Publications

structure of the mammalian antimicrobial peptide bac7(1-16) bound within the exit tunnel of a bacterial ribosome.	proline-rich antimicrobial peptides (pramps) produced as part of the innate immune response of animals, insects and plants represent a vast, untapped resource for the treatment of multidrug-resistant bacterial infections. pramps such as oncocin or bactenecin-7 (bac7) interact with the bacterial ribosome to inhibit translation, but their supposed specificity as inhibitors of bacterial rather than mammalian protein synthesis remains unclear, despite being key to developing drugs with low toxicity. ...	2016	26792896
goniometer-based femtosecond x-ray diffraction of mutant 30s ribosomal subunit crystals.	in this work, we collected radiation-damage-free data from a set of cryo-cooled crystals for a novel 30s ribosomal subunit mutant using goniometer-based femtosecond crystallography. crystal quality assessment for these samples was conducted at the x-ray pump probe end-station of the linac coherent light source (lcls) using recently introduced goniometer-based instrumentation. these 30s subunit crystals were genetically engineered to omit a 26-residue protein, thx, which is present in the wild-ty ...	2015	26798805
multiple nucleic acid cleavage modes in divergent type iii crispr systems.	crispr-cas is an rna-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. type iii systems (cmr, csm) have been shown to cleave rna targets in vitro and some are capable of transcription-dependent dna targeting. the crenarchaeon sulfolobus solfataricus has two divergent subtypes of the type iii system (sso-iiid and a cmr7-containing variant of sso-iiib). here, we report that both the sso-iiid and sso-iiib complexes cleave cognate rna targets with a ruler ...	2016	26801642
structural insights into the quaternary catalytic mechanism of hexameric human quinolinate phosphoribosyltransferase, a key enzyme in de novo nad biosynthesis.	quinolinate phosphoribosyltransferase (qprt) catalyses the production of nicotinic acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous coenzyme nicotinamide adenine dinucleotide. qprt is also essential for maintaining the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing various neurodegenerative diseases. although qprt has been extensively analysed, the molecular basis of the reaction catalysed by human qprt remains unclear. here, we present the c ...	2016	26805589
structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.	with bacterial resistance becoming a serious threat to global public health, antimicrobial peptides (amps) have become a promising area of focus in antibiotic research. amps are derived from a diverse range of species, from prokaryotes to humans, with a mechanism of action that often involves disruption of the bacterial cell membrane. proline-rich antimicrobial peptides (pramps) are instead actively transported inside the bacterial cell where they bind and inactivate specific targets. recently, ...	2016	26809677
identification and characterization of the novel subunit ccom in the cbb3₃cytochrome c oxidase from pseudomonas stutzeri zobell.	cytochrome c oxidases (ccos), members of the heme-copper containing oxidase (hco) superfamily, are the terminal enzymes of aerobic respiratory chains. the cbb3-type cytochrome c oxidases (cbb3-cco) form the c-family and have only the central catalytic subunit in common with the a- and b-family hcos. in pseudomonas stutzeri, two cbb3 operons are organized in a tandem repeat. the atomic structure of the first cbb3 isoform (cbb3-1) was determined at 3.2 å resolution in 2010 (s. buschmann, e. warken ...	2016	26814183
bacterial gcn5-related n-acetyltransferases: from resistance to regulation.	the gcn5-related n-acetyltransferases family (gnat) is an important family of proteins that includes more than 100000 members among eukaryotes and prokaryotes. acetylation appears as a major regulatory post-translational modification and is as widespread as phosphorylation. n-acetyltransferases transfer an acetyl group from acetyl-coa to a large array of substrates, from small molecules such as aminoglycoside antibiotics to macromolecules. acetylation of proteins can occur at two different posit ...	2016	26818562
biological nanomotors with a revolution, linear, or rotation motion mechanism.	the ubiquitous biological nanomotors were classified into two categories in the past: linear and rotation motors. in 2013, a third type of biomotor, revolution without rotation (http://rnanano.osu.edu/movie.html), was discovered and found to be widespread among bacteria, eukaryotic viruses, and double-stranded dna (dsdna) bacteriophages. this review focuses on recent findings about various aspects of motors, including chirality, stoichiometry, channel size, entropy, conformational change, and en ...	2016	26819321
systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5'-phosphate production in e. coli.	recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. understanding the role of such enzymes is an important open question in biology. here we develop a genome-wide method, proper, that uses a permissive psi-blast approach to predict promiscuous activities of metabolic genes. enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous 'replacer' gene rescues lethality caused by ina ...	2016	26821166
acetylome analysis reveals the involvement of lysine acetylation in biosynthesis of antibiotics in bacillus amyloliquefaciens.	lysine acetylation is a major post-translational modification that plays an important regulatory role in almost every aspects in both eukaryotes and prokaryotes. bacillus amyloliquefaciens, a gram-positive bacterium, is very effective for the control of plant pathogens. however, very little is known about the function of lysine acetylation in this organism. here, we conducted the first lysine acetylome in b. amyloliquefaciens through a combination of highly sensitive immune-affinity purification ...	2016	26822828
a structural view of microrna-target recognition.	it is well established that the correct identification of the messenger rna targeted by a given microrna (mirna) is a difficult problem, and that available methods all suffer from low specificity. we hypothesize that the correct identification of the pairing should take into account the effect of the argonaute protein (ago), an essential catalyst of the recognition process. therefore, we developed a strategy named miren for building and scoring three-dimensional models of the ternary complex for ...	2016	26825463
