently accumulate additional 5-methylcytidine (m(5)c) at residues c(48) and c(50) of trna(his), due to the activity of the m(5)c-methy ...201323249748
structural analysis of protein-protein interactions in type i polyketide synthases.polyketide synthases (pkss) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. the pkss consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. recent developments on x-ray crystallography and protein n ...201223249187
structural analysis of protein-protein interactions in type i polyketide synthases.polyketide synthases (pkss) are responsible for synthesizing a myriad of natural products with agricultural, medicinal relevance. the pkss consist of multiple functional domains of which each can catalyze a specified chemical reaction leading to the synthesis of polyketides. biochemical studies showed that protein-substrate and protein-protein interactions play crucial roles in these complex regio-/stereo-selective biochemical processes. recent developments on x-ray crystallography and protein n ...201223249187
application of molecular diagnostic techniques for viral testing.nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. these techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. the increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. this technology has reduced the us ...201223248732
hiv-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mrna entrance channel of the ribosome.the human immunodeficiency virus (hiv) requires a programmed -1 ribosomal frameshift for pol gene expression. the hiv frameshift site consists of a heptanucleotide slippery sequence (uuuuuua) followed by a spacer region and a downstream rna stem-loop structure. here we investigate the role of the rna structure in promoting the -1 frameshift. the stem-loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. no correl ...201223248007
hiv-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mrna entrance channel of the ribosome.the human immunodeficiency virus (hiv) requires a programmed -1 ribosomal frameshift for pol gene expression. the hiv frameshift site consists of a heptanucleotide slippery sequence (uuuuuua) followed by a spacer region and a downstream rna stem-loop structure. here we investigate the role of the rna structure in promoting the -1 frameshift. the stem-loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. no correl ...201223248007
characterization of crispr rna biogenesis and cas6 cleavage-mediated inhibition of a provirus in the haloarchaeon haloferax mediterranei.the adaptive immune system comprising crispr (clustered regularly interspaced short palindromic repeats) arrays and cas (crispr-associated) genes has been discovered in a wide range of bacteria and archaea and has recently attracted comprehensive investigations. however, the subtype i-b crispr-cas system in haloarchaea has been less characterized. here, we investigated cas6-mediated rna processing in haloferax mediterranei. the cas6 cleavage site, as well as the crispr transcription start site, ...201323243301
sediment microbial communities in great boiling spring are controlled by temperature and distinct from water communities.great boiling spring is a large, circumneutral, geothermal spring in the us great basin. twelve samples were collected from water and four different sediment sites on four different dates. microbial community composition and diversity were assessed by pcr amplification of a portion of the small subunit rrna gene using a universal primer set followed by pyrosequencing of the v8 region. analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. wa ...201223235293
sediment microbial communities in great boiling spring are controlled by temperature and distinct from water communities.great boiling spring is a large, circumneutral, geothermal spring in the us great basin. twelve samples were collected from water and four different sediment sites on four different dates. microbial community composition and diversity were assessed by pcr amplification of a portion of the small subunit rrna gene using a universal primer set followed by pyrosequencing of the v8 region. analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. wa ...201223235293
give it ago: the search for mirna-argonaute sorting signals in arabidopsis thaliana indicates a relevance of sequence positions other than the 5'-position alone.the specific recognition of mirnas by argonaute (ago) proteins, the effector proteins of the rna-induced silencing complex, constitutes the final step of the biogenesis of mirnas and is crucial for their target interaction. in the genome of arabidopsis thaliana (ath), 10 different ago proteins are encoded and the sorting decision, which mirna associates with which ago protein, was reported to depend exclusively on the identity of the 5'-sequence position of mature mirnas. hence, with only four d ...201223233858
