Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
|---|
| amylose recognition and ring-size determination of amylomaltase. | starch is a major carbon and energy source throughout all kingdoms of life. it consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. hence, the enzymatic breakdown by glycoside hydrolases (ghs) is of great biological and societal importance. amylomaltases (ams) are ghs specialized in the hydrolysis of α-1,4-linked sugar chains such as amylose. they are able to catalyze an intramolecular transglycosylation of a bound sugar chain yiel ... | 2017 | 28097217 |
| an ambiguity principle for assigning protein structural domains. | ambiguity is the quality of being open to several interpretations. for an image, it arises when the contained elements can be delimited in two or more distinct ways, which may cause confusion. we postulate that it also applies to the analysis of protein three-dimensional structure, which consists in dividing the molecule into subunits called domains. because different definitions of what constitutes a domain can be used to partition a given structure, the same protein may have different but equa ... | 2017 | 28097215 |
| integrating mass spectrometry with md simulations reveals the role of lipids in na(+)/h(+) antiporters. | na(+)/h(+) antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the na(+)/h(+) exchanger napa from thermus thermophilus and compare this to the prototypical antiporter nhaa from escherichia coli and the human homologue nha2. we find that napa and nha2, but ... | 2017 | 28071645 |
| exploring conformational equilibria of a heterodimeric abc transporter. | abc exporters pump substrates across the membrane by coupling atp-driven movements of nucleotide binding domains (nbds) to the transmembrane domains (tmds), which switch between inward- and outward-facing (if, of) orientations. deer measurements on the heterodimeric abc exporter tm287/288 from thermotoga maritima, which contains a non-canonical atp binding site, revealed that in the presence of nucleotides the transporter exists in an if/of equilibrium. while atp binding was sufficient to partia ... | 2017 | 28051765 |
| thermophilic bacteria are potential sources of novel rieske non-heme iron oxygenases. | rieske non-heme iron oxygenases, which have a rieske-type [2fe-2s] cluster and a non-heme catalytic iron center, are an important family of oxidoreductases involved mainly in regio- and stereoselective transformation of a wide array of aromatic hydrocarbons. though present in all domains of life, the most widely studied rieske non-heme iron oxygenases are found in mesophilic bacteria. the present study explores the potential for isolating novel rieske non-heme iron oxygenases from thermophilic s ... | 2017 | 28050858 |
| activation of respiratory complex i from escherichia coli studied by fluorescent probes. | respiratory complex i from e. coli may exist in two interconverting forms: resting (r) and active (a). the r/a transition of purified, solubilized complex i occurring upon turnover was studied employing two different fluorescent probes, annine 6+, and ndb-acetogenin. nadh-induced fluorescent changes of both dyes bound to solubilized complex i from e. coli were characterized as a function of the protein:dye ratio, temperature, ubiquinone redox state and the enzyme activity. analysis of this data ... | 2017 | 28070565 |
| metagenomic analysis of hot springs in central india reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. | extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. india harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. the aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central india namel ... | 2016 | 28105025 |
| 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 ... | 2016 | 26733581 |
| 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 |
| 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 ... | 2016 | 26790714 |
| cryo-em structures of the autoinhibited e. coli atp synthase in three rotational states. | a molecular model that provides a framework for interpreting the wealth of functional information obtained on the e. coli f-atp synthase has been generated using cryo-electron microscopy. three different states that relate to rotation of the enzyme were observed, with the central stalk's ε subunit in an extended autoinhibitory conformation in all three states. the fo motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate th ... | 2016 | 28001127 |
| 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 ... | 2016 | 26721206 |
| characterization of the nqo5 subunit of bacterial complex i in the isolated state. | the subunits that comprise bacterial complex i (nadh:ubiquinone oxidoreductase) are also found in more complicated mitochondrial enzymes in eukaryotic organisms. although the nqo5 subunit is one of these conserved components and important for the formation of complex, it has been little studied. here, we report structure analyses of isolated nqo5 from thermus thermophilus. biochemical studies indicated that the c-terminal region following the 30-kd subunit motif is disordered in the isolated sta ... | 2016 | 27398308 |
