Publications

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
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
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
cold and hot extremozymes: industrial relevance and current trends.	the development of enzymes for industrial applications relies heavily on the use of microorganisms. the intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. these microorganisms have developed unique mechanisms and molecular means to cope with extreme ...	2015	26539430
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
structural basis for gene regulation by a b12-dependent photoreceptor.	photoreceptor proteins enable organisms to sense and respond to light. the newly discovered carh-type photoreceptors use a vitamin b12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. here we present crystal structures of thermus thermophilus carh in all three relevant states: in the dark, both free and bound to operator dna, and after light exposure. these structures provide visualizations of how adenosylcobalamin mediates carh tetramer ...	2015	26416754
identification of middle chain fatty acyl-coa ligase responsible for the biosynthesis of 2-alkylmalonyl-coas for polyketide extender unit.	understanding the biosynthetic mechanism of the atypical polyketide extender unit is important for the development of bioactive natural products. reveromycin (rm) derivatives produced by streptomyces sp. sn-593 possess several aliphatic extender units. here, we studied the molecular basis of 2-alkylmalonyl-coa formation by analyzing the revr and revs genes, which form a transcriptional unit with the revt gene, a crotonyl-coa carboxylase/reductase homolog. we mainly focused on the uncharacterized ...	2015	26378232
the photochemical mechanism of a b12-dependent photoreceptor protein.	the coenzyme b12-dependent photoreceptor protein, carh, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. on binding of coenzyme b12 the monomeric apoprotein forms tetramers in the dark, which bind operator dna thus blocking transcription. under illumination the carh tetramer dissociates, weakening its affinity for dna and allowing transcription. the mechanism by which this occurs is unknown. here we describe the photochemistry in carh t ...	2015	26264192
the transcription factor carh safeguards use of adenosylcobalamin as a light sensor by altering the photolysis products.	the newly discovered light-dependent transcription factor carh uses adenosylcobalamin as a light sensor to regulate expression of protective genes in bacteria upon exposure to sunlight. this use of adenosylcobalamin is a clever adaptation of a classic enzyme cofactor, taking advantage of its photolabile co-c bond. however, it is also puzzling in that photolysis of adenosylcobalamin generates the 5'-deoxyadenosyl radical that could damage dna. here, using liquid chromatography and spectroscopic t ...	2015	25966286
role and function of litr, an adenosyl b12-bound light-sensitive regulator of bacillus megaterium qm b1551, in regulation of carotenoid production.	the litr/carh family of proteins is a light-sensitive merr family of transcriptional regulators that contain an adenosyl b12 (coenzyme b12 or adob12)-binding domain at the c terminus. the genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from gram-positive bacteria remain poorly understood. we performed genetic and biochemical analyses of a homolog of the litr protein from bacillus megaterium qm b1551, a gr ...	2015	25917914
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
low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition.	previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. however, the relationship between high and low temperature adaptations remains unclear. to investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substit ...	2015	26614525
x-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and o2-reduction states.	during x-ray data collection from a multicopper oxidase (mco) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the x-ray-induced reduction of o2 to 2h2o at the trinuclear copper cluster (tnc) of the enzyme. in this work, 12 crystallographic structures of thermus thermophilus hb27 multicopper oxidase (tth-mco) in holo, apo and hg-bound forms and with different x-ray absorbed doses have been determined. in holo tth-mco structures w ...	2015	26627648
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
high-resolution structures of lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate.	probiotic bacterial strains have been shown to enhance the health of the host through a range of mechanisms including colonization, resistance against pathogens, secretion of antimicrobial compounds and modulation of the activity of the innate immune system. lactobacillus salivarius ucc118 is a well characterized probiotic strain which survives intestinal transit and has many desirable host-interaction properties. probiotic bacteria display a wide range of catabolic activities, which determine t ...	2015	26457526