disruption of ionic interactions between the nucleotide binding domain 1 (nbd1) and middle (m) domain in hsp100 disaggregase unleashes toxic hyperactivity and partial independence from hsp70.hsp100 chaperones cooperate with the hsp70 chaperone system to disaggregate and reactivate heat-denatured aggregated proteins to promote cell survival after heat stress. the homology models of hsp100 disaggregases suggest the presence of a conserved network of ionic interactions between the first nucleotide binding domain (nbd1) and the coiled-coil middle subdomain, the signature domain of disaggregating chaperones. mutations intended to disrupt the putative ionic interactions in yeast hsp104 an ...201223233670
disruption of ionic interactions between the nucleotide binding domain 1 (nbd1) and middle (m) domain in hsp100 disaggregase unleashes toxic hyperactivity and partial independence from hsp70.hsp100 chaperones cooperate with the hsp70 chaperone system to disaggregate and reactivate heat-denatured aggregated proteins to promote cell survival after heat stress. the homology models of hsp100 disaggregases suggest the presence of a conserved network of ionic interactions between the first nucleotide binding domain (nbd1) and the coiled-coil middle subdomain, the signature domain of disaggregating chaperones. mutations intended to disrupt the putative ionic interactions in yeast hsp104 an ...201223233670
a gating motif in the translocation channel sets the hydrophobicity threshold for signal sequence function.a critical event in protein translocation across the endoplasmic reticulum is the structural transition between the closed and open conformations of sec61, the eukaryotic translocation channel. channel opening allows signal sequence insertion into a gap between the n- and c-terminal halves of sec61. we have identified a gating motif that regulates the transition between the closed and open channel conformations. polar amino acid substitutions in the gating motif cause a gain-of-function phenotyp ...201223229898
ebec 2012--an energetic time in freiburg.the seventeenth european bioenergetics conference (ebec) took place in september 2012 at the albert-ludwigs-university in freiburg, germany, and was hosted by thorsten friedrich. the conference is a biannual event that brings together researchers from across the globe to discuss progress in this diverse and challenging field.201223229583
ebec 2012--an energetic time in freiburg.the seventeenth european bioenergetics conference (ebec) took place in september 2012 at the albert-ludwigs-university in freiburg, germany, and was hosted by thorsten friedrich. the conference is a biannual event that brings together researchers from across the globe to discuss progress in this diverse and challenging field.201223229583
the genome of pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.the bacterium pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. the genome of p. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing geobacter species.201223227809
in vivo protein interactions and complex formation in the pectobacterium atrosepticum subtype i-f crispr/cas system.clustered regularly interspaced short palindromic repeats (crispr) and their associated proteins (cas; crispr associated) are a bacterial defense mechanism against extra-chromosomal elements. crispr/cas systems are distinct from other known defense mechanisms insofar as they provide acquired and heritable immunity. resistance is accomplished in multiple stages in which the cas proteins provide the enzymatic machinery. importantly, subtype-specific proteins have been shown to form complexes in co ...201223226499
isolation and characterization of rna polymerase rpob mutations that alter transcription slippage during elongation in escherichia coli.transcription fidelity is critical for maintaining the accurate flow of genetic information. the study of transcription fidelity has been limited because the intrinsic error rate of transcription is obscured by the higher error rate of translation, making identification of phenotypes associated with transcription infidelity challenging. slippage of elongating rna polymerase (rnap) on homopolymeric a/t tracts in dna represents a special type of transcription error leading to disruption of open re ...201223223236
isolation and characterization of rna polymerase rpob mutations that alter transcription slippage during elongation in escherichia coli.transcription fidelity is critical for maintaining the accurate flow of genetic information. the study of transcription fidelity has been limited because the intrinsic error rate of transcription is obscured by the higher error rate of translation, making identification of phenotypes associated with transcription infidelity challenging. slippage of elongating rna polymerase (rnap) on homopolymeric a/t tracts in dna represents a special type of transcription error leading to disruption of open re ...201223223236
promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.in all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. molecular models have been reported for complete bacterial 70s and eukaryotic 80s ribosomes; however, only molecular models of large 50s subunits have been reported for archaea. here, we present a complete molecular model for the pyrococcus furiosus 70s ribosome based on a 6.6 å cryo-electron microscopy map. moreover, we have determined cryo-electron microscopy reconstructions of the euryarchaeota meth ...201223222135
promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.in all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. molecular models have been reported for complete bacterial 70s and eukaryotic 80s ribosomes; however, only molecular models of large 50s subunits have been reported for archaea. here, we present a complete molecular model for the pyrococcus furiosus 70s ribosome based on a 6.6 å cryo-electron microscopy map. moreover, we have determined cryo-electron microscopy reconstructions of the euryarchaeota meth ...201223222135
archaeal β-casp ribonucleases of the acpsf1 family are orthologs of the eukaryal cpsf-73 factor.bacterial rnase j and eukaryal cleavage and polyadenylation specificity factor (cpsf-73) are members of the β-casp family of ribonucleases involved in mrna processing and degradation. here we report an in-depth phylogenomic analysis that delineates arnase j and archaeal cpsf (acpsf) as distinct orthologous groups and establishes their repartition in 110 archaeal genomes. the acpsf1 subgroup, which has been inherited vertically and is strictly conserved, is characterized by an n-terminal extensio ...201223222134
archaeal β-casp ribonucleases of the acpsf1 family are orthologs of the eukaryal cpsf-73 factor.bacterial rnase j and eukaryal cleavage and polyadenylation specificity factor (cpsf-73) are members of the β-casp family of ribonucleases involved in mrna processing and degradation. here we report an in-depth phylogenomic analysis that delineates arnase j and archaeal cpsf (acpsf) as distinct orthologous groups and establishes their repartition in 110 archaeal genomes. the acpsf1 subgroup, which has been inherited vertically and is strictly conserved, is characterized by an n-terminal extensio ...201223222134
selection of trna charging quality control mechanisms that increase mistranslation of the genetic code.mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer rna (trna) pairs by aminoacyl-trna synthetases (aarss) and inaccurate selection of aminoacyl-trnas by the ribosome. many aarss actively edit non-cognate amino acids, but editing mechanisms are not evolutionarily conserved, and their physiological significance remains unclear. to address the connection between aarss and mistranslation, the evolutionary divergence of tyrosine editing by phe ...201223222133
selection of trna charging quality control mechanisms that increase mistranslation of the genetic code.mistranslation can follow two events during protein synthesis: production of non-cognate amino acid:transfer rna (trna) pairs by aminoacyl-trna synthetases (aarss) and inaccurate selection of aminoacyl-trnas by the ribosome. many aarss actively edit non-cognate amino acids, but editing mechanisms are not evolutionarily conserved, and their physiological significance remains unclear. to address the connection between aarss and mistranslation, the evolutionary divergence of tyrosine editing by phe ...201223222133
uv damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different dna lesions.repairing damaged dna is essential for an organism's survival. uv damage endonuclease (uvde) is a dna-repair enzyme that can recognize and incise different types of damaged dna. we present the structure of sulfolobus acidocaldarius uvde on its own and in a pre-catalytic complex with uv-damaged dna containing a 6-4 photoproduct showing a novel 'dual dinucleotide flip' mechanism for recognition of damaged dipyrimidines: the two purines opposite to the damaged pyrimidine bases are flipped into a di ...201223221644
uv damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different dna lesions.repairing damaged dna is essential for an organism's survival. uv damage endonuclease (uvde) is a dna-repair enzyme that can recognize and incise different types of damaged dna. we present the structure of sulfolobus acidocaldarius uvde on its own and in a pre-catalytic complex with uv-damaged dna containing a 6-4 photoproduct showing a novel 'dual dinucleotide flip' mechanism for recognition of damaged dipyrimidines: the two purines opposite to the damaged pyrimidine bases are flipped into a di ...201223221644