| 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 |
| 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 |
| 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 |
| trueprime is a novel method for whole-genome amplification from single cells based on tthprimpol. | sequencing of a single-cell genome requires dna amplification, a process prone to introducing bias and errors into the amplified genome. here we introduce a novel multiple displacement amplification (mda) method based on the unique dna primase features of thermus thermophilus (tth) primpol. tthprimpol displays a potent primase activity preferring dntps as substrates unlike conventional primases. a combination of tthprimpol's unique ability to synthesize dna primers with the highly processive phi ... | 2016 | 27897270 |
| high-resolution phenotypic landscape of the rna polymerase ii trigger loop. | the active sites of multisubunit rna polymerases have a "trigger loop" (tl) that multitasks in substrate selection, catalysis, and translocation. to dissect the saccharomyces cerevisiae rna polymerase ii tl at individual-residue resolution, we quantitatively phenotyped nearly all tl single variants en masse. three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among tl residues. we find that mutations disrupting an intra-tl ... | 2016 | 27898685 |
| adaptation in bacillus cereus: from stress to disease. | bacillus cereus is a food-borne pathogen that causes diarrheal disease in humans. after ingestion, b. cereus experiences in the human gastro-intestinal tract abiotic physical variables encountered in food, such as acidic ph in the stomach and changing oxygen conditions in the human intestine. b. cereus responds to environmental changing conditions (stress) by reversibly adjusting its physiology to maximize resource utilization while maintaining structural and genetic integrity by repairing and m ... | 2016 | 27757102 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| origin of a folded repeat protein from an intrinsically disordered ancestor. | repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. many of these originated in a non-repetitive context as cofactors of rna-based replication and catalysis, and required the rna to assume their active conformation. in search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (tpr), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the put ... | 2016 | 27623012 |
| visualizing the phage t4 activated transcription complex of dna and e. coli rna polymerase. | the ability of rna polymerase (rnap) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. however, there is only one crystallized structure of a complete activator/rnap/dna complex. in a process called σ appropriation, bacteriophage t4 activates a class of phage promoters using an activator (mota) and a co-activator (asia), which function through interactions with the σ(70) subunit of rnap. we have developed a holistic, struct ... | 2016 | 27458207 |
| cold shock proteins: a minireview with special emphasis on csp-family of enteropathogenic yersinia. | bacteria have evolved a number of mechanisms for coping with stress and adapting to changing environmental conditions. many bacteria produce small cold shock proteins (csp) as a response to rapid temperature downshift (cold shock). during cold shock, the cell membrane fluidity and enzyme activity decrease, and the efficiency of transcription and translation is reduced due to stabilization of nucleic acid secondary structures. moreover, protein folding is inefficient and ribosome function is hamp ... | 2016 | 27499753 |
| 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 |
| 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 ... | 2016 | 26637598 |
| 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 |
| 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 |
| 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 ... | 2016 | 26763898 |
| flagellin glycosylation in paenibacillus alvei ccm 2051t. | flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. the basis of flagellin glycosylation has been studied for various gram-negative bacteria, but less is known about flagellin glycans of gram-positive bacteria including paenibacillus alvei, a secondary invader of honeybee colonies diseased with european foulbrood. paenibacillus alvei ccm 2051(t) swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evide ... | 2016 | 26405108 |
| flagellin glycosylation in paenibacillus alvei ccm 2051t. | flagellin glycosylation impacts, in several documented cases, the functionality of bacterial flagella. the basis of flagellin glycosylation has been studied for various gram-negative bacteria, but less is known about flagellin glycans of gram-positive bacteria including paenibacillus alvei, a secondary invader of honeybee colonies diseased with european foulbrood. paenibacillus alvei ccm 2051(t) swarms vigorously on solidified culture medium, with swarming relying on functional flagella as evide ... | 2016 | 26405108 |