structural basis of transcription inhibition by cbr hydroxamidines and cbr pyrazoles.	cbr hydroxamidines are small-molecule inhibitors of bacterial rna polymerase (rnap) discovered through high-throughput screening of synthetic-compound libraries. cbr pyrazoles are structurally related rnap inhibitors discovered through scaffold hopping from cbr hydroxamidines. cbr hydroxamidines and pyrazoles selectively inhibit gram-negative bacterial rnap and exhibit selective antibacterial activity against gram-negative bacteria. here, we report crystal structures of the prototype cbr hydroxa ...	2015	26190576
structural biology of bacterial rna polymerase.	since its discovery and characterization in the early 1960s (hurwitz, j. the discovery of rna polymerase. j. biol. chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial rna polymerase (rnap). in the late 1990s, structural information pertaining to bacterial rnap has emerged that provided unprecedented insights into the function and mechanism of rna transcription. in this review, i list all structures related to bacterial rn ...	2015	25970587
time-dependent transcriptional changes in axenic giardia duodenalis trophozoites.	giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. although g. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. the present study employed rna sequencing to characterize the mrna transcriptome of g. duodenalis trophozoites in axenic culture, at log (48 h of g ...	2015	26636323
a conserved histidine in switch-ii of ef-g moderates release of inorganic phosphate.	elongation factor g (ef-g), a translational gtpase responsible for trna-mrna translocation possesses a conserved histidine (h91 in escherichia coli) at the apex of switch-ii, which has been implicated in gtpase activation and gtp hydrolysis. while h91a, h91r and h91e mutants showed different degrees of defect in ribosome associated gtp hydrolysis, h91q behaved like the wt. however, all these mutants, including h91q, are much more defective in inorganic phosphate (pi) release, thereby suggesting ...	2015	26264741
evaluation and directed evolution for thermostability improvement of a gh 13 thermostable α-glucosidase from thermus thermophilus tc11.	thermal stable α-glucosidases with transglycosylation activity could be applied to the industrial production of oligosaccharides as well as conjugation of sugars to biologically useful materials. therefore, α-glucosidases isolated from thermophiles have gained attention over the past decade. in this study, the characterization of a highly thermostable α-glucosidase and its thermostability improved mutant from newly isolated strain thermus thermophilus tc11 were investigated.	2015	26490269
aminopeptidase t of m29 family acts as a novel intracellular virulence factor for listeria monocytogenes infection.	the foodborne pathogen listeria monocytogenes employs a number of virulence determinants including metalloproteases to infect hosts. here for the first time, we identified an m29 family aminopeptidase t (encoded by lmo1603) from l. monocytogenes that possesses a typical feature to catalyze the cleavage of amino acids from peptide substrates, with a preference for arginine. the purified recombinant lmo1603 was activated by fe(3+), zn(2+) and mn(2+), but strongly stimulated by co(2+), indicating t ...	2015	26610705
adaptation of the autotrophic acetogen sporomusa ovata to methanol accelerates the conversion of co2 to organic products.	acetogens are efficient microbial catalysts for bioprocesses converting c1 compounds into organic products. here, an adaptive laboratory evolution approach was implemented to adapt sporomusa ovata for faster autotrophic metabolism and co2 conversion to organic chemicals. s. ovata was first adapted to grow quicker autotrophically with methanol, a toxic c1 compound, as the sole substrate. better growth on different concentrations of methanol and with h2-co2 indicated the adapted strain had a more ...	2015	26530351
structural dissection of the maltodextrin disproportionation cycle of the arabidopsis plastidial disproportionating enzyme 1 (dpe1).	the degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. however, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. in order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (dpe1; a 4-α-glucanotransferase) ...	2015	26504082
complete genome sequence of thermus aquaticus y51mc23.	thermus aquaticus y51mc23 was isolated from a boiling spring in the lower geyser basin of yellowstone national park. remarkably, this t. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. y51mc23 is a gram-negative, rod-shaped organism that grows well between 50°c and 80°c with maximum growth rate at 65°c to 70°c. growth studies suggest that y51mc23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular ...	2015	26465632
complete genome sequence of the thermophilic thermus sp. ccb_us3_uf1 from a hot spring in malaysia.	thermus sp. strain ccb_us3_uf1 is a thermophilic bacterium of the genus thermus, a member of the family thermaceae. members of the genus thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. here, we present the complete genome sequence of thermus sp. ccb_us3_uf1 isolated from a hot spring in malaysia, which is the fifth member of the genus thermus with a completely sequenced and publ ...	2015	26457128
