Publications

convergent evolution of aua decoding in bacteria and archaea.	deciphering aua codons is a difficult task for organisms, because aua and aug specify isoleucine (ile) and methionine (met), separately. each of the other purine-ending sense co-don sets (nnr) specifies a single amino acid in the universal genetic code. in bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (l or lysidine) and 2-agmatinylcytidine (agm(2)c or agmatidine), respectively, are found at the first letter of the anticodon of trna(ile) responsible for aua codons. these modifi ...	2014	25629511
a new window into the molecular physiology of membrane proteins.	integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ...	2014	25630257
a new window into the molecular physiology of membrane proteins.	integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ...	2014	25630257
diversity in (p)ppgpp metabolism and effectors.	bacteria produce guanosine tetraphosphate and pentaphosphate, collectively named (p)ppgpp, in response to a variety of environmental stimuli. these two remarkable molecules regulate many cellular processes, including the central dogma processes and metabolism, to ensure survival and adaptation. work in escherichia coli laid the foundation for understanding the molecular details of (p)ppgpp and its cellular functions. as recent studies expand to other species, it is apparent that there exists con ...	2015	25636134
ubiquitous transcription factors display structural plasticity and diverse functions: nusg proteins - shifting shapes and paradigms.	numerous accessory factors modulate rna polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional rna processing. transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. nusg/spt5 elongation factors comprise the only universally conserved and ancient family of regulators. they bind to the conserved clamp helices domain of rna polymerase, which also interacts with non-homologous initiation ...	2015	25640595
an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations.	several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ...	2014	25642242
an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations.	several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ...	2014	25642242
structural basis for transcription reactivation by rapa.	rna polymerase (rnap) loses activity during transcription as it stalls at various inactive states due to erratic translocation. reactivation of these stalled rnaps is essential for efficient rna synthesis. here we report a 4.7-å resolution crystal structure of the escherichia coli rnap core enzyme in complex with atpase rapa that is involved in reactivating stalled rnaps. the structure reveals that rapa binds at the rna exit channel of the rnap and makes the channel unable to accommodate the for ...	2015	25646438
distinct pathways of rna polymerase regulation by a phage-encoded factor.	transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. here, we dissect the transcription antitermination mechanism of xanthomonas oryzae virus xp10 protein p7, which binds host rna polymerase (rnap) and regulates both transcription initiation and termination. we show that p7 suppresses intrinsic termination by decreasing rnap pausing and increasing the transcription complex stability, in ...	2015	25646468
association between intrinsic disorder and serine/threonine phosphorylation in mycobacterium tuberculosis.	serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. in eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important m. tuberculosis. here i show that serine/threonine phosphorylation s ...	2015	25648268
pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients.	pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ...	2014	25653647
pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients.	pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ...	2014	25653647
molecular mechanism and evolution of guanylate kinase regulation by (p)ppgpp.	the nucleotide (p)ppgpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. here, we characterize the molecular interaction between (p)ppgpp and guanylate kinase (gmk), revealing the importance of this interaction in adaptation to starvation. combining structural and kinetic analyses, we show that (p)ppgpp binds the gmk active site and competitively inhibits the enzyme. the (p)ppgpp-gmk interact ...	2015	25661490
structure of the vacuolar h+-atpase rotary motor reveals new mechanistic insights.	vacuolar h(+)-atpases are multisubunit complexes that operate with rotary mechanics and are essential for membrane proton transport throughout eukaryotes. here we report a ∼ 1 nm resolution reconstruction of a v-atpase in a different conformational state from that previously reported for a lower-resolution yeast model. the stator network of the v-atpase (and by implication that of other rotary atpases) does not change conformation in different catalytic states, and hence must be relatively rigid ...	2015	25661654
eukaryotic lyr proteins interact with mitochondrial protein complexes.	in eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. lyr (leucine/tyrosine/arginine) motif proteins (lyrms) of the complex1_lyr-like superfamily interact with protein complexes of bacterial origin. many lyr proteins function as extra subunits (lyrm3 and lyrm6) or novel assembly factors (lyrm7, lyrm8, acn9 and fmc1) of the oxidative phosphorylation (oxphos) core complexes. structural insights into complex i accessory subunits lyrm6 and lyrm3 have been p ...	2015	25686363
arginine-rhamnosylation as new strategy to activate translation elongation factor p.	ribosome stalling at polyproline stretches is common and fundamental. in bacteria, translation elongation factor p (ef-p) rescues such stalled ribosomes, but only when it is post-translationally activated. in escherichia coli, activation of ef-p is achieved by (r)-β-lysinylation and hydroxylation of a conserved lysine. here we have unveiled a markedly different modification strategy in which a conserved arginine of ef-p is rhamnosylated by a glycosyltransferase (earp) using dtdp-l-rhamnose as a ...	2015	25686373