| the novel aminomethylcycline omadacycline has high specificity for the primary tetracycline-binding site on the bacterial ribosome. | omadacycline is an aminomethylcycline antibiotic with potent activity against many gram-positive and gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. this makes it a promising candidate for therapy of severe infectious diseases. omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. its interactions with the 70s ribosome were, therefore, analyzed in great detail and comp ... | 2016 | 27669321 |
| conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. | protein-protein interactions are fundamental for the proper functioning of the cell. as a result, protein interaction surfaces are subject to strong evolutionary constraints. recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. so far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compi ... | 2016 | 27965389 |
| 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 ... | 2016 | 26741367 |
| crispr-mediated epigenome editing. | mounting evidence has called into question our understanding of the role that the central dogma of molecular biology plays in human pathology. the conventional view that elucidating the mechanisms for translating genes into proteins can account for a panoply of diseases has proven incomplete. landmark studies point to epigenetics as a missing piece of the puzzle. however, technological limitations have hindered the study of specific roles for histone post-translational modifications, dna modific ... | 2016 | 28018139 |
| vapcs of mycobacterium tuberculosis cleave rnas essential for translation. | the major human pathogen mycobacterium tuberculosis can survive in the host organism for decades without causing symptoms. a large cohort of toxin-antitoxin (ta) modules contribute to this persistence. of these, 48 ta modules belong to the vapbc (virulence associated protein) gene family. vapc toxins are pin domain endonucleases that, in enterobacteria, inhibit translation by site-specific cleavage of initiator trna. in contrast, vapc20 of m. tuberculosis inhibits translation by site-specific cl ... | 2016 | 27599842 |
| 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 |
| 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 |
| 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 ... | 2016 | 26764017 |
| driving apart and segregating genomes in archaea. | genome segregation is a fundamental biological process in organisms from all domains of life. how this stage of the cell cycle unfolds in eukarya has been clearly defined and considerable progress has been made to unravel chromosome partition in bacteria. the picture is still elusive in archaea. the lineages of this domain exhibit different cell-cycle lifestyles and wide-ranging chromosome copy numbers, fluctuating from 1 up to 55. this plurality of patterns suggests that a variety of mechanisms ... | 2016 | 27450111 |
| mglc, a paralog of myxococcus xanthus gtpase-activating protein mglb, plays a divergent role in motility regulation. | in order to optimize interactions with their environment and one another, bacteria regulate their motility. in the case of the rod-shaped cells of myxococcus xanthus, regulated motility is essential for social behaviors. m. xanthus moves over surfaces using type iv pilus-dependent motility and gliding motility. these two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small g protein mgla, the cognate mgla gtp ... | 2016 | 26574508 |
| bacterial rna polymerase-dna interaction-the driving force of gene expression and the target for drug action. | dna-dependent multisubunit rna polymerase (rnap) is the key enzyme of gene expression and a target of regulation in all kingdoms of life. it is a complex multifunctional molecular machine which, unlike other dna-binding proteins, engages in extensive and dynamic interactions (both specific and nonspecific) with dna, and maintains them over a distance. these interactions are controlled by dna sequences, dna topology, and a host of regulatory factors. here, we summarize key recent structural and b ... | 2016 | 27882317 |
| discovery and structural characterisation of new fold type iv-transaminases exemplify the diversity of this enzyme fold. | transaminases are useful biocatalysts for the production of amino acids and chiral amines as intermediates for a broad range of drugs and fine chemicals. here, we describe the discovery and characterisation of new transaminases from microorganisms which were enriched in selective media containing (r)-amines as sole nitrogen source. while most of the candidate proteins were clearly assigned to known subgroups of the fold iv family of plp-dependent enzymes by sequence analysis and characterisation ... | 2016 | 27905516 |
