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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 ...201627030968
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 ...201627023615
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 ...201627016741
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.199727006575
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 ...201627001509
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 ...201627000559
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 ...201626994077
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 ...201626984495
(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 ...201626983940
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.201626976861
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 ...201626973877
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 ...201626973090
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 ...201626969705
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.201626968756
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 ...201626963521
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 ...201626954034
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 ...201626951669
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 ...201626950603
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.201626944551
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 ...201626941731
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, ...201626941711
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 ...201626921320
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. ...201626916802
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 ...201626912459
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 ...201626909079
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. ...201626906548
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.201626897180
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 ...201626896801
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 ...201626891220
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 ...201626883824
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 ...201626879262
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 ...201626876483
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 ...201626861307
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 ...201626858461
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 ...201626857547
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 ...201626845082
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.201626843368
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 ...201626840407
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 ...201626833419
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 ...201626830344
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 ...201626825463
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 ...201626822828
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 ...201626821166
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 ...201626819321
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 ...201626818562
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 ...201626814183
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, ...201626809677
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 ...201626805589
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 ...201626801642
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 ...201526798805
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. ...201626792896
novel base-pairing interactions at the trna wobble position crucial for accurate reading of the genetic code.posttranscriptional modifications at the wobble position of transfer rnas play a substantial role in deciphering the degenerate genetic code on the ribosome. the number and variety of modifications suggest different mechanisms of action during messenger rna decoding, of which only a few were described so far. here, on the basis of several 70s ribosome complex x-ray structures, we demonstrate how escherichia coli trna(lys)(uuu) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)u) at ...201626791911
cysteine biosynthesis in lactobacillus casei: identification and characterization of a serine acetyltransferase.in bacteria, cysteine can be synthesized from serine by two steps involving an l-serine o-acetyltransferase (sat) and a cysteine synthase (cysk). while cysk is found in the publicly available annotated genome from lactobacillus casei atcc 334, a gene encoding sat (cyse) is missing. in this study, we found that various strains of l. casei grew in a chemically defined medium containing sulfide as the sole sulfur source, indicating the presence of a serine o-acetyltransferase. the gene lying upstre ...201626790714
functional determinants of metal ion transport and selectivity in paralogous cation diffusion facilitator transporters czcd and mnte in streptococcus pneumoniae.cation diffusion facilitators (cdfs) are a large family of divalent metal transporters that collectively possess broad metal specificity and contribute to intracellular metal homeostasis and virulence in bacterial pathogens. streptococcus pneumoniae expresses two homologous cdf efflux transporters, mnte and czcd. cells lacking mnte or czcd are sensitive to manganese (mn) or zinc (zn) toxicity, respectively, and specifically accumulate mn or zn, respectively, thus suggesting that mnte selectively ...201626787764
the dna polymerase iii holoenzyme contains γ and is not a trimeric polymerase.there is widespread agreement that the clamp loader of the escherichia coli replicase has the composition dnax3δδ'χψ. two dnax proteins exist in e. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds dna polymerase iii tightly; γ does not. there is a controversy as to whether or not dna polymerase iii holoenzyme (pol iii he) contains γ. a three-τ form of pol iii he would contain three pol iiis. proponents of the three-τ hypothesis have claimed that γ found i ...201626786318
centers of motion associated with ef-tu binding to the ribosome.structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rrna resulting from ef-g gtp hydrolysis. this series of measurements is extended here to the ribosome's interactions with the cofactor ef-tu. four recent ef-tu bound ribosome structures were compared to unbound structures. a total of 16 pivots were identified, of which 4 are unique to the ef-tu interaction. pivots in the gtpase associated center and the sarcin-ric ...201626786136