from structure-function analyses to protein engineering for practical applications of dna ligase.	dna ligases are indispensable in all living cells and ubiquitous in all organs. dna ligases are broadly utilized in molecular biology research fields, such as genetic engineering and dna sequencing technologies. here we review the utilization of dna ligases in a variety of in vitro gene manipulations, developed over the past several decades. during this period, fewer protein engineering attempts for dna ligases have been made, as compared to those for dna polymerases. we summarize the recent pro ...	2015	26508902
mismatch repair.	highly conserved muts homologs (msh) and mutl homologs (mlh/pms) are the fundamental components of mismatch repair (mmr). after decades of debate, it appears clear that the msh proteins initiate mmr by recognizing a mismatch and forming multiple extremely stable atp-bound sliding clamps that diffuse without hydrolysis along the adjacent dna. the function(s) of mlh/pms proteins is less clear, although they too bind atp and are targeted to mmr by msh sliding clamps. structural analysis combined wi ...	2015	26354434
cbr antimicrobials inhibit rna polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.	rna polymerase inhibitors like the cbr class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. catalysis by rna polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound ntp and two mg(2+) ions from a preinsertion state to a reactive configuration. cbr inhibitors target a crevice between the n-terminal portion of the bridge helix and a surrounding cap region within ...	2015	26195788
structural basis for the interconversion of maltodextrins by malq, the amylomaltase of escherichia coli.	amylomaltase malq is essential for the metabolism of maltose and maltodextrins in escherichia coli. it catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. to elucidate the molecular basis of transglycosylation by malq, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine- ...	2015	26139606
thermus parvatiensis rl(t) sp. nov., isolated from a hot water spring, located atop the himalayan ranges at manikaran, india.	a gram negative, yellow pigmented, rod shaped bacterium designated as rl(t) was isolated from a hot water spring (90-98 °c) located at manikaran in northern india. the isolate grows at 60-80 °c (optimum, 70 °c) and at ph 7.0-9.0 (optimum ph 7.2). phylogenetic analysis of 16s rrna gene sequences and levels of dna-dna relatedness together indicate that the new isolate represents a novel species of the genus thermus with closest affinity to thermus thermophilus hb8(t) (99.5 %) followed by thermus a ...	2015	26543260
protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor.	in nature, most organisms experience conditions that are suboptimal for growth. to survive, cells must fine-tune energy-demanding metabolic processes in response to nutrient availability. here, we describe a novel mechanism by which protein synthesis in starved cells is down-regulated by phosphorylation of the universally conserved elongation factor tu (ef-tu). phosphorylation impairs the essential gtpase activity of ef-tu, thereby preventing its release from the ribosome. as a consequence, phos ...	2015	26056311
first glycoside hydrolase family 2 enzymes from thermus antranikianii and thermus brockianus with β-glucosidase activity.	two glycoside hydrolase encoding genes (tagh2 and tbgh2) were identified from different thermus species using functional screening. based on amino acid similarities, the enzymes were predicted to belong to glycoside hydrolase (gh) family 2. surprisingly, both enzymes (tagh2 and tbgh2) showed twofold higher activities for the hydrolysis of nitrophenol-linked β-d-glucopyranoside than of -galactopyranoside. specific activities of 3,966 u/mg for tagh2 and 660 u/mg for tbgh2 were observed. in accorda ...	2015	26090361
draft genome sequence of the thermophile thermus filiformis atcc 43280, producer of carotenoid-(di)glucoside-branched fatty acid (di)esters and source of hyperthermostable enzymes of biotechnological interest.	here, we present the draft genome sequence of thermus ﬁliformis strain atcc 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential.	2015	25977443
role of a ribosomal rna phosphate oxygen during the ef-g-triggered gtp hydrolysis.	elongation factor-catalyzed gtp hydrolysis is a key reaction during the ribosomal elongation cycle. recent crystal structures of g proteins, such as elongation factor g (ef-g) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational gtpases (trgtpases) with the sarcin-ricin loop (srl) of ribosomal rna (rrna) is pivotal for hydrolysis. however, the precise mechanism remains elusive and is intensively debated. based on the close prox ...	2015	25941362
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
molecular analysis of codon 548 in the rpob gene involved in mycobacterium tuberculosis resistance to rifampin.	most mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (rrdr) in the gene rpob. however, if this region alone were targeted, rifampin-resistant strains with mutations outside the rrdr would not be detected. in this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long dna fragments containing the rrdr, 47 isolates contained mutations within the rrdr, three isolates conta ...	2015	25534743