| convergent evolution of trna gene targeting preferences in compact genomes. | in gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. the targeting of trna genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba dictyostelium discoideum and the yeast saccharomyces cerevisiae. in d. discoideum, trna gene-targeting retrotransposons have expanded to approximately 3 % of the genome. recently obtained genome sequences o ... | 2016 | 27583033 |
| ribosomal frameshifting and transcriptional slippage: from genetic steganography and cryptography to adventitious use. | genetic decoding is not 'frozen' as was earlier thought, but dynamic. one facet of this is frameshifting that often results in synthesis of a c-terminal region encoded by a new frame. ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. one class of re ... | 2016 | 27436286 |
| 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 |
| in situ spectroscopy reveals that microorganisms in different phyla use different electron transfer biomolecules to respire aerobically on soluble iron. | absorbance spectra were collected on 12 different live microorganisms, representing six phyla, as they respired aerobically on soluble iron at ph 1.5. a novel integrating cavity absorption meter was employed that permitted accurate absorbance measurements in turbid suspensions that scattered light. illumination of each microorganism yielded a characteristic spectrum of electrochemically reduced colored prosthetic groups. a total of six different patterns of reduced-minus-oxidized difference spec ... | 2016 | 28008327 |
| distribution and dynamics of electron transport complexes in cyanobacterial thylakoid membranes. | the cyanobacterial thylakoid membrane represents a system that can carry out both oxygenic photosynthesis and respiration simultaneously. the organization, interactions and mobility of components of these two electron transport pathways are indispensable to the biosynthesis of thylakoid membrane modules and the optimization of bioenergetic electron flow in response to environmental changes. these are of fundamental importance to the metabolic robustness and plasticity of cyanobacteria. this revi ... | 2016 | 26619924 |
| new insight into isoprenoids biosynthesis process and future prospects for drug designing in plasmodium. | the mep (methyl erythritol phosphate) isoprenoids biosynthesis pathway is an attractive drug target to combat malaria, due to its uniqueness and indispensability for the parasite. it is functional in the apicoplast of plasmodium and its products get transported to the cytoplasm, where they participate in glycoprotein synthesis, electron transport chain, trna modification and several other biological processes. several compounds have been tested against the enzymes involved in this pathway and am ... | 2016 | 27679614 |
| 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 |
| 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 |
| metagenomic analysis of hot springs in central india reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. | extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. india harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. the aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central india namel ... | 2016 | 28105025 |
| editorial: filamentous bacteriophage in bio/nano/technology, bacterial pathogenesis and ecology. | 2016 | 28066406 | |
| coupled atpase-adenylate kinase activity in abc transporters. | atp-binding cassette (abc) transporters, a superfamily of integral membrane proteins, catalyse the translocation of substrates across the cellular membrane by atp hydrolysis. here we demonstrate by nucleotide turnover and binding studies based on (31)p solid-state nmr spectroscopy that the abc exporter and lipid a flippase msba can couple atp hydrolysis to an adenylate kinase activity, where adp is converted into amp and atp. single-point mutations reveal that both atpase and adenylate kinase me ... | 2016 | 28004795 |
| mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. | engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of t ... | 2016 | 27998268 |
| homology-based modeling of universal stress protein from listeria innocua up-regulated under acid stress conditions. | an universal stress protein (usp) expressed under acid stress condition by listeria innocua atcc 33090 was investigated. the usp was up-regulated not only in the stationary phase but also during the exponential growth phase. the three dimensional (3d) structure of usp was predicted using a combined proteomic and bioinformatics approach. phylogenetic analysis showed that the usp from listeria detected in our study was distant from the usps of other bacteria (such as pseudomonas spp., escherichia ... | 2016 | 28066336 |
