| the bacterial cytoskeleton. | in recent years it has been shown that bacteria contain a number of cytoskeletal structures. the bacterial cytoplasmic elements include homologs of the three major types of eukaryotic cytoskeletal proteins (actin, tubulin, and intermediate filament proteins) and a fourth group, the mind-para group, that appears to be unique to bacteria. the cytoskeletal structures play important roles in cell division, cell polarity, cell shape regulation, plasmid partition, and other functions. the proteins sel ... | 2006 | 16959967 |
| a kernel for open source drug discovery in tropical diseases. | conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. for this reason, the past decade has seen extensive experimentation with alternative r&d institutions ranging from private-public partnerships to development prizes. despite extensive discussion, however, one of the most promising avenues-open source drug discovery-has remained elusive. we argue that the stumbling block has been the absence of a c ... | 2009 | 19381286 |
| structure and function of enzymes in heme biosynthesis. | tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. further, enzymes such as catalases, peroxidases, or cytochromes p450 rely on heme as essential cofactors. heme is synthesized in most organisms via a highly conserved biosynthetic route. in h ... | 2010 | 20506125 |
| crispr interference: rna-directed adaptive immunity in bacteria and archaea. | sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. the importance of such pathways is highlighted by the extensive study of rna interference (rnai) and related processes in eukaryotes. in many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (crisprs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. crisp ... | 2010 | 20125085 |
| the crispr system: small rna-guided defense in bacteria and archaea. | all cellular systems evolve ways to combat predators and genomic parasites. in bacteria and archaea, numerous resistance mechanisms have developed against phage. our understanding of this defensive repertoire has recently been expanded to include the crispr system of clustered, regularly interspaced short palindromic repeats. in this remarkable pathway, short sequence tags from invading genetic elements are actively incorporated into the host's crispr locus to be transcribed and processed into a ... | 2010 | 20129051 |
| heme ligand identification and redox properties of the cytochrome c synthetase, ccmf. | cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein ccmf, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. we previously reported that the e. coli ccmf protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. here, we show that mutation of either of two conserved ... | 2011 | 22066495 |
| eukaryote-like serine/threonine kinases and phosphatases in bacteria. | genomic studies have revealed the presence of ser/thr kinases and phosphatases in many bacterial species, although their physiological roles have largely been unclear. here we review bacterial ser/thr kinases (estks) that show homology in their catalytic domains to eukaryotic ser/thr kinases and their partner phosphatases (estps) that are homologous to eukaryotic phosphatases. we first discuss insights into the enzymatic mechanism of estk activation derived from structural studies on both the li ... | 2011 | 21372323 |
| the porphyrias: advances in diagnosis and treatment. | the inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as "acute hepatic," "hepatic cutaneous," and "erythropoietic cutaneous" diseases. recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment. these advances include dna-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of th ... | 2012 | 22791288 |
| chemosensory signaling controls motility and subcellular polarity in myxococcus xanthus. | myxococcus xanthus is a model system for the study of dynamic protein localization and cell polarity in bacteria. m. xanthus cells are motile on solid surfaces enabled by two forms of motility. motility is controlled by the che-like frz pathway, which is essential for fruiting body formation and differentiation. the frz signal is mediated by a gtpase/gap protein pair that establishes cell polarity and directs the motility systems. pilus driven motility at the leading pole of the cell requires dy ... | 2012 | 23142584 |
| function and regulation of clustered regularly interspaced short palindromic repeats (crispr) / crispr associated (cas) systems. | phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. in contrast, the clustered regularly interspaced short palindromic repeats (crispr) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. re ... | 2012 | 23202464 |
| interaction of card with rna polymerase mediates mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis. | mycobacterium tuberculosis infection continues to cause substantial human suffering. new chemotherapeutic strategies, which require insight into the pathways essential for m. tuberculosis pathogenesis, are imperative. we previously reported that depletion of the card protein in mycobacteria compromises viability, resistance to oxidative stress and fluoroquinolones, and pathogenesis. card associates with the rna polymerase (rnap), but it has been unknown which of the diverse functions of card are ... | 2012 | 22904282 |
| phosphoproteomic analysis reveals the effects of pilf phosphorylation on type iv pilus and biofilm formation in thermus thermophilus hb27. | thermus thermophilus hb27 is an extremely thermophilic eubacteria with a high frequency of natural competence. this organism is therefore often used as a thermophilic model to investigate the molecular basis of type iv pili-mediated functions, such as the uptake of free dna, adhesion, twitching motility, and biofilm formation, in hot environments. in this study, the phosphoproteome of t. thermophilus hb27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. ninety-three uniqu ... | 2013 | 23828892 |