a selb/ef-tu/aif2γ-like protein from methanosarcina mazei in the gtp-bound form binds cysteinyl-trna(cys.).	the putative translation elongation factor mbar_a0971 from the methanogenic archaeon methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of ef-tu ("ef-pyl"). in the present study, the crystal structures of its homologue from methanosarcina mazei (mm1309) were determined in the gmppnp-bound, gdp-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. the three mm1309 structures are quite similar (r.m.s.d. < 0.1 å). the three domains, correspond ...	2015	25618148
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
draft genome sequence of thermus sp. isolate 2.9, obtained from a hot water spring located in salta, argentina.	thermus sp. isolate 2.9 was obtained from a hot water spring in salta, argentina. here, we report the draft genome sequence (2,485,434 bp) of this isolate, which consists of 11 scaffolds of >10 kbp and 2,719 protein-coding sequences.	2015	25593256
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
detecting conformational differences between rna 3d structures.	a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ...	2015	27330250
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
human holliday junction resolvase gen1 uses a chromodomain for efficient dna recognition and cleavage.	holliday junctions (hjs) are key dna intermediates in homologous recombination. they link homologous dna strands and have to be faithfully removed for proper dna segregation and genome integrity. here, we present the crystal structure of human hj resolvase gen1 complexed with dna at 3.0 å resolution. the gen1 core is similar to other rad2/xpg nucleases. however, unlike other members of the superfamily, gen1 contains a chromodomain as an additional dna interaction site. chromodomains are known fo ...	2015	26682650
resveratrol directly binds to mitochondrial complex i and increases oxidative stress in brain mitochondria of aged mice.	resveratrol is often described as a promising therapeutic molecule for numerous diseases, especially in metabolic and neurodegenerative disorders. while the mechanism of action is still debated, an increasing literature reports that resveratrol regulates the mitochondrial respiratory chain function. in a recent study we have identified mitochondrial complex i as a direct target of this molecule. nevertheless, the mechanisms and consequences of such an interaction still require further investigat ...	2015	26684010
co-evolution of bacterial ribosomal protein s15 with diverse mrna regulatory structures.	rna-protein interactions are critical in many biological processes, yet how such interactions affect the evolution of both partners is still unknown. rna and protein structures are impacted very differently by mechanisms of genomic change. while most protein families are identifiable at the nucleotide level across large phylogenetic distances, rna families display far less nucleotide similarity and are often only shared by closely related bacterial species. ribosomal protein s15 has two rna bind ...	2015	26675164
mechanisms of ribosome stalling by secm at multiple elongation steps.	regulation of translating ribosomes is a major component of gene expression control network. in escherichia coli, ribosome stalling by the c-terminal arrest sequence of secm regulates the seca-dependent secretion pathway. previous studies reported many residues of secm peptide and ribosome exit tunnel are critical for stalling. however, the underlying molecular mechanism is still not clear at the atomic level. here, we present two cryo-em structures of the secm-stalled ribosomes at 3.3-3.7 å res ...	2015	26670735
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
initiation factor 2 stabilizes the ribosome in a semirotated conformation.	intersubunit rotation and movement of the l1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. the initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. bacterial initiation factors (ifs) 1, 2, and 3 mediate the binding of initiator trna and mrna to the small r ...	2015	26668356
synergistic effect of atp for ruva-ruvb-holliday junction dna complex formation.	the escherichia coli ruvb hexameric ring motor proteins, together with ruvas, promote branch migration of holliday junction dna. zero mode waveguides (zmws) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of ruva-ruvb-holliday junction dna complex. in this study, we used zmws and counted the number of ruvbs binding to ruva-holliday junction dna complex. our data ...	2015	26658024
microbial rhodopsins: wide distribution, rich diversity and great potential.	one of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. in this review, we sum ...	2015	27493861
structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle.	the bacterial sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. intermediates in the sox pathway are covalently attached to the heterodimeric carrier protein soxyz through conjugation to a cysteine on a protein swinging arm. we have investigated how the carrier protein shuttles intermediates between the enzymes of the sox pathway using the interaction between soxyz and the enzyme soxb as our model. the carrier protein and enzyme interact only w ...	2015	26655737
deciphering the dynamics of non-covalent interactions affecting thermal stability of a protein: molecular dynamics study on point mutant of thermus thermophilus isopropylmalate dehydrogenase.	thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. in this study dynamic changes in the non-covalent interac ...	2015	26657745