evidence for niche partitioning revealed by the distribution of sulfur oxidation genes collected from areas of a terrestrial sulfidic spring with differing geochemical conditions.the diversity and phylogenetic significance of bacterial genes in the environment has been well studied, but comparatively little attention has been devoted to understanding the functional significance of different variations of the same metabolic gene that occur in the same environment. we analyzed the geographic distribution of 16s rrna pyrosequences and soxb genes along a geochemical gradient in a terrestrial sulfidic spring to identify how different taxonomic variations of the soxb gene were ...201323220955
effects of select histidine to cysteine mutations on transcriptional regulation by escherichia coli rcnr.the rcnr metalloregulator represses the transcription of the co(ii) and ni(ii) exporter, rcnab. previous studies have shown that co(ii) and ni(ii) bind to rcnr in six-coordinate sites, resulting in derepression. here, the roles of his60, his64, and his67 in specific metal recognition are examined. his60 and his64 correspond to ligands that are important for cu(i) binding in the homologous cu(i)-responsive metalloregulator, csor. these residues are known to be functionally important in rcnr trans ...201223215580
effects of select histidine to cysteine mutations on transcriptional regulation by escherichia coli rcnr.the rcnr metalloregulator represses the transcription of the co(ii) and ni(ii) exporter, rcnab. previous studies have shown that co(ii) and ni(ii) bind to rcnr in six-coordinate sites, resulting in derepression. here, the roles of his60, his64, and his67 in specific metal recognition are examined. his60 and his64 correspond to ligands that are important for cu(i) binding in the homologous cu(i)-responsive metalloregulator, csor. these residues are known to be functionally important in rcnr trans ...201223215580
functional diversification of rok-family transcriptional regulators of sugar catabolism in the thermotogae phylum.large and functionally heterogeneous families of transcription factors have complex evolutionary histories. what shapes specificities toward effectors and dna sites in paralogous regulators is a fundamental question in biology. bacteria from the deep-branching lineage thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (rok) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. we applied an integrated genomic approach ...201223209028
functional diversification of rok-family transcriptional regulators of sugar catabolism in the thermotogae phylum.large and functionally heterogeneous families of transcription factors have complex evolutionary histories. what shapes specificities toward effectors and dna sites in paralogous regulators is a fundamental question in biology. bacteria from the deep-branching lineage thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (rok) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. we applied an integrated genomic approach ...201223209028
direct interactions between the coiled-coil tip of dksa and the trigger loop of rna polymerase mediate transcriptional regulation.escherichia coli dksa is a transcription factor that binds to rna polymerase (rnap) without binding to dna, destabilizing rnap-promoter interactions, sensitizing rnap to the global regulator ppgpp, and regulating transcription of several hundred target genes, including those encoding rrna. previously, we described promoter sequences and kinetic properties that account for dksa's promoter specificity, but how dksa exerts its effects on rnap has remained unclear. to better understand dksa's mechan ...201223207918
development of novel sugar isomerases by optimization of active sites in phosphosugar isomerases for monosaccharides.phosphosugar isomerases can catalyze the isomerization of not only phosphosugar but also of monosaccharides, suggesting that the phosphosugar isomerases can be used as sugar isomerases that do not exist in nature. determination of active-site residues of phosphosugar isomerases, including ribose-5-phosphate isomerase from clostridium difficile (cdrpi), mannose-6-phosphate isomerase from bacillus subtilis (bsmpi), and glucose-6-phosphate isomerase from pyrococcus furiosus (pfgpi), was accomplishe ...201323204422
proteins of unknown function in the protein data bank (pdb): an inventory of true uncharacterized proteins and computational tools for their analysis.proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the protein data bank (pdb). our analysis of recent pdb data revealed that only 42.53% of pdb entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. the remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, b ...201223202924