long-range pcr amplification of dna by dna polymerase iii holoenzyme from thermus thermophilus.	dna replication in bacteria is accomplished by a multicomponent replicase, the dna polymerase iii holoenzyme (pol iii he). the three essential components of the pol iii he are the α polymerase, the β sliding clamp processivity factor, and the dnax clamp-loader complex. we report here the assembly of the functional holoenzyme from thermus thermophilus (tth), an extreme thermophile. the minimal holoenzyme capable of dna synthesis consists of α, β and dnax (τ and γ), δ and δ' components of the clam ...	2015	25688300
synergistic effects of atp and rna binding to human dead-box protein ddx1.	rna helicases of the dead-box protein family form the largest group of helicases. the human dead-box protein 1 (ddx1) plays an important role in trna and mrna processing, is involved in tumor progression and is also hijacked by several virus families such as hiv-1 for replication and nuclear export. although important in many cellular processes, the mechanism of ddx1's enzymatic function is unknown. we have performed equilibrium titrations and transient kinetics to determine affinities for nucle ...	2015	25690890
rna polymerase-induced remodelling of nusa produces a pause enhancement complex.	pausing during transcription elongation is a fundamental activity in all kingdoms of life. in bacteria, the essential protein nusa modulates transcriptional pausing, but its mechanism of action has remained enigmatic. by combining structural and functional studies we show that a helical rearrangement induced in nusa upon interaction with rna polymerase is the key to its modulatory function. this conformational change leads to an allosteric re-positioning of conserved basic residues that could en ...	2015	25690895
2-thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in rna and dna duplexes.	2-thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. in particular, the 5-substituted-2-thiouridines (s2us) present in trna play an important role in tuning the translation process through codon-anticodon interactions. the enhanced thermodynamic stability of s2u-containing rna duplexes and the preferred s2u-a versus s2u-g base pairing are appreciated characteristics of s2u-modified molecular probes. recently, we have demonstrated that 2-thiouri ...	2015	25690900
identification of a second gtp-bound magnesium ion in archaeal initiation factor 2.	eukaryotic and archaeal translation initiation processes involve a heterotrimeric gtpase e/aif2 crucial for accuracy of start codon selection. in eukaryotes, the gtpase activity of eif2 is assisted by a gtpase-activating protein (gap), eif5. in archaea, orthologs of eif5 are not found and aif2 gtpase activity is thought to be non-assisted. however, no in vitro gtpase activity of the archaeal factor has been reported to date. here, we show that aif2 significantly hydrolyses gtp in vitro. within a ...	2015	25690901
a prokaryotic twist on argonaute function.	argonaute proteins can be found in all three domains of life. in eukaryotic organisms, argonaute is, as the functional core of the rna-silencing machinery, critically involved in the regulation of gene expression. despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic argonaute proteins, the biological function of bacterial and archaeal argonautes has remained elusive. this review discusses new findings in the field that shed light on the structure and fun ...	2015	25692904
structure of escherichia coli dgtp triphosphohydrolase: a hexameric enzyme with dna effector molecules.	the escherichia coli dgt gene encodes a dgtp triphosphohydrolase whose detailed role still remains to be determined. deletion of dgt creates a mutator phenotype, indicating that the dgtpase has a fidelity role, possibly by affecting the cellular dntp pool. in the present study, we have investigated the structure of the dgt protein at 3.1-å resolution. one of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded dna. the presence of dna caused signific ...	2015	25694425
aida: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.	most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available.	2015	25701568
production of dioxygen in the dark: dismutases of oxyanions.	o₂-generating reactions are exceedingly rare in biology and difficult to mimic synthetically. perchlorate-respiring bacteria enzymatically detoxify chlorite (clo₂(-) ), the end product of the perchlorate (clo(4)(-) ) respiratory pathway, by rapidly converting it to dioxygen (o₂) and chloride (cl(-)). this reaction is catalyzed by a heme-containing protein, called chlorite dismutase (cld), which bears no structural or sequence relationships with known peroxidases or other heme proteins and is par ...	2015	25707466
hemq: an iron-coproporphyrin oxidative decarboxylase for protoheme synthesis in firmicutes and actinobacteria.	genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some archaea. it is now known that among the firmicutes and actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. these proteins, named hemq, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme iii into protoheme ix. as purified, hemqs do not contain bound heme, but readily bind ex ...	2015	25711532
identification of two structural elements important for ribosome-dependent gtpase activity of elongation factor 4 (ef4/lepa).	the bacterial translational gtpase ef4/lepa is structurally similar to the canonical elongation factor ef-g. while sharing core structural features with other translational gtpases, the function of ef4 remains unknown. recent structural data locates the unique c-terminal domain (ctd) of ef4 in proximity to the ribosomal peptidyl transferase center (ptc). to investigate the functional role of ef4's ctd we have constructed three c-terminal truncation variants. these variants are fully functional w ...	2015	25712150
analysis of the cooperative atpase cycle of the aaa+ chaperone clpb from thermus thermophilus by using ordered heterohexamers with an alternating subunit arrangement.	the clpb/hsp104 chaperone solubilizes and reactivates protein aggregates in cooperation with dnak/hsp70 and its cofactors. the clpb/hsp104 protomer has two aaa+ modules, aaa-1 and aaa-2, and forms a homohexamer. in the hexamer, these modules form a two-tiered ring in which each tier consists of homotypic aaa+ modules. by atp binding and its hydrolysis at these aaa+ modules, clpb/hsp104 exerts the mechanical power required for protein disaggregation. although atpase cycle of this chaperone has be ...	2015	25713084