| structure of the mtb card/rnap β-lobes complex reveals the molecular basis of interaction and presents a distinct dna-binding domain for mtb card. | card from mycobacterium tuberculosis (mtb) is an essential protein shown to be involved in stringent response through downregulation of rrna and ribosomal protein genes. card interacts with the β-subunit of rnap and this interaction is vital for mtb's survival during the persistent infection state. we have determined the crystal structure of card in complex with the rnap β-subunit β1 and β2 domains at 2.1 å resolution. the structure reveals the molecular basis of card/rnap interaction, providing ... | 2013 | 24055315 |
| crystallization and preliminary x-ray analysis of an alanine dehydrogenase from bacillus megaterium wsh-002. | alanine dehydrogenase (l-aladh) from bacillus megaterium wsh-002 catalyses the nad⁺-dependent interconversion of l-alanine and pyruvate. the enzyme was expressed in escherichia coli bl21 (de3) cells and purified with a his6 tag by ni²⁺-chelating affinity chromatography for x-ray crystallographic analysis. crystals were grown in a solution consisting of 0.1 m hepes ph 8.0, 12%(w/v) polyethylene glycol 8000, 8%(v/v) ethylene glycol at a concentration of 15 mg ml⁻¹ purified protein. the crystal dif ... | 2013 | 23908047 |
| type iv pilus proteins form an integrated structure extending from the cytoplasm to the outer membrane. | the bacterial type iv pilus (t4p) is the strongest biological motor known to date as its retraction can generate forces well over 100 pn. myxococcus xanthus, a δ-proteobacterium, provides a good model for t4p investigations because its social (s) gliding motility is powered by t4p. in this study, the interactions among m. xanthus t4p proteins were investigated using genetics and the yeast two-hybrid (y2h) system. our genetic analysis suggests that there is an integrated t4p structure that crosse ... | 2013 | 23922942 |
| structure and function of card, an essential mycobacterial transcription factor. | card, an essential transcription regulator in mycobacterium tuberculosis, directly interacts with the rna polymerase (rnap). we used a combination of in vivo and in vitro approaches to establish that card is a global regulator that stimulates the formation of rnap-holoenzyme open promoter (rpo) complexes. we determined the x-ray crystal structure of thermus thermophilus card, allowing us to generate a structural model of the card/rpo complex. on the basis of our structural and functional analyse ... | 2013 | 23858468 |
| activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpob) mutations in actinomycetes. | a subset of rifampin resistance (rpob) mutations result in the overproduction of antibiotics in various actinomycetes, including streptomyces, saccharopolyspora, and amycolatopsis, with h437y and h437r rpob mutations effective most frequently. moreover, the rpob mutations markedly activate (up to 70-fold at the transcriptional level) the cryptic/silent secondary metabolite biosynthetic gene clusters of these actinomycetes, which are not activated under general stressful conditions, with the exce ... | 2013 | 23603745 |
| peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly. | the peptidoglycan (pg) cell wall is a unique macromolecule responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria. a quantitative understanding of the relationships between pg architecture, morphogenesis, immune system activation and pathogenesis can provide molecular-scale insights into the function of proteins involved in cell wall synthesis and cell growth. high-performance liquid chromatography (hplc) has played an important role in our ... | 2013 | 23679048 |
| nusg-spt5 proteins-universal tools for transcription modification and communication. | | 2013 | 23638618 |
| pilmnopq from the pseudomonas aeruginosa type iv pilus system form a transenvelope protein interaction network that interacts with pila. | pseudomonas aeruginosa type iv pili (t4p) are virulence factors that promote infection of cystic fibrosis and immunosuppressed patients. as the absence of t4p impairs colonization, they are attractive targets for the development of novel therapeutics. genes in the pilmnopq operon are important for both t4p assembly and a form of bacterial movement, called twitching motility, that is required for pathogenicity. the type ii membrane proteins, piln and pilo, dimerize via their periplasmic domains a ... | 2013 | 23457250 |
| mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card. | escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ... | 2014 | 25510492 |
| mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card. | escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ... | 2014 | 25510492 |
| evolution and diversity of the ras superfamily of small gtpases in prokaryotes. | the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ... | 2014 | 25480683 |
| evolution and diversity of the ras superfamily of small gtpases in prokaryotes. | the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ... | 2014 | 25480683 |