interaction network of tobacco etch potyvirus nia protein with the host proteome during infection.	the genomes of plant viruses have limited coding capacity, and to complete their infectious cycles, viral factors must target, direct or indirectly, many host elements. however, the interaction networks between viruses and host factors are poorly understood. the genus potyvirus is the largest group of plus-strand rna viruses infecting plants. potyviral nuclear inclusion a (nia) plays many roles during infection. nia is a polyprotein consisting of two domains, viral protein genome-linked (vpg) an ...	2016	26830344
different functions of phylogenetically distinct bacterial complex i isozymes.	nadh:quinone oxidoreductase (complex i) is a bioenergetic enzyme that transfers electrons from nadh to quinone, conserving the energy of this reaction by contributing to the proton motive force. while the importance of nadh oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex i to bacterial electron transport chains has been tested in only a few species. here, we analyze the function of two phylogenetically distinct complex i isozymes in rhodobacter spha ...	2016	26833419
neisseria meningitidis translation elongation factor p and its active-site arginine residue are essential for cell viability.	translation elongation factor p (ef-p), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. in escherichia coli and salmonella enterica, the post-translational β-lysyl modification of lys34 of ef-p is important for the ef-p activity. the β-lysyl ef-p modification pathway is conserved among only 26-28% of bacteria. recently, it was found that the shewanella oneidensis and pseudomonas aeruginosa ef-p proteins, containing ...	2016	26840407
mutations in the nucleotide binding and hydrolysis domains of helicobacter pylori muts2 lead to altered biochemical activities and inactivation of its in vivo function.	helicobacter pylori muts2 (hpmuts2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. although hpmuts2 belongs to a highly conserved family of abc transporter atpases, the role of its atp binding and hydrolysis activities remains elusive.	2016	26843368
all the o2 consumed by thermus thermophilus cytochrome ba3 is delivered to the active site through a long, open hydrophobic tunnel with entrances within the lipid bilayer.	cytochrome ba3 is a proton-pumping heme-copper oxygen reductase from the extreme thermophile thermus thermophilus. despite the fact that the enzyme's active site is buried deep within the protein, the apparent second order rate constant for the initial binding of o2 to the active-site heme has been experimentally found to be 10(9) m(-1) s(-1) at 298 k, at or near the diffusion limit, and 2 orders of magnitude faster than for o2 binding to myoglobin. to provide quantitative and microscopic descri ...	2016	26845082
kinetic mechanism and fidelity of nick sealing by escherichia coli nad+-dependent dna ligase (liga).	escherichia coli dna ligase (ecoliga) repairs 3'-oh/5'-po4 nicks in duplex dna via reaction of liga with nad(+) to form a covalent liga-(lysyl-nζ)-amp intermediate (step 1); transfer of amp to the nick 5'-po4 to form an appdna intermediate (step 2); and attack of the nick 3'-oh on appdna to form a 3'-5' phosphodiester (step 3). a distinctive feature of ecoliga is its stimulation by ammonium ion. here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealin ...	2016	26857547
from chlorite dismutase towards hemq - the role of the proximal h-bonding network in haeme binding.	chlorite dismutase (cld) and hemq are structurally and phylogenetically closely related haeme enzymes differing fundamentally in their enzymatic properties. clds are able to convert chlorite into chloride and dioxygen, whereas hemq is proposed to be involved in the haeme b synthesis of gram-positive bacteria. a striking difference between these protein families concerns the proximal haeme cavity architecture. the pronounced h-bonding network in cld, which includes the proximal ligand histidine a ...	2016	26858461
biofuel production based on carbohydrates from both brown and red macroalgae: recent developments in key biotechnologies.	marine macroalgae (green, red and brown macroalgae) have attracted attention as an alternative source of renewable biomass for producing both fuels and chemicals due to their high content of suitable carbohydrates and to their advantages over terrestrial biomass. however, except for green macroalgae, which contain relatively easily-fermentable glucans as their major carbohydrates, practical utilization of red and brown macroalgae has been regarded as difficult due to the major carbohydrates (alg ...	2016	26861307
ribosomal small subunit domains radiate from a central core.	the domain architecture of a large rna can help explain and/or predict folding, function, biogenesis and evolution. we offer a formal and general definition of an rna domain and use that definition to experimentally characterize the rrna of the ribosomal small subunit. here the rrna comprising a domain is compact, with a self-contained system of molecular interactions. a given rrna helix or stem-loop must be allocated uniquely to a single domain. local changes such as mutations can give domain-w ...	2016	26876483
chemical control of xylem differentiation by thermospermine, xylemin, and auxin.	the xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. the vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. procambium formation and xylem differentiation are directed by auxin. in angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. h ...	2016	26879262
mycobacterium tuberculosis transcription machinery: ready to respond to host attacks.	regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. for pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. inappropriate responses have consequences; h ...	2016	26883824
purification and characterization of glutaminase free asparaginase from enterobacter cloacae: in-vitro evaluation of cytotoxic potential against human myeloid leukemia hl-60 cells.	asparaginase is an important antileukemic agent extensively used worldwide but the intrinsic glutaminase activity of this enzymatic drug is responsible for serious life threatening side effects. hence, glutaminase free asparaginase is much needed for upgradation of therapeutic index of asparaginase therapy. in the present study, glutaminase free asparaginase produced from enterobacter cloacae was purified to apparent homogeneity. the purified enzyme was found to be homodimer of approximately 106 ...	2016	26891220
substrate recognition and cleavage-site selection by a single-subunit protein-only rnase p.	rnase p is the enzyme that removes 5' extensions from trna precursors. with its diversity of enzyme forms-either protein- or rna-based, ranging from single polypeptides to multi-subunit ribonucleoproteins-the rnase p enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous rnase p prorp3 from arabidopsis thaliana. compared ...	2016	26896801
the trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by pichia pastoris.	copper is an essential chemical element for life as it is a part of prosthetic groups of enzymes including super oxide dismutase and cytochrome c oxidase; however, it is also toxic at high concentrations. here, we present the trade-off of copper availability and growth inhibition of a common host used for copper-dependent protein production, pichia pastoris.	2016	26897180
systematic evolution and study of uagn decoding trnas in a genomically recoded bacteria.	we report the first systematic evolution and study of trna variants that are able to read a set of uagn (n = a, g, u, c) codons in a genomically recoded e. coli strain that lacks any endogenous in-frame uagn sequences and release factor 1. through randomizing bases in anticodon stem-loop followed by a functional selection, we identified trna mutants with significantly improved uagn decoding efficiency, which will augment the current efforts on genetic code expansion through quadruplet decoding. ...	2016	26906548
role of protein phosphorylation in the regulation of cell cycle and dna-related processes in bacteria.	in all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. in eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. protein phosphorylation is also involved in the global control of dna replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. similar to eukaryotes, bacteria use hanks-type kinases and phosphatases for signal transductio ...	2016	26909079
atp binding by the p-loop ntpase osychf1 (an unconventional g protein) contributes to biotic but not abiotic stress responses.	g proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze gtp. the ychf subfamily, interestingly, possesses the unique ability to bind both atp and gtp, and is possibly an ancestral form of g proteins based on phylogenetic studies and is present in all kingdoms of life. however, the biological significance of such a relaxed ligand specificity has long eluded researchers. here, we have elucidated the different conformational chan ...	2016	26912459
in-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.	precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. we developed a system for producing high-quality protein crystals with high throughput. using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. in addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. ...	2016	26916802
naturally occurring isoleucyl-trna synthetase without trna-dependent pre-transfer editing.	isoleucyl-trna synthetase (ilers) is unusual among aminoacyl-trna synthetases in having a trna-dependent pre-transfer editing activity. alongside the typical bacterial ilers (such as escherichia coli ilers), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic ilerss and exhibit low sensitivity to the antibiotic mupirocin. our phylogenetic analysis suggests that the iles1 and iles2 genes of contemporary bacteria are the descendants of genes that might have arisen by ...	2016	26921320
physiological properties and genome structure of the hyperthermophilic filamentous phage φoh3 which infects thermus thermophilus hb8.	a filamentous bacteriophage, φoh3, was isolated from hot spring sediment in obama hot spring in japan with the hyperthermophilic bacterium thermus thermophilus hb8 as its host. phage φoh3, which was classified into the inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φoh3 was stable at temperatures ranging from 70 to 90°c and at phs ranging from 6 to 9. a one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, ...	2016	26941711
metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines.	soda lakes are salt lakes with a naturally alkaline ph due to evaporative concentration of sodium carbonates in the absence of major divalent cations. hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. we present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from th ...	2016	26941731
genomic and transcriptomic analysis of the streptomycin-dependent mycobacterium tuberculosis strain 18b.	the ability of mycobacterium tuberculosis to establish a latent infection (ltbi) in humans confounds the treatment of tuberculosis. consequently, there is a need to discover new therapeutic agents that can kill m. tuberculosis both during active disease and ltbi. the streptomycin-dependent strain of m. tuberculosis, 18b, provides a useful tool for this purpose since upon removal of streptomycin (str) it enters a non-replicating state that mimics latency both in vitro and in animal models.	2016	26944551
crystal structure of a substrate-engaged secy protein-translocation channel.	hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic secy or eukaryotic sec61 complex. how signal sequences are recognized is poorly understood, particularly because they are diverse in sequence and length. structures of the inactive channel show that the largest subunit, secy or sec61α, consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membr ...	2016	26950603
models for the a subunits of the thermus thermophilus v/a-atpase and saccharomyces cerevisiae v-atpase enzymes by cryo-em and evolutionary covariance.	rotary atpases couple atp synthesis or hydrolysis to proton translocation across a membrane. however, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. the v/a-atpase from the eubacterium thermus thermophilus is similar in structure to the eukaryotic v-atpase but has a simpler subunit composition and functions in vivo to synthesize atp rather than pump protons. we determined the t. thermophilus v/a-atpase structure by cr ...	2016	26951669
the inhibitory effect of non-substrate and substrate dna on the ligation and self-adenylylation reactions catalyzed by t4 dna ligase.	dna ligases are essential both to in vivo replication, repair and recombination processes, and in vitro molecular biology protocols. prior characterization of dna ligases through gel shift assays has shown the presence of a nick site to be essential for tight binding between the enzyme and its dsdna substrate, with no interaction evident on dsdna lacking a nick. in the current study, we observed a significant substrate inhibition effect, as well as the inhibition of both the self-adenylylation a ...	2016	26954034
stability of ensemble models predicts productivity of enzymatic systems.	stability in a metabolic system may not be obtained if incorrect amounts of enzymes are used. without stability, some metabolites may accumulate or deplete leading to the irreversible loss of the desired operating point. even if initial enzyme amounts achieve a stable steady state, changes in enzyme amount due to stochastic variations or environmental changes may move the system to the unstable region and lose the steady-state or quasi-steady-state flux. this situation is distinct from the pheno ...	2016	26963521
illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.	illumina's sequencing platforms are currently the most utilised sequencing systems worldwide. the technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read-lengths and true paired-end reads. however, data from any sequencing technology contains noise and our understanding of the peculiarities and sequencing errors encountered in illumina data has lagged behind this rapid development.	2016	26968756
application of a euryarchaeota-specific helicase from thermococcus kodakarensis for noise reduction in pcr.	dna/rna helicases, which are enzymes for eliminating hydrogen bonds between bases of dna/dna, dna/rna, and rna/rna using the energy of atp hydrolysis, contribute to various biological activities. in the present study, the euryarchaeota-specific helicase esha (tk0566) from the hyperthermophilic archaeon thermococcus kodakarensis (tk-esha) was obtained as a recombinant form, and its enzymatic properties were examined. tk-esha exhibited maximal atpase activity in the presence of rna at 80°c. unwind ...	2016	26969705
unlocking the bacterial secy translocon.	the sec translocon performs protein secretion and membrane protein insertion at the plasma membrane of bacteria and archaea (secyeg/β), and the endoplasmic reticular membrane of eukaryotes (sec61). despite numerous structures of the complex, the mechanism underlying translocation of pre-proteins, driven by the atpase seca in bacteria, remains unresolved. here we present a series of biochemical and computational analyses exploring the consequences of signal sequence binding to secyeg. the data de ...	2016	26973090
structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.	throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trgtpase). although the structural basis for trgtpase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trgtpase, initiation factor 2 (if2), complexed with the ribosome, remains elusive. we determine t ...	2016	26973877
a polymorphism in leus confers reduced susceptibility to gsk2251052 in a clinical isolate of staphylococcus aureus.	gsk2251052 is a broad-spectrum antibacterial inhibitor of leucyl trna-synthetase (leurs) that has been evaluated in phase ii clinical trials. here, we report the identification of a clinical isolate of staphylococcus aureus that exhibits reduced susceptibility to gsk2251052 without prior exposure to the compound and demonstrate that this phenotype is attributable to a single amino acid polymorphism (p329) within the editing domain of leurs.	2016	26976861
(1)h, (13)c and (15)n resonance assignments and secondary structure analysis of translation initiation factor 1 from pseudomonas aeruginosa.	pseudomonas aeruginosa is a gram-negative opportunistic pathogen and a primary cause of infection in humans. p. aeruginosa can acquire resistance against multiple groups of antimicrobial agents, including β-lactams, aminoglycosides and fluoroquinolones, and multidrug resistance is increasing in this organism which makes treatment of the infections difficult and expensive. this has led to the unmet need for discovery of new compounds distinctly different from present antimicrobials. protein synth ...	2016	26983940
insight into the flagella type iii export revealed by the complex structure of the type iii atpase and its regulator.	flii and flij form the flii6flij atpase complex of the bacterial flagellar export apparatus, a member of the type iii secretion system. the flii6flij complex is structurally similar to the α3β3γ complex of f1-atpase. the flih homodimer binds to flii to connect the atpase complex to the flagellar base, but the details are unknown. here we report the structure of the homodimer of a c-terminal fragment of flih (flihc2) in complex with flii. flihc2 shows an unusually asymmetric homodimeric structure ...	2016	26984495
silica-induced protein (sip) in thermophilic bacterium thermus thermophilus responds to low iron availability.	thermus thermophilus hb8 expresses silica-induced protein (sip) when cultured in medium containing supersaturated silicic acids. using genomic information, sip was identified as a fe(3+)-binding abc transporter. detection of a 1-kb hybridized band in northern analysis revealed that sip transcription is monocistronic and that sip has its own terminator and promoter. the sequence of the sip promoter showed homology with that of the σ(a)-dependent promoter, which is known as a housekeeping promoter ...	2016	26994077
targeting antibiotic resistance.	finding strategies against the development of antibiotic resistance is a major global challenge for the life sciences community and for public health. the past decades have seen a dramatic worldwide increase in human-pathogenic bacteria that are resistant to one or multiple antibiotics. more and more infections caused by resistant microorganisms fail to respond to conventional treatment, and in some cases, even last-resort antibiotics have lost their power. in addition, industry pipelines for th ...	2016	27000559
mechanism of fusidic acid inhibition of rrf- and ef-g-dependent splitting of the bacterial post-termination ribosome.	the antibiotic drug fusidic acid (fa) is commonly used in the clinic against gram-positive bacterial infections. fa targets ribosome-bound elongation factor g (ef-g), a translational gtpase that accelerates both messenger rna (mrna) translocation and ribosome recycling. how fa inhibits translocation was recently clarified, but fa inhibition of ribosome recycling by ef-g and ribosome recycling factor (rrf) has remained obscure. here we use fast kinetics techniques to estimate mean times of riboso ...	2016	27001509
sequencing of hepatitis c virus cdna with polymerase chain reaction directed sequencing.	to explore a rapid and easy sequencing method for hepatitis c virus (hcv) genome and establish a new sequencing method in china.	1997	27006575
a critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.	k-turns are commonly-occurring motifs that introduce sharp kinks into duplex rna, thereby facilitating tertiary contacts. both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called n3 and n1, that differ in the pattern of hydrogen bonding in the core. we show here that this is determined by the basepair adjacent to the critical g•a pairs. we determined crystal structures of a series of kt-7 variants in which this 3b,3 ...	2016	27016741