novel flp pilus biogenesis-dependent natural transformation.	natural transformation has been described in bacterial species spread through nearly all major taxonomic groups. however, the current understanding of the structural components and the regulation of competence development is derived from only a few model organisms. although natural transformation was discovered in members of the actinobacteria (high gc gram-positive bacteria) more than four decades ago, the structural components or the regulation of the competence system have not been studied in ...	2015	25713572
studying the active-site loop movement of the são paolo metallo-β-lactamase-1†electronic supplementary information (esi) available: procedures for protein expression and purification, (19)f-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. see doi: 10.1039/c4sc01752hclick here for additional data file.	metallo-β-lactamases (mbls) catalyse the hydrolysis of almost all β-lactam antibiotics. we report biophysical and kinetic studies on the são paulo mbl (spm-1), which reveal its zn(ii) ion usage and mechanism as characteristic of the clinically important di-zn(ii) dependent b1 mbl subfamily. biophysical analyses employing crystallography, dynamic (19)f nmr and ion mobility mass spectrometry, however, reveal that spm-1 possesses loop and mobile element regions characteristic of the b2 mbls. these ...	2014	25717359
studying the active-site loop movement of the são paolo metallo-β-lactamase-1†electronic supplementary information (esi) available: procedures for protein expression and purification, (19)f-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. see doi: 10.1039/c4sc01752hclick here for additional data file.	metallo-β-lactamases (mbls) catalyse the hydrolysis of almost all β-lactam antibiotics. we report biophysical and kinetic studies on the são paulo mbl (spm-1), which reveal its zn(ii) ion usage and mechanism as characteristic of the clinically important di-zn(ii) dependent b1 mbl subfamily. biophysical analyses employing crystallography, dynamic (19)f nmr and ion mobility mass spectrometry, however, reveal that spm-1 possesses loop and mobile element regions characteristic of the b2 mbls. these ...	2014	25717359
unraveling the mechanistic features of rna polymerase ii termination by the 5'-3' exoribonuclease rat1.	within a complex with rai1, the 5'-3' exoribonuclease rat1 promotes termination of rna polymerase ii (rnapii) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. using in vitro transcription termination assays, we have found that rnapii is prone to more effective termination by rat1/rai1 when its catalytic site is disrupted due to ntp misincorporation, implying that paused rnapii, which is often found in vivo near termination sites, could adopt a similar c ...	2015	25722373
structural basis for recognition of g-1-containing trna by histidyl-trna synthetase.	aminoacyl-trna synthetases (aarss) play a crucial role in protein translation by linking trnas with cognate amino acids. among all the trnas, only trna(his) bears a guanine base at position -1 (g-1), and it serves as a major recognition element for histidyl-trna synthetase (hisrs). despite strong interests in the histidylation mechanism, the trna recognition and aminoacylation details are not fully understood. we herein present the 2.55 å crystal structure of hisrs complexed with trna(his), whic ...	2015	25722375
supramolecular protein assembly supports immobilization of a cytochrome p450 monooxygenase system as water-insoluble gel.	diverse applications of the versatile bacterial cytochrome p450 enzymes (p450s) are hampered by their requirement for the auxiliary proteins, ferredoxin reductases and ferredoxins, that transfer electrons to p450s. notably, this limits the use of p450s as immobilized enzymes for industrial purposes. herein, we demonstrate the immobilization of a bacterial p450 and its redox protein partners by supramolecular complex formation using a self-assembled heterotrimeric protein. employment of homodimer ...	2015	25733255
heterotrimeric nadh-oxidizing methylenetetrahydrofolate reductase from the acetogenic bacterium acetobacterium woodii.	the methylenetetrahydrofolate reductase (mthfr) of acetogenic bacteria catalyzes the reduction of methylene-thf, which is highly exergonic with nadh as the reductant. therefore, the enzyme was suggested to be involved in energy conservation by reducing ferredoxin via electron bifurcation, followed by na(+) translocation by the rnf complex. the enzyme was purified from acetobacterium woodii and shown to have an unprecedented subunit composition containing the three subunits rnfc2, metf, and metv. ...	2015	25733614
mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site.	the ba3-type cytochrome c oxidase from thermus thermophilus is a membrane-bound protein complex that couples electron transfer to o2 to proton translocation across the membrane. to elucidate the mechanism of the redox-driven proton pumping, we investigated the kinetics of electron and proton transfer in a structural variant of the ba3 oxidase where a putative "pump site" was modified by replacement of asp372 by ile. in this structural variant, proton pumping was uncoupled from internal electron ...	2015	25733886
trna biology in mitochondria.	mitochondria are the powerhouses of eukaryotic cells. they are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. these organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. among them, mitochondria use many specific pathways to obtain complete and functional sets of trnas as required for translatio ...	2015	25734984
evolution of the metazoan mitochondrial replicase.	the large number of complete mitochondrial dna (mtdna) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. by investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtdna polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by ex ...	2015	25740821
regulation of the rply gene encoding 5s rrna binding protein l25 in escherichia coli and related bacteria.	ribosomal protein (r-protein) l25 is one of the three r-proteins (l25, l5, l18) that interact with 5s rrna in eubacteria. specific binding of l25 with a certain domain of 5s r-rna, a so-called loop e, has been studied in detail, but information about regulation of l25 synthesis has remained totally lacking. in contrast to the rple (l5) and rplr (l18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein s8, the rply (l25) gene forms an independ ...	2015	25749694