atp regulation in bioproduction.	adenosine-5'-triphosphate (atp) is consumed as a biological energy source by many intracellular reactions. thus, the intracellular atp supply is required to maintain cellular homeostasis. the dependence on the intracellular atp supply is a critical factor in bioproduction by cell factories. recent studies have shown that changing the atp supply is critical for improving product yields. in this review, we summarize the recent challenges faced by researchers engaged in the development of engineere ...	2015	26655598
nmr structure and function of helicoverpa armigera sterol carrier protein-2, an important insecticidal target from the cotton bollworm.	the cotton bollworm, helicoverpa armigera, has developed strong resistance to many insecticides. sterol carrier protein-2 (scp-2) is an important non-specific lipid transfer protein in insects and appears to be a potential new target. in order to elucidate the structure and function of helicoverpa armigera scp-2 (hascp-2), nmr spectroscopy, docking simulations, mutagenesis and bioassays were performed. hascp-2 composed of five α-helices and four stranded β-sheets. the folds of α-helices and β-sh ...	2015	26655641
evolutionary limitation and opportunities for developing trna synthetase inhibitors with 5-binding-mode classification.	aminoacyl-trna synthetases (aarss) are enzymes that catalyze the transfer of amino acids to their cognate trnas as building blocks for translation. each of the aars families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. in addition, aarss in higher species have evolved important non-translational functions. these translational and non-translational functions of aars are attractive for developing antibacterial, antifungal, and antiparasitic agents ...	2015	26670257
consistency analysis of genome-scale models of bacterial metabolism: a metamodel approach.	genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. with the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. the results showed that a large number of reactions (~22%) are blocked in all the models where they are present. to unravel the nature of such inconsistencies a metamodel was construed by joining the 130 mo ...	2015	26629901
non-specific blocking of mir-17-5p guide strand in triple negative breast cancer cells by amplifying passenger strand activity.	conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (mirna) precursor duplex is selected as the active mirna guide strand. the complementary mirna passenger strand, however, is thought to be inactive. high levels of the oncogenic mirna (oncomir) guide strand called mir-17-5p is overexpressed in triple negative breast cancer (tnbc) and can inhibit ribosomal translation of tumor suppressor gene mrnas, such as programmed cell death 4 (pdcd4) or phosphatase and ten ...	2015	26629823
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
clinical metagenomic identification of balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.	primary amoebic meningoencephalitis (pam) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes.	2015	26620704
activities of the peptidyl transferase center of ribosomes lacking protein l27.	the ribosome is the molecular machine responsible for protein synthesis in all living organisms. its catalytic core, the peptidyl transferase center (ptc), is built of rrna, although several proteins reach close to the inner rrna shell. in the escherichia coli ribosome, the flexible n-terminal tail of the ribosomal protein l27 contacts the a- and p-site trna. based on computer simulations of the ptc and on previous biochemical evidence, the n-terminal α-amino group of l27 was suggested to take p ...	2015	26475831
an s6:s18 complex inhibits translation of e. coli rpsf.	more than half of the ribosomal protein operons in escherichia coli are regulated by structures within the mrna transcripts that interact with specific ribosomal proteins to inhibit further protein expression. this regulation is accomplished using a variety of mechanisms and the rna structures responsible for regulation are often not conserved across bacterial phyla. a widely conserved mrna structure preceding the ribosomal protein operon containing rpsf and rpsr (encoding s6 and s18) was recent ...	2015	26447183
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013
clpb n-terminal domain plays a regulatory role in protein disaggregation.	clpb/hsp100 is an atp-dependent disaggregase that solubilizes and reactivates protein aggregates in cooperation with the dnak/hsp70 chaperone system. the clpb-substrate interaction is mediated by conserved tyrosine residues located in flexible loops in nucleotide-binding domain-1 that extend into the clpb central pore. in addition to the tyrosines, the clpb n-terminal domain (ntd) was suggested to provide a second substrate-binding site; however, the manner in which the ntd recognizes and binds ...	2015	26621746
dancing through life: molecular dynamics simulations and network-centric modeling of allosteric mechanisms in hsp70 and hsp110 chaperone proteins.	hsp70 and hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. although many aspects of allosteric regulatory mechanisms in hsp70 and hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. in this work, ...	2015	26619280