the rna polymerase bridge helix yfi motif in catalysis, fidelity and translocation.the bridge α-helix in the β' subunit of rna polymerase (rnap) borders the active site and may have roles in catalysis and translocation. in escherichia coli rnap, a bulky hydrophobic segment near the n-terminal end of the bridge helix is identified (β' 772-yfi-774; the yfi motif). yfi is located at a distance from the active center and adjacent to a glycine hinge (β' 778-garkg-782) involved in dynamic bending of the bridge helix. remarkably, amino acid substitutions in yfi significantly alter in ...201223202476
the rna polymerase bridge helix yfi motif in catalysis, fidelity and translocation.the bridge α-helix in the β' subunit of rna polymerase (rnap) borders the active site and may have roles in catalysis and translocation. in escherichia coli rnap, a bulky hydrophobic segment near the n-terminal end of the bridge helix is identified (β' 772-yfi-774; the yfi motif). yfi is located at a distance from the active center and adjacent to a glycine hinge (β' 778-garkg-782) involved in dynamic bending of the bridge helix. remarkably, amino acid substitutions in yfi significantly alter in ...201223202476
function and regulation of clustered regularly interspaced short palindromic repeats (crispr) / crispr associated (cas) systems.phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. in contrast, the clustered regularly interspaced short palindromic repeats (crispr) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. re ...201223202464
malolactic enzyme from oenococcus oeni: heterologous expression in escherichia coli and biochemical characterization.malolactic enzymes (mle) are known to directly convert l-malic acid into l-lactic acid with a catalytical requirement of nicotinamide adenine dinucleotide (nad (+) ) and mn ( 2+) ; however, the reaction mechanism is still unclear. to study a mle, the structural gene from oenococcus oeni strain dsm 20255 was heterologously expressed in escherichia coli, yielding 22.9 ku l (-1) fermentation broth. after affinity chromatography and removal of apparently inactive protein by precipitation, purified r ...201223196745
malolactic enzyme from oenococcus oeni: heterologous expression in escherichia coli and biochemical characterization.malolactic enzymes (mle) are known to directly convert l-malic acid into l-lactic acid with a catalytical requirement of nicotinamide adenine dinucleotide (nad (+) ) and mn ( 2+) ; however, the reaction mechanism is still unclear. to study a mle, the structural gene from oenococcus oeni strain dsm 20255 was heterologously expressed in escherichia coli, yielding 22.9 ku l (-1) fermentation broth. after affinity chromatography and removal of apparently inactive protein by precipitation, purified r ...201223196745
coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads.showerheads support the development of multi-species biofilms that can be unsightly, produce malodor, and may harbor pathogens. the outer-surface spray-plates of many showerheads support visible biofilms that likely contain a mixture of bacteria from freshwater and potentially from human users. coaggregation, a mechanism by which genetically distinct bacteria specifically recognize one another, may contribute to the retention and enrichment of different species within these biofilms. the aim of ...201323194413
investigation of stable and transient protein-protein interactions: past, present, and future.this article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (ppis) with a focus on their function within cells, organs, and organisms. the significance of ptms within the ppis is also discussed. we focus on methods to study ppis and methods of detecting ppis, with particular emphasis on electrophoresis-based and ms-based investigation of ppis, including specific examples. the validation of ppis is emphas ...201323193082
crystallization and preliminary x-ray analysis of the open form of human ecto-5'-nucleotidase (cd73).eukaryotic ecto-5'-nucleotidase (e5nt) catalyses the hydrolysis of extracellular amp to adenosine and plays a pivotal role in switching on adenosine signalling via the p1 receptors of the purinergic signalling pathway. with such an important regulatory role, e5nt has become an appealing new drug target, with potential applications in the treatment of inflammation, chronic pain, hypoxia and cancer. in order to gain insight into the structure and function of the eukaryotic e5nt enzymes and to assi ...201223192044