structural characterization of an alternative mode of tigecycline binding to the bacterial ribosome.	although both tetracycline and tigecycline inhibit protein synthesis by sterically hindering the binding of trna to the ribosomal a site, tigecycline shows increased efficacy in both in vitro and in vivo activity assays and escapes the most common resistance mechanisms associated with the tetracycline class of antibiotics. these differences in activities are attributed to the tert-butyl-glycylamido side chain found in tigecycline. our structural analysis by x-ray crystallography shows that tigec ...	2015	25753625
how fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization.	maximization of growth rate is an important fitness strategy for bacteria. bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. this is exemplified for escherichia coli by the increase of its ribosomal protein-fraction with growth rate, which precisely matches the increased protein synthesis demand. these findings and others have led to the hypothesis that e. coli aims to maximize its growth rate in environments that support growth. howe ...	2015	25754869
the ingenious structure of central rotor apparatus in vov1; key for both complex disassembly and energy coupling between v1 and vo.	vacuolar type rotary h+-atpases (vov1) couple atp synthesis/hydrolysis by v1 with proton translocation by vo via rotation of a central rotor apparatus composed of the v1-df rotor shaft, a socket-like vo-c (eukaryotic vo-d) and the hydrophobic rotor ring. reconstitution experiments using subcomplexes revealed a weak binding affinity of v1-df to vo-c despite the fact that torque needs to be transmitted between v1-df and vo-c for the tight energy coupling between v1 and vo. mutation of a short heli ...	2015	25756791
crystal structure of the c-terminal 2',5'-phosphodiesterase domain of group a rotavirus protein vp3.	in response to viral infections, the mammalian innate immune system induces the production of the second messenger 2'-5' oligoadenylate (2-5a) to activate latent ribonuclease l (rnase l) that restricts viral replication and promotes apoptosis. a subset of rotaviruses and coronaviruses encode 2',5'-phosphodiesterase enzymes that hydrolyze 2-5a, thereby inhibiting rnase l activation. we report the crystal structure of the 2',5'-phosphodiesterase domain of group a rotavirus protein vp3 at 1.39 å re ...	2015	25758703
an intermolecular binding mechanism involving multiple lysm domains mediates carbohydrate recognition by an endopeptidase.	lysm domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing n-acetylglucosamine (glcnac) moieties, such as chitin and peptidoglycan. in bacteria, the functional significance of the involvement of multiple lysm domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. here, a structural study of the thermus thermophilus nlpc/p60 endopeptidase cont ...	2015	25760608
a prime/boost strategy using dna/fowlpox recombinants expressing the genetically attenuated e6 protein as a putative vaccine against hpv-16-associated cancers.	considering the high number of new cases of cervical cancer each year that are caused by human papilloma viruses (hpvs), the development of an effective vaccine for prevention and therapy of hpv-associated cancers, and in particular against the high-risk hpv-16 genotype, remains a priority. vaccines expressing the e6 and e7 proteins that are detectable in all hpv-positive pre-cancerous and cancer cells might support the treatment of hpv-related lesions and clear already established tumors.	2015	25763880
transcription elongation. heterogeneous tracking of rna polymerase and its biological implications.	regulation of transcription elongation via pausing of rna polymerase has multiple physiological roles. the pausing mechanism depends on the sequence heterogeneity of the dna being transcribed, as well as on certain interactions of polymerase with specific dna sequences. in order to describe the mechanism of regulation, we introduce the concept of heterogeneity into the previously proposed alternative models of elongation, power stroke and brownian ratchet. we also discuss molecular origins and p ...	2014	25764114
the old and new testaments of gene regulation. evolution of multi-subunit rna polymerases and co-evolution of eukaryote complexity with the rnap ii ctd.	i relate a story of genesis told from the point of view of multi-subunit rna polymerases (rnaps) including an old testament (core rnap motifs in all cellular life) and a new testament (the rnap ii heptad repeat carboxy terminal domain (ctd) and ctd interactome in eukarya). the old testament: at their active site, one class of eukaryotic interfering rnap and ubiquitous multi-subunit rnaps each have two-double psi β barrel (dpbb) motifs (a distinct pattern for compact 6-β sheet barrels). between β ...	2014	25764332
novel type ii and monomeric nad+ specific isocitrate dehydrogenases: phylogenetic affinity, enzymatic characterization, and evolutionary implication.	nad(+) use is an ancestral trait of isocitrate dehydrogenase (idh), and the nadp(+) phenotype arose through evolution as an ancient adaptation event. however, no nad(+)-specific idhs have been found among type ii idhs and monomeric idhs. in this study, novel type ii homodimeric nad-idhs from ostreococcus lucimarinus cce9901 idh (olidh) and micromonas sp. rcc299 (miidh), and novel monomeric nad-idhs from campylobacter sp. fobrc14 idh (caidh) and campylobacter curvus (ccidh) were reported for the ...	2015	25775177
high-resolution structure of the escherichia coli ribosome.	protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. moreover, the functions of modifications to ribosomal rna and ribosomal proteins have also been unclear. here we present the structure of the escherichia coli 70s ribosome at 2.4-å resolution. the structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and it suggests how sol ...	2015	25775265
structural insights into the role of rrna modifications in protein synthesis and ribosome assembly.	we report crystal structures of the thermus thermophilus ribosome at 2.3- to 2.5-å resolution, which have enabled modeling of rrna modifications. the structures reveal contacts of modified nucleotides with mrna and trnas or protein py, and contacts within the ribosome interior stabilizing the functional fold of rrna. our work provides a resource to explore the roles of rrna modifications and yields a more comprehensive atomic model of a bacterial ribosome.	2015	25775268