| the predatory bacterium bdellovibrio bacteriovorus aspartyl-trna synthetase recognizes trnaasn as a substrate. | the predatory bacterium bdellovibrio bacteriovorus preys on other gram-negative bacteria and was predicted to be an asparagine auxotroph. however, despite encoding asparaginyl-trna synthetase and glutaminyl-trna synthetase, b. bacteriovorus also contains the amidotransferase gatcab. deinococcus radiodurans, and thermus thermophilus also encode both of these aminoacyl-trna synthetases with gatcab. both also code for a second aspartyl-trna synthetase and use the additional aspartyl-trna synthetase ... | 2014 | 25338061 |
| zinc and atp binding of the hexameric aaa-atpase pilf from thermus thermophilus: role in complex stability, piliation, adhesion, twitching motility, and natural transformation. | the traffic aaa-atpase pilf is essential for pilus biogenesis and natural transformation of thermus thermophilus hb27. recently, we showed that pilf forms hexameric complexes containing six zinc atoms coordinated by conserved tetracysteine motifs. here we report that zinc binding is essential for complex stability. however, zinc binding is neither required for pilus biogenesis nor natural transformation. a number of the mutants did not exhibit any pili during growth at 64 °c but still were trans ... | 2014 | 25202014 |
| a review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. | microbial cell factories (mcfs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. this review highlights the progress of computational models for the rational design of an mcf to produce a target bio-commodity. in particular, the rational design of an mcf involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) mcf chassis selection, (iv) enzyme engineering of ... | 2014 | 25379147 |
| molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix. | tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ... | 2014 | 25108393 |
| multiple regulatory mechanisms control the expression of the geobacillus stearothermophilus gene for extracellular xylanase. | geobacillus stearothermophilus t-6 produces a single extracellular xylanase (xyn10a) capable of producing short, decorated xylo-oligosaccharides from the naturally branched polysaccharide, xylan. gel retardation assays indicated that the master negative regulator, xylr, binds specifically to xylr operators in the promoters of xylose and xylan-utilization genes. this binding is efficiently prevented in vitro by xylose, the most likely molecular inducer. expression of the extracellular xylanase is ... | 2014 | 25070894 |
| outside-in assembly pathway of the type iv pilus system in myxococcus xanthus. | type iv pili (t4p) are ubiquitous bacterial cell surface structures that undergo cycles of extension, adhesion, and retraction. t4p function depends on a highly conserved envelope-spanning macromolecular machinery consisting of 10 proteins that localizes polarly in myxococcus xanthus. using this localization, we investigated the entire t4p machinery assembly pathway by systematically profiling the stability of all and the localization of eight of these proteins in the absence of other t4p machin ... | 2014 | 24187092 |
| type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2. | natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ... | 2014 | 24212586 |
| structural basis for gene regulation by a b12-dependent photoreceptor. | photoreceptor proteins enable organisms to sense and respond to light. the newly discovered carh-type photoreceptors use a vitamin b12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. here we present crystal structures of thermus thermophilus carh in all three relevant states: in the dark, both free and bound to operator dna, and after light exposure. these structures provide visualizations of how adenosylcobalamin mediates carh tetramer ... | 2015 | 26416754 |
| identification of middle chain fatty acyl-coa ligase responsible for the biosynthesis of 2-alkylmalonyl-coas for polyketide extender unit. | understanding the biosynthetic mechanism of the atypical polyketide extender unit is important for the development of bioactive natural products. reveromycin (rm) derivatives produced by streptomyces sp. sn-593 possess several aliphatic extender units. here, we studied the molecular basis of 2-alkylmalonyl-coa formation by analyzing the revr and revs genes, which form a transcriptional unit with the revt gene, a crotonyl-coa carboxylase/reductase homolog. we mainly focused on the uncharacterized ... | 2015 | 26378232 |
| the photochemical mechanism of a b12-dependent photoreceptor protein. | the coenzyme b12-dependent photoreceptor protein, carh, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. on binding of coenzyme b12 the monomeric apoprotein forms tetramers in the dark, which bind operator dna thus blocking transcription. under illumination the carh tetramer dissociates, weakening its affinity for dna and allowing transcription. the mechanism by which this occurs is unknown. here we describe the photochemistry in carh t ... | 2015 | 26264192 |
| the transcription factor carh safeguards use of adenosylcobalamin as a light sensor by altering the photolysis products. | the newly discovered light-dependent transcription factor carh uses adenosylcobalamin as a light sensor to regulate expression of protective genes in bacteria upon exposure to sunlight. this use of adenosylcobalamin is a clever adaptation of a classic enzyme cofactor, taking advantage of its photolabile co-c bond. however, it is also puzzling in that photolysis of adenosylcobalamin generates the 5'-deoxyadenosyl radical that could damage dna. here, using liquid chromatography and spectroscopic t ... | 2015 | 25966286 |