crystallization and preliminary x-ray crystallographic analysis of human apaf-1-interacting protein.apaf-1-interacting protein (apip) is known to inhibit two different types of cell death: caspase-1-dependent pyroptosis and caspase-9-dependent apoptosis. apip is also involved in the methionine-salvage pathway, where it is called 5-methylthioribulose-1-phosphate dehydratase (mtnb). the enzyme activity seems to be essential for inhibition of pyroptosis by apip, but not for inhibition of apoptosis. in this study, human apip was overproduced in escherichia coli, purified and crystallized. an x-ray ...201223192037
crystallization and preliminary x-ray crystallographic analysis of quinolinate phosphoribosyltransferase from porcine kidney in complex with nicotinate mononucleotide.quinolinate phosphoribosyltransferase (qaprtase) is a key enzyme in nad biosynthesis; it catalyzes the formation of nicotinate mononucleotide (namn) from quinolinate and 5-phosphoribosyl-1-pyrophosphate. in order to elucidate the mechanism of namn biosynthesis, crystals of sus scrofa qaprtase (ss-qaprtase) purified from porcine kidney in complex with namn were obtained and diffraction data were collected and processed to 2.1 å resolution. the ss-qaprtase-namn cocrystals belonged to space group p ...201223192029
inorganic pyrophosphatase crystals from thermococcus thioreducens for x-ray and neutron diffraction.inorganic pyrophosphatase (ippase) from the archaeon thermococcus thioreducens was cloned, overexpressed in escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. ippase is thermally stable and is able to resist denaturation at temperatures above 348 k. owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and x-ray and n ...201223192028
structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc118.the structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc188 has been determined at 1.72 å resolution. the structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. comparison to other related structures revealed high homology in the active site, allo ...201223192019
plasmodium falciparum uvrd helicase translocates in 3' to 5' direction, colocalizes with mlh and modulates its activity through physical interaction.malaria is a global disease and a major health problem. the control of malaria is a daunting task due to the increasing drug resistance. therefore, there is an urgent need to identify and characterize novel parasite specific drug targets. in the present study we report the biochemical characterization of parasite specific uvrd helicase from plasmodium falciparum. the n-terminal fragment (pfudn) containing uvrd helicase domain, which consists of helicase motifs q, ia-id, ii, iii and most of motif ...201223185322
cellular and molecular mechanisms of mitochondrial function.mitochondria are membrane bound organelles present in almost all eukaryotic cells. responsible for orchestrating cellular energy production, they are central to the maintenance of life and the gatekeepers of cell death. thought to have originated from symbiotic ancestors, they carry a residual genome as mtdna encoding 13 proteins essential for respiratory chain function. mitochondria comprise an inner and outer membrane that separate and maintain the aqueous regions, the intermembrane space and ...201223168274
post-translation modification in archaea: lessons from haloferax volcanii and other haloarchaea.as an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. of the various sources of proteomic variability, post-translational modifications (ptms) most greatly serve to expand the variety of proteins found in the cell. likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. while both strategies for generating pro ...201223167813
post-translation modification in archaea: lessons from haloferax volcanii and other haloarchaea.as an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. of the various sources of proteomic variability, post-translational modifications (ptms) most greatly serve to expand the variety of proteins found in the cell. likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. while both strategies for generating pro ...201223167813
catalysis of dioxygen reduction by thermus thermophilus strain hb27 laccase on ketjen black electrodes.we present electrochemical analyses of the catalysis of dioxygen reduction by thermus thermophilus strain hb27 laccase on ketjen black substrates. our cathodes reliably produce 0.56 ma cm(-2) at 0.0 v vs ag|agcl reference at 30 °c in air-saturated buffer, under conditions of nonlimiting o(2) flux. we report the electrochemical activity of this laccase as a function of temperature, ph, time, and the efficiency of its conversion of dioxygen to water. we have measured the surface concentration of e ...201223163614