characterization of aspartate kinase from corynebacterium pekinense and the critical site of arg169.	aspartate kinase (ak) is the key enzyme in the biosynthesis of aspartate-derived amino acids. recombinant ak was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. homogeneous ak was predicted as a decamer with a molecular weight of ~48 kda and a half-life of 4.5 h. the enzymatic activity was enhanced by ethanol and ni(2+). moreover, steady-state kinetic study confirmed that ak is an allosteric enzyme, and it ...	2015	26633359
active site coupling in plasmodium falciparum gmp synthetase is triggered by domain rotation.	gmp synthetase (gmps), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. crystal structures of plasmodium falciparum gmps in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the gatase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. we suggest that conformational ...	2015	26592566
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
metagenomics of an alkaline hot spring in galicia (spain): microbial diversity analysis and screening for novel lipolytic enzymes.	a fosmid library was constructed with the metagenomic dna from the water of the lobios hot spring (76°c, ph = 8.2) located in ourense (spain). metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 mbp. 23,207 orfs (open reading frames) were predicted from the assembly. biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. the six ...	2015	26635759
metagenomics: retrospect and prospects in high throughput age.	in recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. in the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. a brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenom ...	2015	26664751
natural guided genome engineering reveals transcriptional regulators controlling quorum-sensing signal degradation.	quorum-quenching (qq) are natural or engineered processes disrupting the quorum-sensing (qs) signalling which controls virulence and persistence (e.g. biofilm) in numerous bacteria. qq involves different enzymes including lactonases, amidases, oxidases and reductases which degrade the qs molecules such as n-acylhomoserine lactones (nahl). rhodococcus erythropolis known to efficiently degrade nahl is proposed as a biocontrol agent and a reservoir of qq-enzymes for biotechnology. in r. erythropoli ...	2015	26554837
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals.	enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few ...	2015	26594201
thermus thermophilus as a source of thermostable lipolytic enzymes.	lipolytic enzymes, esterases (ec 3.1.1.1) and lipases (ec 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. at present, they represent about 20% of commercialized enzymes for industrial use. lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. however, the production at an indus ...	2015	27682117
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
the presence of highly disruptive 16s rrna mutations in clinical samples indicates a wider role for mutations of the mitochondrial ribosome in human disease.	mitochondrial dna mutations are well recognized as an important cause of disease, with over two hundred variants in the protein encoding and mt-trna genes associated with human disorders. in contrast, the two genes encoding the mitochondrial rrnas (mt-rrnas) have been studied in far less detail. this is because establishing the pathogenicity of mt-rrna mutations is a major diagnostic challenge. only two disease causing mutations have been identified at these loci, both mapping to the small subun ...	2015	26349026
coevolution of rtcb and archease created a multiple-turnover rna ligase.	rtcb is a noncanonical rna ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. the genes encoding rtcb and archease constitute a trna splicing operon in many organisms. archease is a cofactor of rtcb that accelerates rna ligation and alters the ntp specificity of the ligase from pyrococcus horikoshii. yet, not all organisms that encode rtcb also encode archease. here we sought to understand the differences between archease-dependent and archease-indepe ...	2015	26385509
structure and function of mitochondrial membrane protein complexes.	biological energy conversion in mitochondria is carried out by the membrane protein complexes of the respiratory chain and the mitochondrial atp synthase in the inner membrane cristae. recent advances in electron cryomicroscopy have made possible new insights into the structural and functional arrangement of these complexes in the membrane, and how they change with age. this review places these advances in the context of what is already known, and discusses the fundamental questions that remain ...	2015	26515107
current and future resources for functional metagenomics.	functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted dna of mixed microbial populations. a functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain dna cloned from environmental metagenomes. the information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. in this perspective, we b ...	2015	26579102