| role and function of litr, an adenosyl b12-bound light-sensitive regulator of bacillus megaterium qm b1551, in regulation of carotenoid production. | the litr/carh family of proteins is a light-sensitive merr family of transcriptional regulators that contain an adenosyl b12 (coenzyme b12 or adob12)-binding domain at the c terminus. the genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from gram-positive bacteria remain poorly understood. we performed genetic and biochemical analyses of a homolog of the litr protein from bacillus megaterium qm b1551, a gr ... | 2015 | 25917914 |
| ubiquitous transcription factors display structural plasticity and diverse functions: nusg proteins - shifting shapes and paradigms. | numerous accessory factors modulate rna polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional rna processing. transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. nusg/spt5 elongation factors comprise the only universally conserved and ancient family of regulators. they bind to the conserved clamp helices domain of rna polymerase, which also interacts with non-homologous initiation ... | 2015 | 25640595 |
| 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 |
| prediction and analysis of the modular structure of cytochrome p450 monooxygenases. | cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague. | 2010 | 20950472 |
| whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. | the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ... | 2012 | 23145189 |
| integron gene cassettes: a repository of novel protein folds with distinct interaction sites. | mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. in most cases, functional annotation of gene cassettes directly recovered by cassette-pcr is obscured by their characteristically high sequence novelty. this inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. a structural genomics approach incorporating x-ray crystallograph ... | 2013 | 23349695 |
| evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera? | evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ... | 2014 | 24521160 |
| 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 |
| mustang-mr structural sieving server: applications in protein structural analysis and crystallography. | a central tenet of structural biology is that related proteins of common function share structural similarity. this has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. this paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program mustang. | 2010 | 20386610 |
| the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family. | we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins. | 2014 | 24908050 |
| structural basis of thermal stability of the tungsten cofactor synthesis protein moab from pyrococcus furiosus. | molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. the biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (mpt) by adenylylation before the respective metal is incorporated. in the hyperthermophilic organism pyrococcus furiosus, the hexameric protein moab (pfumoab) has been shown to catalyse mpt-ad ... | 2014 | 24465852 |
| the class iii cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways. | photolyases are proteins with an fad chromophore that repair uv-induced pyrimidine dimers on the dna in a light-dependent manner. the cyclobutane pyrimidine dimer class iii photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. here we present the crystal structure of a class iii photolyase termed photolyase-related protein a (phra) of agrobacterium tumefaciens at 1.67-å resolution. phra contains 5,10-methenyltetrahydrofolate (m ... | 2015 | 25784552 |
| a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene. | genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ... | 2015 | 25883135 |
| bioprocessing data for the production of marine enzymes. | this review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. submerged, immobilized and solid-state processes in batch mode were widely employed. the fed-batch process was also applied in several b ... | 2010 | 20479981 |
| branchclust: a phylogenetic algorithm for selecting gene families. | automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ... | 2007 | 17425803 |
| identification of genes encoding trna modification enzymes by comparative genomics. | as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ... | 2007 | 17673083 |
| a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. | bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ... | 2011 | 21673094 |
| 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 |
| dna polymerases engineered by directed evolution to incorporate non-standard nucleotides. | dna polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. however, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. the focus of this review is on non-standard nucleotides that expand the genetic "alphabet." this review focuses on experiments that, by directed evolution, ha ... | 2014 | 25400626 |
| 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 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution. | we present a novel analysis of compositional order (co) based on the occurrence of frequent amino-acid triplets (fts) that appear much more than random in protein sequences. the method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. we introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and t ... | 2013 | 24278003 |
| extremophiles 2002. | | 2003 | 12813059 |
| soda: an mn/fe superoxide dismutase prediction and design server. | superoxide dismutases (sods) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. we focus here on the sod family that uses fe or mn as cofactor. | 2008 | 18518943 |
| initiation of mrna decay in bacteria. | the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ... | 2013 | 24064983 |