universal pathway for posttransfer editing reactions: insights from the crystal structure of ttphers with puromycin.	at the amino acid binding and recognition step, phenylalanyl-trna synthetase (phers) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. resampling of tyr-trna(phe) to phers increasing the number of correctly charged trna molecules has recently been revealed. thus, the very same editing site of phers promotes hydrolysis of misacylated trna species, associated both with cis- and trans-editing pathways. here we report the crystal structure o ...	2015	25775602
substrate, product, and cofactor: the extraordinarily flexible relationship between the cde superfamily and heme.	pfam clan 0032, also known as the cde superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most im ...	2015	25778630
reflections on the 20th anniversary of rna.		2015	25780133
rrna--the evolution of that magic molecule.		2015	25780167
ribosome biochemistry in crystal structure determination.		2015	25780230
the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.	photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ...	2015	25784552
overexpression of a novel thermostable and chloride-tolerant laccase from thermus thermophilus sg0.5jp17-16 in pichia pastoris and its application in synthetic dye decolorization.	laccases have been used for the decolorization and detoxification of synthetic dyes due to their ability to oxidize a wide variety of dyes with water as the sole byproduct. a putative laccase gene (lactt) from thermus thermophilus sg0.5jp17-16 was screened using the genome mining approach, and it was highly expressed in pichia pastoris, yielding a high laccase activity of 6130 u/l in a 10-l fermentor. the lactt open reading frame encoded a protein of 466 amino acid residues with four putative cu ...	2015	25790466
asc1, homolog of human rack1, prevents frameshifting in yeast by ribosomes stalled at cga codon repeats.	quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. in yeast, ribosome stalling occurs at arg cga codon repeats, with even two consecutive cga codons able to reduce translation by up to 50%. the conserved eukaryotic asc1 protein limits translation through internal arg cga codon repeats. we show that, in the absence of asc1 protein, ribosomes continue translatin ...	2015	25792604
unraveling the specific regulation of the central pathway for anaerobic degradation of 3-methylbenzoate.	the mbd cluster encodes the anaerobic degradation of 3-methylbenzoate in the β-proteobacterium azoarcus sp. cib. the specific transcriptional regulation circuit that controls the expression of the mbd genes was investigated. the po, pb 1, and p3 r promoters responsible for the expression of the mbd genes, their cognate mbdr transcriptional repressor, as well as the mbdr operator regions (atacn10gtat) have been characterized. the three-dimensional structure of mbdr has been solved revealing a con ...	2015	25795774
bacterial transfer rnas.	transfer rna is an essential adapter molecule that is found across all three domains of life. the primary role of transfer rna resides in its critical involvement in the accurate translation of messenger rna codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. this review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer rn ...	2015	25796611
x-ray crystal structures of escherichia coli rna polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein.	squaramides constitute a novel class of rna polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the rna polymerase switch region. an iterative chemistry program increased the fraction unbound to human plasma protein from below minimum detection levels, i.e., <1% to 4-6%, while retaining biochemical potency. since in vitro antimicrobial activity against an efflux-negative strain of haemophilus influenz ...	2015	25798859
structural and functional studies of phosphoenolpyruvate carboxykinase from mycobacterium tuberculosis.	tuberculosis, the second leading infectious disease killer after hiv, remains a top public health priority. the causative agent of tuberculosis, mycobacterium tuberculosis (mtb), which can cause both acute and clinically latent infections, reprograms metabolism in response to the host niche. phosphoenolpyruvate carboxykinase (pck) is the enzyme at the center of the phosphoenolpyruvate-pyruvate-oxaloacetate node, which is involved in regulating the carbon flow distribution to catabolism, anabolis ...	2015	25798914
ph dependence of the stress regulator dksa.	dksa controls transcription of genes associated with diverse stress responses, such as amino acid and carbon starvation, oxidative stress, and iron starvation. dksa binds within the secondary channel of rna polymerase, extending its long coiled-coil domain towards the active site. the cellular expression of dksa remains constant due to a negative feedback autoregulation, raising the question of whether dksa activity is directly modulated during stress. here, we show that escherichia coli dksa is ...	2015	25799498
inducible expression of a resistance-nodulation-division-type efflux pump in staphylococcus aureus provides resistance to linoleic and arachidonic acids.	although staphylococcus aureus is exposed to antimicrobial fatty acids on the skin, in nasal secretions, and in abscesses, a specific mechanism of inducible resistance to this important facet of innate immunity has not been identified. here, we have sequenced the genome of s. aureus usa300 variants selected for their ability to grow at an elevated concentration of linoleic acid. the fatty acid-resistant clone far7 had a single nucleotide polymorphism resulting in an h₁₂₁y substitution in an unch ...	2015	25802299
a universal stress protein (usp) in mycobacteria binds camp.	mycobacteria are endowed with rich and diverse machinery for the synthesis, utilization, and degradation of camp. the actions of cyclic nucleotides are generally mediated by binding of camp to conserved and well characterized cyclic nucleotide binding domains or structurally distinct cgmp-specific and -regulated cyclic nucleotide phosphodiesterase, adenylyl cyclase, and e. coli transcription factor fhla (gaf) domain-containing proteins. proteins with cyclic nucleotide binding and gaf domains can ...	2015	25802331