catalysis of dioxygen reduction by thermus thermophilus strain hb27 laccase on ketjen black electrodes.we present electrochemical analyses of the catalysis of dioxygen reduction by thermus thermophilus strain hb27 laccase on ketjen black substrates. our cathodes reliably produce 0.56 ma cm(-2) at 0.0 v vs ag|agcl reference at 30 °c in air-saturated buffer, under conditions of nonlimiting o(2) flux. we report the electrochemical activity of this laccase as a function of temperature, ph, time, and the efficiency of its conversion of dioxygen to water. we have measured the surface concentration of e ...201223163614
mechanical modulation of atp-binding affinity of v1-atpase.v(1)-atpase is a rotary motor protein that rotates the central shaft in a counterclockwise direction hydrolyzing atp. although the atp-binding process is suggested to be the most critical reaction step for torque generation in f(1)-atpase (the closest relative of v(1)-atpase evolutionarily), the role of atp binding for v(1)-atpase in torque generation has remained unclear. in the present study, we performed single-molecule manipulation experiments on v(1)-atpase from thermus thermophilus to inve ...201223155048
mechanical modulation of atp-binding affinity of v1-atpase.v(1)-atpase is a rotary motor protein that rotates the central shaft in a counterclockwise direction hydrolyzing atp. although the atp-binding process is suggested to be the most critical reaction step for torque generation in f(1)-atpase (the closest relative of v(1)-atpase evolutionarily), the role of atp binding for v(1)-atpase in torque generation has remained unclear. in the present study, we performed single-molecule manipulation experiments on v(1)-atpase from thermus thermophilus to inve ...201223155048
structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in rna crystal structures.tetraloop-receptor interactions are prevalent structural units in rnas, and include the gaaa/11-nt and gnra-minor groove interactions. in this study, we have compiled a set of 78 nonredundant loop-helix interactions from x-ray crystal structures, and examined them for the extent of their sequence and structural variation. of the 78 interactions in the set, only four were classical gaaa/11-nt motifs, while over half (48) were gnra-minor groove interactions. the gnra-minor groove interactions were ...201223152878
crystal structures and kinetics of monofunctional proline dehydrogenase provide insight into substrate recognition and conformational changes associated with flavin reduction and product release.proline dehydrogenase (prodh) catalyzes the fad-dependent oxidation of proline to δ(1)-pyrroline-5-carboxylate, which is the first step of proline catabolism. here, we report the structures of proline dehydrogenase from deinococcus radiodurans in the oxidized state complexed with the proline analogue l-tetrahydrofuroic acid and in the reduced state with the proline site vacant. the analogue binds against the si face of the fad isoalloxazine and is protected from bulk solvent by helix α8 and the ...201223151026
weakly antiferromagentic coupling via superexchange interaction between mn(ii)-mn(ii) atoms: a qm/mm study of the active site of human cytosolic x-propyl aminopeptidase p.we investigate the dinuclear manganese, mn(ii)-mn(ii), active site of human cytosolic x-propyl aminopeptidase (xpnpep1) employing the qm/mm method. the optimized structure supports two manganese atoms at the active site and excludes the possibility of a single mn(ii) atom or other combination of divalent metal ions: ca(ii), fe(ii), mg(ii). a broken symmetry solution verifies an antiferromagnetically coupled state between the mn(ii)-mn(ii) pair, which is the ground state. from the energy differen ...201223145216
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...201223145189
chemosensory signaling controls motility and subcellular polarity in myxococcus xanthus.myxococcus xanthus is a model system for the study of dynamic protein localization and cell polarity in bacteria. m. xanthus cells are motile on solid surfaces enabled by two forms of motility. motility is controlled by the che-like frz pathway, which is essential for fruiting body formation and differentiation. the frz signal is mediated by a gtpase/gap protein pair that establishes cell polarity and directs the motility systems. pilus driven motility at the leading pole of the cell requires dy ...201223142584
unraveling the dynamics of ribosome translocation.translocation is one of the key events in translation, requiring large-scale conformational changes in the ribosome, movements of two transfer rnas (trnas) across a distance of more than 20å, and the coupled movement of the messenger rna (mrna) by one codon, completing one cycle of peptide-chain elongation. translocation is catalyzed by elongation factor g (ef-g in bacteria), which hydrolyzes gtp in the process. however, how the conformational rearrangements of the ribosome actually drive the mo ...201223142574
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