trna core hypothesis for the transition from the rna world to the ribonucleoprotein world.	herein we present the trna core hypothesis, which emphasizes the central role of trnas molecules in the origin and evolution of fundamental biological processes. trnas gave origin to the first genes (mrna) and the peptidyl transferase center (rrna), proto-trnas were at the core of a proto-translation system, and the anticodon and operational codes then arose in trnas molecules. metabolic pathways emerged from evolutionary pressures of the decoding systems. the transitions from the rna world to t ...	2016	27023615
investigating the proton donor in the no reductase from paracoccus denitrificans.	variant nomenclature: the variants were made in the norb subunit if not indicated by the superscript c, which are variants in the norc subunit (e.g. e122a = exchange of glu-122 in norb for an ala, e71cd; exchange of glu-71 in norc for an asp). bacterial no reductases (nors) are integral membrane proteins from the heme-copper oxidase superfamily. most heme-copper oxidases are proton-pumping enzymes that reduce o2 as the last step in the respiratory chain. with electrons from cytochrome c, no redu ...	2016	27030968
structures of e. coli σs-transcription initiation complexes provide new insights into polymerase mechanism.	in bacteria, multiple σ factors compete to associate with the rna polymerase (rnap) core enzyme to form a holoenzyme that is required for promoter recognition. during transcription initiation rnap remains associated with the upstream promoter dna via sequence-specific interactions between the σ factor and the promoter dna while moving downstream for rna synthesis. as rna polymerase repetitively adds nucleotides to the 3'-end of the rna, a pyrophosphate ion is generated after each nucleotide inco ...	2016	27035955
a bacterial argonaute with noncanonical guide rna specificity.	eukaryotic argonaute proteins induce gene silencing by small rna-guided recognition and cleavage of mrna targets. although structural similarities between human and prokaryotic argonautes are consistent with shared mechanistic properties, sequence and structure-based alignments suggested that argonautes encoded within crispr-cas [clustered regularly interspaced short palindromic repeats (crispr)-associated] bacterial immunity operons have divergent activities. we show here that the crispr-associ ...	2016	27035975
crystal structure of cota laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site.	the cota laccase from bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. the crystal structure of cota complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in a hole motif has been solved. the novel binding site was about 26 å away from the t1 binding pocket. comparison with known structures of other laccases revealed that the hole is a specific feature of cota. the key residues arg476 and ser360 were directly bo ...	2016	27050268
escherichia coli dnae polymerase couples pyrophosphatase activity to dna replication.	dna polymerases generate pyrophosphate every time they catalyze a step of dna elongation. this elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphatases. however, the specific action of inorganic pyrophosphatases coupled to dna replication in vivo was never demonstrated. here we show that the polymerase-histidinol-phosphatase (php) domain of escherichia coli dna polymerase iii α subunit features pyrophospha ...	2016	27050298
structural basis for dna 5´-end resection by recj.	the resection of dna strand with a 5´ end at double-strand breaks is an essential step in recombinational dna repair. recj, a member of dhh family proteins, is the only 5´ nuclease involved in the recf recombination pathway. here, we report the crystal structures of deinococcus radiodurans recj in complex with deoxythymidine monophosphate (dtmp), ssdna, the c-terminal region of single-stranded dna-binding protein (ssb-ct) and a mechanistic insight into the recf pathway. a terminal 5´-phosphate-b ...	2016	27058167
the chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in new zealand's taupō volcanic zone.	chthonomonas calidirosea t49(t) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. we hypothesized that the c. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. we tested this hypothesis by sequencing the genomes of four c. calidirosea isolates obtained from four separate geoth ...	2016	27060125
global association between thermophilicity and vancomycin susceptibility in bacteria.	exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 ph) mid-temperature (55-85°c) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. to gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media w ...	2016	27065976
inhibition of translation initiation complex formation by ge81112 unravels a 16s rrna structural switch involved in p-site decoding.	in prokaryotic systems, the initiation phase of protein synthesis is governed by the presence of initiation factors that guide the transition of the small ribosomal subunit (30s) from an unlocked preinitiation complex (30s preic) to a locked initiation complex (30sic) upon the formation of a correct codon-anticodon interaction in the peptidyl (p) site. biochemical and structural characterization of ge81112, a translational inhibitor specific for the initiation phase, indicates that the main mech ...	2016	27071098
insights into rna binding by the anticancer drug cisplatin from the crystal structure of cisplatin-modified ribosome.	cisplatin is a widely prescribed anticancer drug, which triggers cell death by covalent binding to a broad range of biological molecules. among cisplatin targets, cellular rnas remain the most poorly characterized molecules. although cisplatin was shown to inactivate essential rnas, including ribosomal, spliceosomal and telomeric rnas, cisplatin binding sites in most rna molecules are unknown, and therefore it remains challenging to study how modifications of rna by cisplatin contributes to its ...	2016	27079977
crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous β-keto acid.	the enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. in a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria pseudomonas putida g7. in this organism, the 83 kb nah7 plasmid carries several genes involved in this biotransformation process. one enzyme in this route, nahk, ...	2016	27082660
evolutionary relationships between heme-binding ferredoxin α + β barrels.	the α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. the barrel architecture of these proteins is formed by either homo-/hetero-dimerization or duplication and fusion of ferredoxin-like domains. several members of this superfamily bind heme in order to carry out their functions.	2016	27089923