autonomously folding protein fragments reveal differences in the energy landscapes of homologous rnases h.	an important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. in this work, we compare e. coli and t. thermophilus homologs of the protein rnase h. using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (i(core) and i(core+1)) hypothesized to be present on the energy landscapes of these two proteins. we observe that ...	2015	25803034
glycosylation of phenolic compounds by the site-mutated β-galactosidase from lactobacillus bulgaricus l3.	β-galactosidases can transfer the galactosyl from lactose or galactoside donors to various acceptors and thus are especially useful for the synthesis of important glycosides. however, these enzymes have limitations in the glycosylation of phenolic compounds that have many physiological functions. in this work, the β-galactosidase from lactobacillus bulgaricus l3 was subjected to site-saturation mutagenesis at the w980 residue. the recombinant pet-21b plasmid carrying the enzyme gene was used as ...	2015	25803778
deinococcus as new chassis for industrial biotechnology: biology, physiology and tools.	deinococcus spp are among the most radiation-resistant micro-organisms that have been discovered. they show remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation and oxidizing agents. traditionally, escherichia coli and saccharomyces cerevisiae have been the two platforms of choice for engineering micro-organisms for biotechnological applications, because they are well understood and easy to work with. however, in recent years, researchers have begun ...	2015	25809882
the conserved endoribonuclease ybey is required for chloroplast ribosomal rna processing in arabidopsis.	maturation of chloroplast ribosomal rnas (rrnas) comprises several endoribonucleolytic and exoribonucleolytic processing steps. however, little is known about the specific enzymes involved and the cleavage steps they catalyze. here, we report the functional characterization of the single arabidopsis (arabidopsis thaliana) gene encoding a putative ybey endoribonuclease. atybey null mutants are seedling lethal, indicating that atybey function is essential for plant growth. knockdown plants display ...	2015	25810095
structure-function dissection of myxococcus xanthus card n-terminal domain, a defining member of the card_cdnl_trcf family of rna polymerase interacting proteins.	two prototypes of the large card_cdnl_trcf family of bacterial rna polymerase (rnap)-binding proteins, myxococcus xanthus card and cdnl, have distinct functions whose molecular basis remain elusive. card, a global regulator linked to the action of several extracytoplasmic function (ecf) σ-factors, binds to the rnap β subunit (rnap-β) and to protein carg via an n-terminal domain, cardnt, and to dna via an intrinsically unfolded c-terminal domain resembling eukaryotic high-mobility-group a (hmga) ...	2015	25811865
triaminopyrimidine is a fast-killing and long-acting antimalarial clinical candidate.	the widespread emergence of plasmodium falciparum (pf) strains resistant to frontline agents has fuelled the search for fast-acting agents with novel mechanism of action. here, we report the discovery and optimization of novel antimalarial compounds, the triaminopyrimidines (taps), which emerged from a phenotypic screen against the blood stages of pf. the clinical candidate (compound 12) is efficacious in a mouse model of pf malaria with an ed99 <30 mg kg(-1) and displays good in vivo safety mar ...	2015	25823686
the vrra srna controls a stationary phase survival factor vrp of vibrio cholerae.	small non-coding rnas (srnas) are emerging regulatory elements in bacteria. the vibrio cholerae srna vrra has previously been shown to down-regulate outer membrane proteins (ompa and ompt) and biofilm matrix protein (rbmc) by base-pairing with the 5' region of the corresponding mrnas. in this study, we present an additional target of vrra in v. cholerae, the mrna coding for the ribosome binding protein vrp. vrp is homologous to ribosome-associated inhibitor a (raia) of escherichia coli which fac ...	2015	25826569
interaction of trna with eukaryotic ribosome.	this paper is a review of currently available data concerning interactions of trnas with the eukaryotic ribosome at various stages of translation. these data include the results obtained by means of cryo-electron microscopy and x-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of trna derivatives bearing chemically or photochemically reactive groups in the cca-terminal fragment and chemical probing of 28s rrna in the region of the peptid ...	2015	25830484
a functional role of rv1738 in mycobacterium tuberculosis persistence suggested by racemic protein crystallography.	protein 3d structure can be a powerful predictor of function, but it often faces a critical roadblock at the crystallization step. rv1738, a protein from mycobacterium tuberculosis that is strongly implicated in the onset of nonreplicating persistence, and thereby latent tuberculosis, resisted extensive attempts at crystallization. chemical synthesis of the l- and d-enantiomeric forms of rv1738 enabled facile crystallization of the d/l-racemic mixture. the structure was solved by an ab initio ap ...	2015	25831534
two duplicated genes ddi2 and ddi3 in budding yeast encode a cyanamide hydratase and are induced by cyanamide.	two dna damage-inducible genes in saccharomyces cerevisiae, ddi2 and ddi3, are identical and encode putative hd domain-containing proteins, whose functions are currently unknown. because ddi2/3 also shows limited homology to a fungal cyanamide hydratase that converts cyanamide to urea, we tested the enzymatic activity of recombinant ddi2. to this end, we developed a novel enzymatic assay and determined that the km value of the recombinant ddi2/3 for cyanamide is 17.3 ± 0.05 mm, and its activity ...	2015	25847245
productive mrna stem loop-mediated transcriptional slippage: crucial features in common with intrinsic terminators.	escherichia coli and yeast dna-dependent rna polymerases are shown to mediate efficient nascent transcript stem loop formation-dependent rna-dna hybrid realignment. the realignment was discovered on the heteropolymeric sequence t5c5 and yields transcripts lacking a c residue within a corresponding u5c4. the sequence studied is derived from a roseiflexus insertion sequence (is) element where the resulting transcriptional slippage is required for transposase synthesis. the stability of the rna str ...	2015	25848054