a target-protection mechanism of antibiotic resistance at atomic resolution: insights into fusb-type fusidic acid resistance.antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. we present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the fusb fusidic acid resistance protein and the drug target (ef-g) it acts to protect. binding ...201626781961
bacterial transcription as a target for antibacterial drug development.transcription, the first step of gene expression, is carried out by the enzyme rna polymerase (rnap) and is regulated through interaction with a series of protein transcription factors. rnap and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. the determination ...201626764017
a comprehensive benchmarking study of protocols and sequencing platforms for 16s rrna community profiling.in the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. the most common phylogenetic marker for microbial community diversity studies is the 16s ribosomal rna gene and in the last 10 years the field h ...201626763898
structural basis for the endoribonuclease activity of the type iii-a crispr-associated protein csm6.prokaryotic crispr-cas systems provide an rna-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. in type iii-a crispr-cas systems, the rna-guided multisubunit csm effector complex targets both single-stranded rnas and double-stranded dnas. in addition to the csm complex, efficient anti-plasmid immunity mediated by type iii-a systems also requires the crispr-associated protein csm6. here we report the crystal structure of csm6 from thermus thermophil ...201626763118
impact of different target sequences on type iii crispr-cas immunity.clustered regularly interspaced short palindromic repeat (crispr) loci encode an adaptive immune system of prokaryotes. within these loci, sequences intercalated between repeats known as "spacers" specify the targets of crispr immunity. the majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. we studied this issue using the staphylococcus epidermidis crispr system, which ...201626755632
two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. direct structural evidence on the transient cytochrome c oxidase-cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. here, we report on the 2d crystallization of monomeric bovine cytochrome c oxidase with tightly bound c ...201626754561
n(6)-methyladenosine in mrna disrupts trna selection and translation-elongation dynamics.n(6)-methylation of adenosine (forming m(6)a) is the most abundant post-transcriptional modification within the coding region of mrna, but its role during translation remains unknown. here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)a in mrna decoding. although m(6)a base-pairs with uridine during decoding, as shown by x-ray crystallographic analyses of thermus thermophilus ribosomal complexes, our measurements in an escherichia coli translation system revealed t ...201626751643
the bioactive secondary metabolites from talaromyces species.the focus of this review is placed on the chemical structures from the species of the genus talaromyces reported with reference to their biological activities. 221 secondary metabolites, including 43 alkaloids and peptides, 88 esters, 31 polyketides, 19 quinones, 15 steroid and terpenoids, and 25 other structure type compounds, have been included, and 66 references are cited.201626746215
comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms.understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. while multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. in this work we compare equivalent clusters of spatially neighboring residues between paired thermophili ...201626741367
a model for genesis of transcription systems.repeating sequences generated from rna gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. a simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-ψ-β-barrel (dpbb) type rna polymerases (rnaps), general transcription factors (gtfs), and promoters. a general rule that emerges is that biological complexity that arises through generation of repea ...201626735411
lineage-specific variations in the trigger loop modulate rna proofreading by bacterial rna polymerases.rna cleavage by bacterial rna polymerase (rnap) has been implicated in transcriptional proofreading and reactivation of arrested transcription elongation complexes but its molecular mechanism is less understood than the mechanism of nucleotide addition, despite both reactions taking place in the same active site. rnap from the radioresistant bacterium deinococcus radiodurans is characterized by highly efficient intrinsic rna cleavage in comparison with escherichia coli rnap. we find that the enh ...201626733581
gbtools: interactive visualization of metagenome bins in r.improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ...201526732662
redirection of the reaction specificity of a thermophilic acetolactate synthase toward acetaldehyde formation.acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. in this study, the reaction specificity of acetolactate synthase from thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxyla ...201626731734
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 ...201526721932
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 ...201526721932
energy conversion, redox catalysis and generation of reactive oxygen species by respiratory complex i.complex i (nadh:ubiquinone oxidoreductase) is critical for respiration in mammalian mitochondria. it oxidizes nadh produced by the krebs' tricarboxylic acid cycle and β-oxidation of fatty acids, reduces ubiquinone, and transports protons to contribute to the proton-motive force across the inner membrane. complex i is also a significant contributor to cellular oxidative stress. in complex i, nadh oxidation by a flavin mononucleotide, followed by intramolecular electron transfer along a chain of i ...201626721206