structure and two-metal mechanism of a eukaryal nick-sealing rna ligase.	atp-dependent rna ligases are agents of rna repair that join 3'-oh and 5'-po4 rna ends. naegleria gruberi rna ligase (ngrrnl) exemplifies a family of rna nick-sealing enzymes found in bacteria, viruses, and eukarya. crystal structures of ngrrnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-nζ)-amp•mn(2+) intermediate; ligase•atp•(mn(2+))2 michaelis complex; and ligase•mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound " ...	2015	26512110
enzyme-modified particles for selective biocatalytic hydrogenation by hydrogen-driven nadh recycling.	we describe a new approach to selective h2-driven hydrogenation that exploits a sequence of enzymes immobilised on carbon particles. we used a catalyst system that comprised alcohol dehydrogenase, hydrogenase and an nad(+) reductase on carbon black to demonstrate a greater than 98 % conversion of acetophenone to phenylethanol. oxidation of h2 by the hydrogenase provides electrons through the carbon for nad(+) reduction to recycle the nadh cofactor required by the alcohol dehydrogenase. this bioc ...	2015	26613009
defining the mrna recognition signature of a bacterial toxin protein.	bacteria contain multiple type ii toxins that selectively degrade mrnas bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (a) site, but how these endonucleases achieve substrate specificity remains poorly understood. here, we identify the critical features for how the host inhibition of growth b (higb) toxin recognizes each of the three a-sit ...	2015	26508639
thermodynamics of protein denaturation at temperatures over 100 °c: cuta1 mutant proteins substituted with hydrophobic and charged residues.	although the thermodynamics of protein denaturation at temperatures over 100 °c is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. we designed certain hydrophobic mutant proteins of cuta1 from escherichia coli, which have denaturation temperatures (td) ranging from 101 to 113 °c and show a reversible heat denaturation. using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mut ...	2015	26497062
saxs fingerprints of aldehyde dehydrogenase oligomers.	enzymes of the aldehyde dehydrogenase (aldh) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. aldhs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. mutations in genes encoding aldhs cause metabolic disorders, including alcohol flush reaction (aldh2), sjögren-larsson syndrome (aldh3a2), hyperprolinemia type ii (aldh4a1), γ-hydroxybuty ...	2015	26693506
crystal structure of the human trna m(1)a58 methyltransferase-trna(3)(lys) complex: refolding of substrate trna allows access to the methylation target.	human trna3(lys) is the primer for reverse transcription of hiv; the 3' end is complementary to the primer-binding site on hiv rna. the complementarity ends at the 18th base, a58, which in trna3(lys) is modified to remove watson-crick pairing. motivated to test the role of the modification in terminating the primer-binding sequence and thus limiting run-on transcription, we asked how the modification of rna could be accomplished. trna m(1)a58 methyltransferase (m(1)a58 mtase) methylates n1 of a5 ...	2015	26470919
discovery and functional characterization of diverse class 2 crispr-cas systems.	microbial crispr-cas systems are divided into class 1, with multisubunit effector complexes, and class 2, with single protein effectors. currently, only two class 2 effectors, cas9 and cpf1, are known. we describe here three distinct class 2 crispr-cas systems. the effectors of two of the identified systems, c2c1 and c2c3, contain ruvc-like endonuclease domains distantly related to cpf1. the third system, c2c2, contains an effector with two predicted hepn rnase domains. whereas production of mat ...	2015	26593719
how to show the real microbial biodiversity? a comparison of seven dna extraction methods for bacterial population analyses in matrices containing highly charged natural nanoparticles.	a dna extraction that comprises the dna of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged dna molecules after cell lysis within dna extraction. depending on the methodology of dna extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possibl ...	2015	27682112
a non-canonical multisubunit rna polymerase encoded by a giant bacteriophage.	the infection of pseudomonas aeruginosa by the giant bacteriophage phikz is resistant to host rna polymerase (rnap) inhibitor rifampicin. phikz encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit rnaps. polypeptides of one set are encoded by middle phage genes and are found in the phikz virions. polypeptides of the second set are encoded by early phage genes and are absent from virions. here, we report isolation of a five- ...	2015	26490960
mechanism of eif6 release from the nascent 60s ribosomal subunit.	sbds protein (deficient in the inherited leukemia-predisposition disorder shwachman-diamond syndrome) and the gtpase efl1 (an ef-g homolog) activate nascent 60s ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eif6 from nascent 60s ribosomal subunits. however, the mechanism is completely unknown. here, we present cryo-em structures of human sbds and sbds-efl1 bound to dictyostelium discoideum 60s ribosomal subunits with and without endogenous eif6. sbds ass ...	2015	26479198