the human 18s rrna base methyltransferases dimt1l and wbscr22-trmt112 but not rrna modification are required for ribosome biogenesis.	at the heart of the ribosome lie rrnas, whose catalytic function in translation is subtly modulated by posttranscriptional modifications. in the small ribosomal subunit of budding yeast, on the 18s rrna, two adjacent adenosines (a1781/a1782) are n(6)-dimethylated by dim1 near the decoding site, and one guanosine (g1575) is n(7)-methylated by bud23-trm112 at a ridge between the p- and e-site trnas. here we establish human dimt1l and wbscr22-trmt112 as the functional homologues of yeast dim1 and b ...	2015	25851604
the phenotypic expression of mitochondrial trna-mutations can be modulated by either mitochondrial leucyl-trna synthetase or the c-terminal domain thereof.	mutations in mitochondrial (mt) dna determine important human diseases. the majority of the known pathogenic mutations are located in transfer rna (trna) genes and are responsible for a wide range of currently untreatable disorders. experimental evidence both in yeast and in human cells has shown that the detrimental effects of mt-trna point mutations can be attenuated by increasing the expression of the cognate mt-aminoacyl-trna synthetases (aarss). in addition, constitutive high levels of isol ...	2015	25852750
salinity regulation of the interaction of halovirus snj1 with its host and alteration of the halovirus replication strategy to adapt to the variable ecosystem.	halovirus is a major force that affects the evolution of extreme halophiles and the biogeochemistry of hypersaline environments. however, until now, the systematic studies on the halovirus ecology and the effects of salt concentration on virus-host systems are lacking. to provide more valuable information for understanding ecological strategies of a virus-host system in the hypersaline ecosystem, we studied the interaction between halovirus snj1 and its host natrinema sp.j7-2 under various nacl ...	2015	25853566
recent functional insights into the role of (p)ppgpp in bacterial physiology.	the alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppgpp) are involved in regulating growth and several different stress responses in bacteria. in recent years, substantial progress has been made in our understanding of the molecular mechanisms of (p)ppgpp metabolism and (p)ppgpp-mediated regulation. in this review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the rela/spot homologue (rsh) ...	2015	25853779
marine extremophiles: a source of hydrolases for biotechnological applications.	the marine environment covers almost three quarters of the planet and is where evolution took its first steps. extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. the ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. hydrolases including amylases, cellulases, peptidases and lipases from hyper ...	2015	25854643
molecular determinants of the interactions between proteins and ssdna.	ssdna binding proteins (ssbs) protect ssdna from chemical and enzymatic assault that can derail dna processing machinery. complexes between ssbs and ssdna are often highly stable, but predicting their structures is challenging, mostly because of the inherent flexibility of ssdna and the geometric and energetic complexity of the interfaces that it forms. here, we report a newly developed coarse-grained model to predict the structure of ssb-ssdna complexes. the model is successfully applied to pre ...	2015	25855635
zinc regulates a switch between primary and alternative s18 ribosomal proteins in mycobacterium tuberculosis.	the mycobacterium tuberculosis genome encodes five putative 'alternative' ribosomal proteins whose expression is repressed at high zn(2+) concentration. each alternative protein has a primary homologue that is predicted to bind zn(2+). we hypothesized that zinc triggers a switch between these paired homologous proteins and therefore chose one of these pairs, s18-1/s18-2, to study mechanisms of the predicted competition for their incorporation into ribosomes. our data show that zn(2+)-depletion c ...	2015	25858183
trnaglu increases the affinity of glutamyl-trna synthetase for its inhibitor glutamyl-sulfamoyl-adenosine, an analogue of the aminoacylation reaction intermediate glutamyl-amp: mechanistic and evolutionary implications.	for trna-dependent protein biosynthesis, amino acids are first activated by aminoacyl-trna synthetases (aarss) yielding the reaction intermediates aminoacyl-amp (aa-amp). stable analogues of aa-amp, such as aminoacyl-sulfamoyl-adenosines, inhibit their cognate aarss. glutamyl-sulfamoyl-adenosine (glu-ams) is the best known inhibitor of escherichia coli glutamyl-trna synthetase (glurs). thermodynamic parameters of the interactions between glu-ams and e. coli glurs were measured in the presence an ...	2015	25860020
parallel structural evolution of mitochondrial ribosomes and oxphos complexes.	the five macromolecular complexes that jointly mediate oxidative phosphorylation (oxphos) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal rna ...	2015	25861818
isolation and characterization of a hybrid respiratory supercomplex consisting of mycobacterium tuberculosis cytochrome bcc and mycobacterium smegmatis cytochrome aa3.	recently, energy production pathways have been shown to be viable antitubercular drug targets to combat multidrug-resistant tuberculosis and eliminate pathogen in the dormant state. one family of drugs currently under development, the imidazo[1,2-a]pyridine derivatives, is believed to target the pathogen's homolog of the mitochondrial bc1 complex. this complex, denoted cytochrome bcc, is highly divergent from mitochondrial complex iii both in subunit structure and inhibitor sensitivity, making i ...	2015	25861988
multiple mutations and increased rna expression in tetracycline-resistant streptococcus pneumoniae as determined by genome-wide dna and mrna sequencing.	the objective of this study was to characterize chromosomal mutations associated with resistance to tetracycline in streptococcus pneumoniae.	2015	25862682
atomic-resolution structures of discrete stages on the reaction coordinate of the [fe4s4] enzyme ispg (gcpe).	ispg is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the ispg-catalyzed conversion of 2-c- ...	2015	25868383