cooperation between two periplasmic copper chaperones is required for full activity of the cbb3 -type cytochrome c oxidase and copper homeostasis in rhodobacter capsulatus.copper (cu) is an essential micronutrient that functions as a cofactor in several important enzymes, such as respiratory heme-copper oxygen reductases. yet, cu is also toxic and therefore cells engage a highly coordinated cu uptake and delivery system to prevent the accumulation of toxic cu concentrations. in this study, we analyzed cu delivery to the cbb3 -type cytochrome c oxidase (cbb3 -cox) of rhodobacter capsulatus. we identified the pcua c-like periplasmic chaperone pcca and analyzed its c ...201626718481
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 ...201526715760
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 ...201526715760
isc, a novel group of bacterial and archaeal dna transposons that encode cas9 homologs.bacterial genomes encode numerous homologs of cas9, the effector protein of the type ii crispr-cas systems. the homology region includes the arginine-rich helix and the hnh nuclease domain that is inserted into the ruvc-like nuclease domain. these genes, however, are not linked to cas genes or crispr. here, we show that cas9 homologs represent a distinct group of nonautonomous transposons, which we denote isc (insertion sequences cas9-like). we identify many diverse families of full-length isc t ...201626712934
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 ...201526712743
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 ...201526712743
aerobic and anaerobic thiosulfate oxidation by a cold-adapted, subglacial chemoautotroph.geochemical data indicate that protons released during pyrite (fes2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. oxidation of fes2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (s2o3 (2-)), which represents an electron donor capable of supporting microbial metabolism. subglacial meltwaters sampled from robertson glacier (rg), canada, over a seasonal m ...201626712544
curing the megaplasmid ptt27 from thermus thermophilus hb27 and maintaining exogenous plasmids in the plasmid-free strain.stepwise deletions in the only plasmid in thermus thermophilus hb27, megaplasmid ptt27, showed that two distantly located loci were important for maintenance of the plasmid. one is a minimum replicon including one gene, rept, coding a replication initiator, and the other encodes subunits of class i ribonucleotide reductase (rnr) for deoxynucleoside triphosphate (dntp) synthesis. since the initiator protein, rept, bound to direct repeats downstream from its own gene, it was speculated that a more ...201626712540
structural insights into a key carotenogenesis related enzyme phytoene synthase of p. falciparum: a novel drug target for malaria.carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. phytoene synthase (psy), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. psys have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. in an effort ...201526702306
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 ...201526693506
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 ...201526684010
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 ...201526682650
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 ...201526675164
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 ...201526673726
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 ...201526673726
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 ...201526670735
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 ...201526670257
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 ...201526668356
structural similarities and differences between two functionally distinct seca proteins, mycobacterium tuberculosis seca1 and seca2.while seca is the atpase component of the major bacterial secretory (sec) system, mycobacteria and some gram-positive pathogens have a second paralog, seca2. in bacteria with two seca paralogs, each seca is functionally distinct, and they cannot compensate for one another. compared to seca1, seca2 exports a distinct and smaller set of substrates, some of which have roles in virulence. in the mycobacterial system, some seca2-dependent substrates lack a signal peptide, while others contain a signa ...201626668263
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 ...201526664751
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 ...201526658024
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 ...201526657745
markerless gene deletion with cytosine deaminase in thermus thermophilus strain hb27.we developed a counterselectable deletion system for thermus thermophilus hb27 based on cytosine deaminase (encoded by coda) from thermaerobacter marianensis dsm 12885 and the sensitivity of t. thermophilus hb27 to the antimetabolite 5-fluorocytosine (5-fc). the deletion vector comprises the puc18 origin of replication, a thermostable kanamycin resistance marker functional in t. thermophilus hb27, and coda under the control of a constitutive putative trehalose promoter from t. thermophilus hb27. ...201626655764
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 ...201526655737
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 ...201526655641
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 ...201526655598
cytoplasmic copz-like protein and periplasmic rusticyanin and acop proteins as possible copper resistance determinants in acidithiobacillus ferrooxidans atcc 23270.acidophilic organisms, such as acidithiobacillus ferrooxidans, possess high-level resistance to copper and other metals. a. ferrooxidans contains canonical copper resistance determinants present in other bacteria, such as copa atpases and rnd efflux pumps, but these components do not entirely explain its high metal tolerance. the aim of this study was to find other possible copper resistance determinants in this bacterium. transcriptional expression of a. ferrooxidans genes coding for a cytoplas ...201626637599
single-cell-genomics-facilitated read binning of candidate phylum em19 genomes from geothermal spring metagenomes.the vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. this "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. in this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "calescamantes" (em19) to calibrate machine learning algorithms and define metagenomic bins directly ...201626637598
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