| comparison of lipases and glycoside hydrolases as catalysts in synthesis reactions. | lipases and glycoside hydrolases have large similarities concerning reaction mechanisms. acyl-enzyme intermediates are formed during lipase-catalyzed reactions and in an analogous way, retaining glycoside hydrolases form glycosyl-enzyme intermediates during catalysis. in both cases, the covalent enzyme intermediates can react with water or other nucleophiles containing hydroxyl groups. simple alcohols are accepted as nucleophiles by both types of enzymes. lipases are used very successfully in sy ... | 2016 | 27995311 |
| comparison of lipases and glycoside hydrolases as catalysts in synthesis reactions. | lipases and glycoside hydrolases have large similarities concerning reaction mechanisms. acyl-enzyme intermediates are formed during lipase-catalyzed reactions and in an analogous way, retaining glycoside hydrolases form glycosyl-enzyme intermediates during catalysis. in both cases, the covalent enzyme intermediates can react with water or other nucleophiles containing hydroxyl groups. simple alcohols are accepted as nucleophiles by both types of enzymes. lipases are used very successfully in sy ... | 2016 | 27995311 |
| systematic analysis of the lysine acetylome in fusarium graminearum. | lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. although known for many years, its function remains elusive in fusarium graminearum, one of the most important necrotrophic plant pathogens with huge economic impact. | 2016 | 27964708 |
| the mechanism of a formaldehyde-sensing transcriptional regulator. | most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. therefore, biology has evolved systems to perceive and detoxify formaldehyde. the frmra(b) operon that is present in many bacteria represents one such system. the frmr protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (frma and frmb, when the latter is present). ... | 2016 | 27934966 |
| dynamic complexes in the chaperonin-mediated protein folding cycle. | the groel-groes chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. during this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. despite of almost three decades of research on this oligomeric protein, cer ... | 2016 | 28008398 |
| structures and stabilization of kinetoplastid-specific split rrnas revealed by comparing leishmanial and human ribosomes. | the recent success in ribosome structure determination by cryoem has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. here, by direct electron-counting cryoem, we have determined the structures of the leishmania donovani and human ribosomes at 2.9 å and 3.6 å, respectively. our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rrna (as ... | 2016 | 27752045 |
| characterization of a highly thermostable and organic solvent-tolerant copper-containing polyphenol oxidase with dye-decolorizing ability from kurthia huakuii lam0618t. | laccases are green biocatalysts that possess attractive advantages for the treatment of resistant environmental pollutants and dye effluents. a putative laccase-like gene, laclk, encoding a protein of 29.3 kda and belonging to the cu-oxidase_4 superfamily, was cloned and overexpressed in escherichia coli. the purified recombinant protein laclk (laclk) was able to oxidize typical laccase substrates such as 2,6-dimethoxyphenol and l-dopamine. the characteristic adsorption maximums of typical lacca ... | 2016 | 27741324 |
| structure of the 40s ribosomal subunit of plasmodium falciparum by homology and de novo modeling. | generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. this is especially the case if a homologous crystal structure is already available. high-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of sc ... | 2016 | 28119814 |
| structure of the 40s ribosomal subunit of plasmodium falciparum by homology and de novo modeling. | generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. this is especially the case if a homologous crystal structure is already available. high-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of sc ... | 2016 | 28119814 |
| pb(2+) effects on growth, lipids, and protein and dna profiles of the thermophilic bacterium thermus thermophilus. | extremophiles are organisms able to thrive in extreme environmental conditions and some of them show the ability to survive high doses of heavy metals thanks to defensive mechanisms provided by primary and secondary metabolic products, i.e., extremolytes, lipids, and extremozymes. this is why there is a growing scientific and industrial interest in the use of thermophilic bacteria in a host of tasks, from the environmental detoxification of heavy metal to industrial activities, such as bio-machi ... | 2016 | 27929414 |
| improved in-cell structure determination of proteins at near-physiological concentration. | investigating three-dimensional (3d) structures of proteins in living cells by in-cell nuclear magnetic resonance (nmr) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. in-cell nmr provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cel ... | 2016 | 27910948 |