elongation factor 4 remodels the a-site trna on the ribosome.	during translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. many of those factors are guanosine triphosphatases (gtpases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (gtp) to promote conformational changes. despite numerous studies, the function of elongation factor 4 (ef-4/lepa), a highly conserved translational gtpase, has remained elusive. here, we present the crystal structure at 2.6-å resolution of the thermus thermophilus 7 ...	2016	27092003
the ancient evolutionary history of polyomaviruses.	polyomaviruses are a family of dna tumor viruses that are known to infect mammals and birds. to investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billi ...	2016	27093155
nucleoside modifications in the regulation of gene expression: focus on trna.	both, dna and rna nucleoside modifications contribute to the complex multi-level regulation of gene expression. modified bases in trnas modulate protein translation rates in a highly dynamic manner. synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. nucleoside modifications in the trna anticodon loop can favor the interaction with selected codons by stabilizing specific ...	2016	27094388
computing the origin and evolution of the ribosome from its structure - uncovering processes of macromolecular accretion benefiting synthetic biology.	accretion occurs pervasively in nature at widely different timeframes. the process also manifests in the evolution of macromolecules. here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. phylogenetic trees of protein ...	2015	27096056
engineering a d-lactate dehydrogenase that can super-efficiently utilize nadph and nadh as cofactors.	engineering the cofactor specificity of a natural enzyme often results in a significant decrease in its activity on original cofactor. here we report that a nadh-dependent dehydrogenase (d-ldh) from lactobacillus delbrueckii 11842 can be rationally engineered to efficiently use both nadh and nadph as cofactors. point mutations on three amino acids (d176s, i177r, f178t) predicted by computational analysis resulted in a modified enzyme designated as d-ldh. the kcat/km of the purified d-ldh on na ...	2016	27109778
structural dynamics of human argonaute2 and its interaction with sirnas designed to target mutant tdp43.	the human argonaute2 protein (ago2) is a key player in rna interference pathway and small rna recognition by ago2 is the crucial step in sirna mediated gene silencing mechanism. the present study highlights the structural and functional dynamics of human ago2 and the interaction mechanism of ago2 with a set of seven sirnas for the first time. the human ago2 protein adopts two conformations such as "open" and "close" during the simulation of 25 ns. one of the domains named as paz, which is respon ...	2016	27110240
life without complex i: proteome analyses of an arabidopsis mutant lacking the mitochondrial nadh dehydrogenase complex.	the mitochondrial nadh dehydrogenase complex (complex i) is of particular importance for the respiratory chain in mitochondria. it is the major electron entry site for the mitochondrial electron transport chain (metc) and therefore of great significance for mitochondrial atp generation. we recently described an arabidopsis thaliana double-mutant lacking the genes encoding the carbonic anhydrases ca1 and ca2, which both form part of a plant-specific 'carbonic anhydrase domain' of mitochondrial co ...	2016	27122571
transcription regulation in archaea.	the known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. archaea are reliant on a single rna polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcripti ...	2016	27137495
bioprospecting sponge-associated microbes for antimicrobial compounds.	sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. however, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. this review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. we discuss the current state-of-the-art by grouping the bioact ...	2016	27144573
evidence for fast electron transfer between the high-spin haems in cytochrome bd-i from escherichia coli.	cytochrome bd-i is one of the three proton motive force-generating quinol oxidases in the o2-dependent respiratory chain of escherichia coli. it contains one low-spin haem (b558) and the two high-spin haems (b595 and d) as the redox-active cofactors. in order to examine the flash-induced intraprotein reverse electron transfer (the so-called ''electron backflow''), co was photolyzed from the ferrous haem d in one-electron reduced (b5583+b5953+d2+-co) cytochrome bd-i, and the fully reduced (b5582+ ...	2016	27152644
independent evolution of six families of halogenating enzymes.	halogenated natural products are widespread in the environment, and the halogen atoms are typically vital to their bioactivities. thus far, six families of halogenating enzymes have been identified: cofactor-free haloperoxidases (hpo), vanadium-dependent haloperoxidases (v-hpo), heme iron-dependent haloperoxidases (hi-hpo), non-heme iron-dependent halogenases (ni-hg), flavin-dependent halogenases (f-hg), and s-adenosyl-l-methionine (sam)-dependent halogenases (s-hg). however, these halogenating ...	2016	27153321
comparative transcriptomics across the prokaryotic tree of life.	whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding rnas, cis-antisense transcription and regulatory untranslated regions (utrs). understanding the functional relevance of the plethora of non-coding rnas in a given organism is challenging, especially since some of these rnas were attributed to 'transcriptional noise'. to allow the search for conserved transcriptomic elements we produce ...	2016	27154273
zinc coordination is essential for the function and activity of the type ii secretion atpase epse.	the type ii secretion system eps in vibrio cholerae promotes the extracellular transport of cholera toxin and several hydrolytic enzymes and is a major virulence system in many gram-negative pathogens which is structurally related to the type iv pilus system. the cytoplasmic atpase epse provides the energy for exoprotein secretion through atp hydrolysis. epse contains a unique metal-binding domain that coordinates zinc through a tetracysteine motif (cxxcx29 cxxc), which is also present in type i ...	2016	27168165
the crispr rna-guided surveillance complex in escherichia coli accommodates extended rna spacers.	bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign dna into crispr (clustered regularly interspaced short palindromic repeats) loci. in escherichia coli, crispr-derived rnas (crrnas) assemble with cas proteins into a multi-subunit surveillance complex called cascade (crispr-associated complex for antiviral defense). cascade recognizes dna targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing be ...	2016	27174938