semiquinone intermediates are involved in the energy coupling mechanism of e. coli complex i.	complex i (nadh:quinone oxidoreductase) is central to cellular aerobic energy metabolism, and its deficiency is involved in many human mitochondrial diseases. complex i translocates protons across the membrane using electron transfer energy. semiquinone (sq) intermediates appearing during catalysis are suggested to be key for the coupling mechanism in complex i. however, the existence of sq has remained controversial due to the extreme difficulty in detecting unstable and low intensity sq signal ...	2015	25868873
major centers of motion in the large ribosomal rnas.	major centers of motion in the rrnas of thermus thermophilus are identified by alignment of crystal structures of ef-g bound and ef-g unbound ribosomal subunits. small rigid helices upstream of these 'pivots' are aligned, thereby decoupling their motion from global rearrangements. of the 21 pivots found, six are observed in the large subunit rrna and 15 in the small subunit rrna. although the magnitudes of motion differ, with only minor exceptions equivalent pivots are seen in comparisons of esc ...	2015	25870411
structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral rnase l antagonist.	synthesis of 2'-5'-oligoadenylates (2-5a) by oligoadenylate synthetase (oas) is an important innate cellular response that limits viral replication by activating the latent cellular rnase, rnase l, to degrade single-stranded rna. some rotaviruses and coronaviruses antagonize the oas/rnase l pathway through the activity of an encoded 2h phosphoesterase domain that cleaves 2-5a. these viral 2h phosphoesterases are phylogenetically related to the cellular a kinase anchoring protein 7 (akap7) and sh ...	2015	25878106
applications of cas9 as an rna-programmed rna-binding protein.	the streptococcus pyogenes crispr-cas system has gained widespread application as a genome editing and gene regulation tool as simultaneous cellular delivery of the cas9 protein and guide rnas enables recognition of specific dna sequences. the recent discovery that cas9 can also bind and cleave rna in an rna-programmable manner indicates the potential utility of this system as a universal nucleic acid-recognition technology. rna-targeted cas9 (rcas9) could allow identification and manipulation o ...	2015	25880497
a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene.	genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ...	2015	25883135
identification of a laccase glac15 from ganoderma lucidum 77002 and its application in bioethanol production.	laccases have potential applications in detoxification of lignocellulosic biomass after thermochemical pretreatment and production of value-added products or biofuels from renewable biomass. however, their application in large-scale industrial and environmental processes has been severely thwarted by the high cost of commercial laccases. therefore, it is necessary to identify new laccases with lower cost but higher activity to detoxify lignocellulosic hydrolysates and better efficiency to produc ...	2015	25883681
structural effects of protein aging: terminal marking by deamidation in human triosephosphate isomerase.	deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. despite the importance of this process, there is a lack of detailed structural information explai ...	2015	25884638
biosynthesis of l-sorbose and l-psicose based on c-c bond formation catalyzed by aldolases in an engineered corynebacterium glutamicum strain.	the property of loose stereochemical control at aldol products from aldolases helped to synthesize multiple polyhydroxylated compounds with nonnatural stereoconfiguration. in this study, we discovered for the first time that some fructose 1,6-diphosphate aldolases (frua) and tagatose 1,6-diphosphate (taga) aldolases lost their strict stereoselectivity when using l-glyceraldehyde and synthesized not only l-sorbose but also a high proportion of l-psicose. among the aldolases tested, taga from baci ...	2015	25888171
effects of argonaute on gene expression in thermus thermophilus.	eukaryotic argonaute proteins mediate rna-guided rna interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. recently, it has become evident that prokaryotic argonaute homologs mediate dna-guided dna interference, and play a role in host defense. argonaute of the bacterium thermus thermophilus (ttago) targets invading plasmid dna during and after transformation. using small interfering dna guides, ttago can cleave single and double str ...	2015	25902012
major reorientation of trna substrates defines specificity of dihydrouridine synthases.	the reduction of specific uridines to dihydrouridine is one of the most common modifications in trna. increased levels of the dihydrouridine modification are associated with cancer. dihydrouridine synthases (dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded trna, into dihydrouridine. because the catalytic center of all dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotide ...	2015	25902496
dna interference: dna-induced gene silencing in the appendicularian oikopleura dioica.	rna interference is widely employed as a gene-silencing system in eukaryotes for host defence against invading nucleic acids. in response to invading double-stranded rna (dsrna), mrna is degraded in sequence-specific manner. so far, however, dna interference (dnai) has been reported only in plants, ciliates and archaea, and has not been explored in metazoa. here, we demonstrate that linear double-stranded dna promotes both sequence-specific transcription blocking and mrna degradation in developi ...	2015	25904672
identification of novel esterase-active enzymes from hot environments by use of the host bacterium thermus thermophilus.	functional metagenomic screening strategies, which are independent of known sequence information, can lead to the identification of truly novel genes and enzymes. since e. coli has been used exhaustively for this purpose as a host, it is important to establish alternative expression hosts and to use them for functional metagenomic screening for new enzymes. in this study we show that thermus thermophilus hb27 is an excellent screening host and can be used as an alternative provider of truly nove ...	2015	25904908