| identification of a highly conserved hypothetical protein ton_0340 as a probable manganese-dependent phosphatase. | a hypothetical protein ton_0340 of a thermococcus species is a protein conserved in a variety of organisms including human. herein, we present four different crystal structures of ton_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. biochemical and mutational analyses involving many phosphorous compounds show that ton_0340 is a mn2+-dependent phosphatase. ... | 2016 | 27907125 |
| nusg inhibits rna polymerase backtracking by stabilizing the minimal transcription bubble. | universally conserved factors from nusg family bind at the upstream fork junction of transcription elongation complexes and modulate rna synthesis in response to translation, processing, and folding of the nascent rna. escherichia coli nusg enhances transcription elongation in vitro by a poorly understood mechanism. here we report that e. coli nusg slows gre factor-stimulated cleavage of the nascent rna, but does not measurably change the rates of single nucleotide addition and translocation by ... | 2016 | 27697152 |
| target and non-target site mechanisms developed by glyphosate-resistant hairy beggarticks (bidens pilosa l.) populations from mexico. | in 2014 hairy beggarticks (bidens pilosa l.) has been identified as being glyphosate-resistant in citrus orchards from mexico. the target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (r1 and r2) and one susceptible (s) were studied. experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and 5-enolpyruvyl shikimate-3-phosphate synthase (epsps) gene sequencing were carried out in each population. the r1 ... | 2016 | 27752259 |
| structures of type iv pilins from thermus thermophilus demonstrate similarities with type ii secretion system pseudopilins. | type iv pilins are proteins which form polymers that extend from the surface of the bacterial cell; they are involved in mediating a wide variety of functions, including adhesion, motility and natural competence. here we describe the determination of the crystal structures of three type iva pilins proteins from the thermophile thermus thermophilus. they form part of a cluster of pilus-like proteins within the genome; our results show that one, tt1222, is very closely related to the main structur ... | 2016 | 27612581 |
| structural basis for the disaggregase activity and regulation of hsp104. | the hsp104 disaggregase is a two-ring atpase machine that rescues various forms of non-native proteins including the highly resistant amyloid fibers. the structural-mechanistic underpinnings of how the recovery of toxic protein aggregates is promoted and how this potent unfolding activity is prevented from doing collateral damage to cellular proteins are not well understood. here, we present structural and biochemical data revealing the organization of hsp104 from chaetomium thermophilum at 3.7 ... | 2016 | 27901467 |
| thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability. | nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ... | 2016 | 27899597 |
| thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability. | nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ... | 2016 | 27899597 |
| beyond antibodies: development of a novel protein scaffold based on human chaperonin 10. | human chaperonin 10 (hcpn10) was utilised as a novel scaffold for presenting peptides of therapeutic and diagnostic significance. molecular dynamic simulations and protein sizing analyses identified a peptide linker (p1) optimal for the formation of the quarternary hcpn10 heptamer structure. hcpn10 scaffold displaying peptides targeting factor viia (ce76-p1) and cd44 (cp7) were expressed in e. coli. functional studies of ce76-p1 indicated nanomolar affinity for factor viia (3 nm) similar to the ... | 2016 | 27874025 |
| first resistance mechanisms characterization in glyphosate-resistant leptochloa virgata. | leptochloa virgata (l.) p. beauv. is an annual weed common in citrus groves in the states of puebla and veracruz, mexico limiting their production. since 2010, several l. virgata populations were identified as being resistant to glyphosate, but studies of their resistance mechanisms developed by this species have been conducted. in this work, three glyphosate-resistant populations (r8, r14, and r15) collected in citrus orchards from mexico, were used to study their resistance mechanisms comparin ... | 2016 | 27917189 |
| a natural light-driven inward proton pump. | light-driven outward h(+) pumps are widely distributed in nature, converting sunlight energy into proton motive force. here we report the characterization of an oppositely directed h(+) pump with a similar architecture to outward pumps. a deep-ocean marine bacterium, parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward h(+) pump when expressed in escherichia coli and mouse neural cells. detailed mechanistic analyses of the purified proteins reveal that ... | 2016 | 27853152 |
| redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism. | a major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. this holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. this large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (mo/w-bispgd) and fe/s clusters. here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational cha ... | 2016 | 27886223 |
| computing and applying atomic regulons to understand gene expression and regulation. | understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. an important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. these gene sets, atomic regulons (ars), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes an ... | 2016 | 27933038 |
| boosting functionality of synthetic dna circuits with tailored deactivation. | molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. the function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. here we introduce a mechanism to tune the nonlinearities associated with individual no ... | 2016 | 27845324 |
| two proofreading steps amplify the accuracy of genetic code translation. | aminoacyl-trnas (aa-trnas) are selected by the messenger rna programmed ribosome in ternary complex with elongation factor tu (ef-tu) and gtp and then, again, in a proofreading step after gtp hydrolysis on ef-tu. we use trna mutants with different affinities for ef-tu to demonstrate that proofreading of aa-trnas occurs in two consecutive steps. first, aa-trnas in ternary complex with ef-tu·gdp are selected in a step where the accuracy increases linearly with increasing aa-trna affinity to ef-tu. ... | 2016 | 27837019 |
| identification of ybey-protein interactions involved in 16s rrna maturation and stress regulation in escherichia coli. | ybey is part of a core set of rnases in escherichia coli and other bacteria. this highly conserved endoribonuclease has been implicated in several important processes such as 16s rrna 3' end maturation, 70s ribosome quality control, and regulation of mrnas and small noncoding rnas, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. thus, ybey likely interacts with numerous protein or rna partners that are involved in various aspects of cell ... | 2016 | 27834201 |
| a thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach. | a gene coding for a multicopper oxidase (bopa) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. the recombinant bopa protein produced in escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in the presence of copper, suggesting that bopa is laccase. a bioinformatic analysis of the bopa gene sequence indicated that it has a phylogenetically bacterial origin, possibly der ... | 2016 | 27885197 |
| cryo-em study of start codon selection during archaeal translation initiation. | eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aif1, e/aif1a, the ternary complex (tc, e/aif2-gtp-met-trnai(met)) and mrna bound to the small ribosomal subunit. e/aif2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. here, we present cryo-em structures of the full archaeal 30s initiation complex showing two conformational states of the tc. in the first state, the tc is bound to the riboso ... | 2016 | 27819266 |
| identification of essential genes in the salmonella phage spn3us reveals novel insights into giant phage head structure and assembly. | giant tailed bacterial viruses, or phages, such as pseudomonas aeruginosa phage ϕkz, have long genomes packaged into large, atypical virions. many aspects of ϕkz and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. we hypothesized that the salmonella enterica phage spn3us could be a useful model phage to address this gap in knowledge. the 240-kb spn3us genome shares a core set of 91 genes with ϕkz and related ph ... | 2016 | 27605673 |
| structural characterization of antibiotic self-immunity trna synthetase in plant tumour biocontrol agent. | antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. the biocontrol agrobacterium radiobacter k84 secretes the trojan horse antibiotic agrocin 84 that is selectively transported into the plant pathogen a. tumefaciens and processed into the toxin tm84. we previously showed that tm84 employs a unique trna-dependent mechanism to inhibit leucyl-trna synthetase (leurs), while the tm84-producer prevents self-poisoning by expressing a resistant leurs agnb2. we now identify ... | 2016 | 27713402 |
| in vitro engineering of novel bioactivity in the natural enzymes. | enzymes catalyze various biochemical functions with high efficiency and specificity. in vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. similarly, combined computat ... | 2016 | 27774447 |
| mechanism of ph-dependent activation of the sodium-proton antiporter nhaa. | escherichia coli nhaa is a prototype sodium-proton antiporter, which has been extensively characterized by x-ray crystallography, biochemical and biophysical experiments. however, the identities of proton carriers and details of ph-regulated mechanism remain controversial. here we report constant ph molecular dynamics data, which reveal that nhaa activation involves a net charge switch of a ph sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the fu ... | 2016 | 27708266 |