a water-forming nadh oxidase regulates metabolism in anaerobic fermentation.	water-forming nadh oxidase can oxidize cytosolic nadh to nad(+), thus relieving cytosolic nadh accumulation in saccharomyces cerevisiae. previous studies of the enzyme were conducted under aerobic conditions, as o2 is the recognized electron acceptor of the enzyme. in order to extend its use in industrial production and to study its effect on anaerobes, the effects of overexpression of this oxidase in s. cerevisiae by4741 and clostridium acetobutylicum 428 (cac-428) under anaerobic conditions we ...	2016	27175216
characterization of the flexibility of the peripheral stalk of prokaryotic rotary a-atpases by atomistic simulations.	rotary atpases are involved in numerous physiological processes, with the three distinct types (f/a/v-atpases) sharing functional properties and structural features. the basic mechanism involves the counter rotation of two motors, a soluble atp hydrolyzing/synthesizing domain and a membrane-embedded ion pump connected through a central rotor axle and a stator complex. within the a/v-atpase family conformational flexibility of the eg stators has been shown to accommodate catalytic cycling and is ...	2016	27177595
global quantitative proteomics reveal up-regulation of endoplasmic reticulum stress response proteins upon depletion of eif5a in hela cells.	the eukaryotic translation factor, eif5a, is a translation factor essential for protein synthesis, cell growth and animal development. by use of a adenoviral eif5a shrna, we have achieved an effective depletion of eif5a in hela cells and undertook in vivo comprehensive proteomic analyses to examine the effects of eif5a depletion on the total proteome and to identify cellular pathways influenced by eif5a. the proteome of hela cells transduced with eif5a shrna was compared with that of scramble sh ...	2016	27180817
cyclic amp receptor protein acts as a transcription regulator in response to stresses in deinococcus radiodurans.	the cyclic amp receptor protein family of transcription factors regulates various metabolic pathways in bacteria, and also play roles in response to environmental changes. here, we identify four homologs of the crp family in deinococcus radiodurans, one of which tolerates extremely high levels of oxidative stress and dna-damaging reagents. transcriptional levels of crp were increased under hydrogen peroxide (h2o2) treatment during the stationary growth phase, indicating that crps function in res ...	2016	27182600
anatomy of risc: how do small rnas and chaperones activate argonaute proteins?	rna silencing is a eukaryote-specific phenomenon in which micrornas and small interfering rnas degrade messenger rnas containing a complementary sequence. to this end, these small rnas need to be loaded onto an argonaute protein (ago protein) to form the effector complex referred to as rna-induced silencing complex (risc). risc assembly undergoes multiple and sequential steps with the aid of hsc70/hsp90 chaperone machinery. the molecular mechanisms for this assembly process remain unclear, despi ...	2016	27184117
the diversity of ribonuclease p: protein and rna catalysts with analogous biological functions.	ribonuclease p (rnase p) is an essential endonuclease responsible for catalyzing 5' end maturation in precursor transfer rnas. since its discovery in the 1970s, rnase p enzymes have been identified and studied throughout the three domains of life. interestingly, rnase p is either rna-based, with a catalytic rna subunit, or a protein-only (prorp) enzyme with differential evolutionary distribution. the available structural data, including the active site data, provides insight into catalysis and s ...	2016	27187488
structure of human cdc45 and implications for cmg helicase function.	cell division cycle protein 45 (cdc45) is required for dna synthesis during genome duplication, as a component of the cdc45-mcm-gins (cmg) helicase. despite its essential biological function, its biochemical role in dna replication has remained elusive. here we report the 2.1-å crystal structure of human cdc45, which confirms its evolutionary link with the bacterial recj nuclease and reveals several unexpected features that underpin its function in eukaryotic dna replication. these include a lon ...	2016	27189187
a highly thermostable kanamycin resistance marker expands the tool kit for genetic manipulation of caldicellulosiruptor bescii.	caldicellulosiruptor bescii, an anaerobic gram-positive bacterium with an optimal growth temperature of 78°c, is the most thermophilic cellulose degrader known. it is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the pyrf genome region. the pyrf gene serves as a genetic marker to select for uracil prototro ...	2016	27208106
implications of limited thermophilicity of nitrite reduction for control of sulfide production in oil reservoirs.	nitrate reduction to nitrite in oil fields appears to be more thermophilic than the subsequent reduction of nitrite. concentrated microbial consortia from oil fields reduced both nitrate and nitrite at 40 and 45°c but only nitrate at and above 50°c. the abundance of the nirs gene correlated with mesophilic nitrite reduction activity. thauera and pseudomonas were the dominant mesophilic nitrate-reducing bacteria (mnrb), whereas petrobacter and geobacillus were the dominant thermophilic nrb (tnrb) ...	2016	27208132
functional characterization of the subunits n, h, j, and o of the nad(p)h dehydrogenase complexes in synechocystis sp. strain pcc 6803.	the cyanobacterial nad(p)h dehydrogenase (ndh-1) complexes play crucial roles in variety of bioenergetic reactions such as respiration, co2 uptake, and cyclic electron transport around psi. recently, substantial progress has been made in identifying the composition of subunits of ndh-1 complexes. however, the localization and the physiological roles of several subunits in cyanobacteria are not fully understood. here, by constructing fully segregated ndhn, ndho, ndhh, and ndhj null mutants in syn ...	2016	27208236
the pilin n-terminal domain maintains neisseria gonorrhoeae transformation competence during pilus phase variation.	the obligate human pathogen neisseria gonorrhoeae is the sole aetiologic agent of the sexually transmitted infection, gonorrhea. required for gonococcal infection, type iv pili (tfp) mediate many functions including adherence, twitching motility, defense against neutrophil killing, and natural transformation. critical for immune escape, the gonococcal tfp undergoes antigenic variation, a recombination event at the pile locus that varies the surface exposed residues of the major pilus subunit pil ...	2016	27213957
essential structural elements in trna(pro) for ef-p-mediated alleviation of translation stalling.	the ribosome stalls on translation of polyproline sequences due to inefficient peptide bond formation between consecutive prolines. the translation factor ef-p is able to alleviate this stalling by accelerating pro-pro formation. however, the mechanism by which ef-p recognizes the stalled complexes and accelerates peptide bond formation is not known. here, we use genetic code reprogramming through a flexible in-vitro translation (fit) system to investigate how mutations in trna(pro) affect ef-p ...	2016	27216360
wake me when it's over - bacterial toxin-antitoxin proteins and induced dormancy.	toxin-antitoxin systems are encoded by bacteria and archaea to enable an immediate response to environmental stresses, including antibiotics and the host immune response. during normal conditions, the antitoxin components prevent toxins from interfering with metabolism and arresting growth; however, toxin activation enables microbes to remain dormant through unfavorable conditions that might continue over millions of years. intense investigations have revealed a multitude of mechanisms for both ...	2016	27216598
abundance and temperature dependency of protein-protein interaction revealed by interface structure analysis and stability evolution.	protein complexes are major forms of protein-protein interactions and implement essential biological functions. the subunit interface in a protein complex is related to its thermostability. though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. in the present work, we studied this relationship and found a positive correlation in thermophiles ...	2016	27220911
elongation factor tu prevents misediting of gly-trna(gly) caused by the design behind the chiral proofreading site of d-aminoacyl-trna deacylase.	d-aminoacyl-trna deacylase (dtd) removes d-amino acids mischarged on trnas and is thus implicated in enforcing homochirality in proteins. previously, we proposed that selective capture of d-aminoacyl-trna by dtd's invariant, cross-subunit gly-cispro motif forms the mechanistic basis for its enantioselectivity. we now show, using nuclear magnetic resonance (nmr) spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that dtd effectively mised ...	2016	27224426
characterization of the atp-dependent lon-like protease in methanobrevibacter smithii.	the lon protease is highly evolutionarily conserved. however, little is known about lon in the context of gut microbial communities. a gene encoding a lon-like protease (lon-like-ms) was identified and characterized from methanobrevibacter smithii, the predominant archaeon in the human gut ecosystem. phylogenetic and sequence analyses showed that lon-like-ms and its homologs are newly identified members of the lon family. a recombinant form of the enzyme was purified by affinity chromatography, ...	2016	27239160
a colorimetric microplate assay for dna-binding activity of his-tagged muts protein.	a simple microplate method was designed for rapid testing dna-binding activity of proteins. the principle of the assay involves binding of tested dna by his-tagged protein immobilized on a nickel-coated elisa plate, following colorimetric detection of biotinylated dna with avidin conjugated to horseradish peroxidase. the method was used to compare dna mismatch binding activities of muts proteins from three bacterial species. the assay required relatively low amounts of tested protein (approximat ...	2016	27241123
a mutation in the 16s rrna decoding region attenuates the virulence of mycobacterium tuberculosis.	mycobacterium tuberculosis contains a single rrna operon that encodes targets for antituberculosis agents, including kanamycin. to date, only four mutations in the kanamycin binding sites of 16s rrna have been reported in kanamycin-resistant clinical isolates. we hypothesized that another mutation(s) in the region may dramatically decrease m. tuberculosis viability and virulence. here, we describe an rrna mutation, u1406a, which was generated in vitro and confers resistance to kanamycin while hi ...	2016	27245411
expression and characterization of a novel glycerophosphodiester phosphodiesterase from pyrococcus furiosus dsm 3638 that possesses lysophospholipase d activity.	glycerophosphodiester phosphodiesterases (gdpd) are enzymes which degrade various glycerophosphodiesters to produce glycerol-3-phosphate and the corresponding alcohol moiety. apart from this, a very interesting finding is that this enzyme could be used in the degradation of toxic organophosphorus esters, which has resulted in much attention on the biochemical and application research of gdpds. in the present study, a novel gdpd from pyrococcus furiosus dsm 3638 (pfgdpd) was successfully expresse ...	2016	27248999
mechanism of b-box 2 domain-mediated higher-order assembly of the retroviral restriction factor trim5α.	restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. mammalian trim5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. here, we report crystallographic and functional studies of the trim5α b-box 2 domain, which mediates higher-order assembly of trim5 proteins. the b-box can form both dimers and t ...	2016	27253059
unusually situated binding sites for bacterial transcription factors can have hidden functionality.	a commonly accepted paradigm of molecular biology is that transcription factors control gene expression by binding sites at the 5' end of a gene. however, there is growing evidence that transcription factor targets can occur within genes or between convergent genes. in this work, we have investigated one such target for the cyclic amp receptor protein (crp) of enterotoxigenic escherichia coli. we show that crp binds between two convergent genes. when bound, crp regulates transcription of a small ...	2016	27258043
chloramphenicol derivatives as antibacterial and anticancer agents: historic problems and current solutions.	chloramphenicol (cam) is the d-threo isomer of a small molecule, consisting of a p-nitrobenzene ring connected to a dichloroacetyl tail through a 2-amino-1,3-propanediol moiety. cam displays a broad-spectrum bacteriostatic activity by specifically inhibiting the bacterial protein synthesis. in certain but important cases, it also exhibits bactericidal activity, namely against the three most common causes of meningitis, haemophilus influenzae, streptococcus pneumoniae and neisseria meningitidis. ...	2016	27271676
cloning and expression of dnak gene from bacillus pumilus of hot water spring origin.	a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ...	2013	27275408
cloning and expression of dnak gene from bacillus pumilus of hot water spring origin.	a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ...	2013	27275408