| n-acetylgalatosamine-mediated regulation of the aga operon by agar in streptococcus pneumoniae. | here, we analyze the transcriptomic response of streptococcus pneumoniae d39 to n-acetylgalactosamine (naga). transcriptome comparison of s. pneumoniae d39 grown in nagam17 (0.5% naga + m17) to that grown in gm17 (0.5% glucose + m17) revealed the elevated expression of various carbon metabolic genes/operons, including a pts operon (denoted here as the aga operon), which is putatively involved in naga transport and utilization, in the presence of naga. we further studied the role of a gntr-family ... | 2016 | 27672623 |
| microcystin-bound protein patterns in different cultures of microcystis aeruginosa and field samples. | micocystin (mc) exists in microcystis cells in two different forms, free and protein-bound. we examined the dynamic change in extracellular free mcs, intracellular free mcs and protein-bound mcs in both batch cultures and semi-continuous cultures, using high performance liquid chromatography and western blot. the results showed that the free mc per cell remained constant, while the quantity of protein-bound mcs increased with the growth of microcystis cells in both kinds of culture. significant ... | 2016 | 27754336 |
| functional characterization of a csor-cuea divergon in bradyrhizobium liaoningense ccnwsx0360, involved in copper, zinc and cadmium cotolerance. | random mutagenesis in a symbiotic nitrogen-fixing bradyrhizobium liaoningense ccnwsx0360 (bln0360) using tn5 identified five copper (cu) resistance-related genes. they were functionally sorted into three groups: transmembrane transport (cuea and tolc); oxidation (copa); and protection of the membrane barrier (lpte and ctpa). the gene cuea, together with the upstream csor (cu-sensitive operon repressor), constituted a csor-cuea divergon which plays a crucial role in cu homeostasis. deletion of cu ... | 2016 | 27725778 |
| a cascade of thermophilic enzymes as an approach to the synthesis of modified nucleotides. | we propose a new approach for the synthesis of biologically important nucleotides which includes a multi-enzymatic cascade conversion of d-pentoses into purine nucleotides. the approach exploits nucleic acid exchange enzymes from thermophilic microorganisms: ribokinase, phosphoribosylpyrophosphate synthetase, and adenine phosphoribosyltransferase. we cloned the ribokinase gene from thermus sp. 2.9, as well as two different genes of phosphoribosylpyrophosphate synthetase (prpp-synthetase) and the ... | 2016 | 28050269 |
| ns-μs time-resolved step-scan ftir of ba₃ oxidoreductase from thermus thermophilus: protonic connectivity of w941-w946-w927. | time-resolved step-scan ftir spectroscopy has been employed to probe the dynamics of the ba₃ oxidoreductase from thermus thermophilus in the ns-μs time range and in the ph/pd 6-9 range. the data revealed a ph/pd sensitivity of the d372 residue and of the ring-a propionate of heme a₃. based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the d372 and the ring-a propionate of heme a₃ is described. | 2016 | 27690021 |
| birth of archaeal cells: molecular phylogenetic analyses of g1p dehydrogenase, g3p dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having g1p polar lipids. | bacteria and eukarya have cell membranes with sn-glycerol-3-phosphate (g3p), whereas archaeal membranes contain sn-glycerol-1-phosphate (g1p). determining the time at which cells with either g3p-lipid membranes or g1p-lipid membranes appeared is important for understanding the early evolution of terrestrial life. to clarify this issue, we reconstructed molecular phylogenetic trees of g1pdh (g1p dehydrogenase; egsa/aram) which is responsible for g1p synthesis and g3pdhs (g3p dehydrogenase; gpsa a ... | 2016 | 27774041 |
| quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods. | cultivation-independent investigation of microbial ecology is biased by the dna extraction methods used. we aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different dna extraction methods with different cell lysis principles. our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic dna from the food matrices compared to the widely used ... | 2016 | 27669673 |
| metagenomics of thermophiles with a focus on discovery of novel thermozymes. | microbial populations living in environments with temperatures above 50°c (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. the integrated study of the whole-community dna from an environment, known as metagenomics ... | 2016 | 27729905 |
| specific internalisation of gold nanoparticles into engineered porous protein cages via affinity binding. | porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. protein cages' pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. however, strategies based on nanoparticle transport through the pores are largely unexplored, due to the diffi ... | 2016 | 27622533 |