| initiation of mrna decay in bacteria. | the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ... | 2013 | 24064983 |
| detection, distribution and characterization of novel superoxide dismutases from yersinia enterocolitica biovar 1a. | superoxide dismutases (sods) cause dismutation of superoxide radicals to hydrogen peroxide and oxygen. besides protecting the cells against oxidative damage by endogenously generated oxygen radicals, sods play an important role in intraphagocytic survival of pathogenic bacteria. the complete genome sequences of yersinia enterocolitica strains show presence of three different sod genes. however, not much is known about the types of sods present in y. enterocolitica, their characteristics and role ... | 2013 | 23704955 |
| psychrophily and catalysis. | polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. ... | 2013 | 24832805 |
| structures of protein-protein complexes involved in electron transfer. | electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of atp, and are involved in many reactions of intermediary metabolism. key to these roles is the formation of transient inter-protein electron transfer complexes. the structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic ... | 2013 | 23535590 |
| improved cultivation and metagenomics as new tools for bioprospecting in cold environments. | only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ... | 2014 | 25399309 |
| improved cultivation and metagenomics as new tools for bioprospecting in cold environments. | only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ... | 2014 | 25399309 |
| stability curve prediction of homologous proteins using temperature-dependent statistical potentials. | the unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. in this paper we attempt to gain insight into the thermal stability of proteins by designing a tool to predict the full stability curve as a function of the temperature for a set of 45 proteins belonging to 11 homologou ... | 2014 | 25032839 |
| rna-seq-based analysis of cold shock response in thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene. | although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. thermoanaerobacter tengcongensis mb4, a thermophile harboring only one known cold shock protein gene (ttescpc), can survive from 50° to 80 °c, but has poor natural competence under cold shock at 50 °c. we therefore examined cold shock responses ... | 2014 | 24667527 |
| cold and hot extremozymes: industrial relevance and current trends. | the development of enzymes for industrial applications relies heavily on the use of microorganisms. the intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. these microorganisms have developed unique mechanisms and molecular means to cope with extreme ... | 2015 | 26539430 |
| marine extremophiles: a source of hydrolases for biotechnological applications. | the marine environment covers almost three quarters of the planet and is where evolution took its first steps. extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. the ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. hydrolases including amylases, cellulases, peptidases and lipases from hyper ... | 2015 | 25854643 |
| the fggy carbohydrate kinase family: insights into the evolution of functional specificities. | function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. however, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. here, using the fggy carbohydrate kinase family as an example, we bu ... | 2011 | 22215998 |
| naxd is a deacetylase required for lipid a modification and francisella pathogenesis. | modification of specific gram-negative bacterial cell envelope components, such as capsule, o-antigen and lipid a, are often essential for the successful establishment of infection. francisella species express lipid a molecules with unique characteristics involved in circumventing host defences, which significantly contribute to their virulence. in this study, we show that naxd, a member of the highly conserved ydjc superfamily, is a deacetylase required for an important modification of the oute ... | 2012 | 22966934 |
| magnesium-dependent processes are targets of bacterial manganese toxicity. | a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ... | 2014 | 24975873 |
| 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 |
| 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 |
| angling for uniqueness in enzymatic preparation of glycosides. | in the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. this is a general bird's-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. as far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features ... | 2013 | 24970171 |
| 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 |
| phylogenetic analysis and evolutionary origins of dna polymerase x-family members. | mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ... | 2014 | 25112931 |
| ribonucleotide reduction - horizontal transfer of a required function spans all three domains. | ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ... | 2010 | 21143941 |
| the universally conserved prokaryotic gtpases. | members of the large superclass of p-loop gtpases share a core domain with a conserved three-dimensional structure. in eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. as targets of mutation and toxins, gtpases are involved in the pathogenesis of cancer and infectious diseases. in prokaryotes also, it is hard to overestimate the importance of gtpases in cell physiology. nu ... | 2011 | 21885683 |
| structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc118. | the structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc188 has been determined at 1.72 å resolution. the structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. comparison to other related structures revealed high homology in the active site, allo ... | 2012 | 23192019 |
| high-resolution structures of thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with nad+ and in complex with nad+ and triclosan. | enoyl-acyl carrier protein reductase (enr; the product of the fabi gene) is an important enzyme that is involved in the type ii fatty-acid-synthesis pathway of bacteria, plants, apicomplexan protozoa and mitochondria. harmful pathogens such as mycobacterium tuberculosis and plasmodium falciparum use the type ii fatty-acid-synthesis system, but not mammals or fungi, which contain a type i fatty-acid-synthesis pathway consisting of one or two multifunctional enzymes. for this reason, specific inhi ... | 2012 | 23027736 |
| molecular evolution of hydrogen peroxide degrading enzymes. | for efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2h(2)o(2) → o(2) + 2h(2)o), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. here we report on the updated reconstruction of the molecular phylogeny of these three gene families. ubiquitous typical (monofunctional) heme catalases are found in all domains of life showin ... | 2012 | 22330759 |
| glutamine versus ammonia utilization in the nad synthetase family. | nad is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. the last step of nad synthesis is the atp-dependent amidation of deamido-nad by nad synthetase (nads). members of the nads family are present in nearly all species across the three kingdoms of life. in eukaryotic nads, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. this two-domain nads arrangement enabling ... | 2012 | 22720044 |
| staphylococcus aureus fabi: inhibition, substrate recognition, and potential implications for in vivo essentiality. | methicillin-resistant staphylococcus aureus (mrsa) infections constitute a serious health threat worldwide, and novel antibiotics are therefore urgently needed. the enoyl-acp reductase (safabi) is essential for the s. aureus fatty acid biosynthesis and, hence, serves as an attractive drug target. we have obtained a series of snapshots of this enzyme that provide a mechanistic picture of ligand and inhibitor binding, including a dimer-tetramer transition combined with extensive conformational cha ... | 2012 | 22579249 |
| aggregate reactivation mediated by the hsp100 chaperones. | hsp100 family of molecular chaperones shows a unique capability to resolubilize and reactivate aggregated proteins. the hsp100-mediated protein disaggregation is linked to the activity of other chaperones from the hsp70 and hsp40 families. the best-studied members of the hsp100 family are the bacterial clpb and hsp104 from yeast. hsp100 chaperones are members of a large super-family of energy-driven conformational "machines" known as aaa+ atpases. this review describes the current mechanistic mo ... | 2012 | 22306514 |
| type iv pili in gram-positive bacteria. | type iv pili (t4p) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, dna uptake (competence), and protein secretion and that can act as nanowires carrying electric current. t4p are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type ii secretion systems in eubacteria and the flagella of archaea. t4p are found throughout gram-negative bacterial families and have been studied most ... | 2013 | 24006467 |
| replacing sulfa drugs with novel dhps inhibitors. | more research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. the enzyme dhps has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. the use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. despite the large amount of structural information available for dhps, few recent publi ... | 2013 | 23859210 |
| crystal structures and kinetic properties of enoyl-acyl carrier protein reductase i from candidatus liberibacter asiaticus. | huanglongbing (hlb) is a destructive citrus disease. the leading cause of hlb is candidatus liberibacter asiaticus. fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. enoyl-acyl carrier protein reductase (also called enr or fabi and a product of the fabi gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agen ... | 2014 | 24407918 |
| the moxr atpase rava and its cofactor viaa interact with the nadh:ubiquinone oxidoreductase i in escherichia coli. | moxr atpases are widespread throughout bacteria and archaea. the experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. in escherichia coli, the moxr atpase rava and its putative cofactor viaa are found to exist in early stationary-phase cells at 37 °c at low levels of about 350 and 90 molecules per cell, respectively. both proteins are predominantly localized to the cytopla ... | 2014 | 24454883 |
| cpf1 is a single rna-guided endonuclease of a class 2 crispr-cas system. | the microbial adaptive immune system crispr mediates defense against foreign genetic elements through two classes of rna-guided nuclease effectors. class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized cas9. here, we report characterization of cpf1, a putative class 2 crispr effector. we demonstrate that cpf1 mediates robust dna interference with features distinct from cas9. cpf1 is a single rna-guid ... | 2015 | 26422227 |
| the origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. | the tree of life is usually rooted between archaea and bacteria. we have previously presented three arguments that support placing the root of the tree of life in bacteria. the data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. | 2011 | 21356104 |
| architecture and conservation of the bacterial dna replication machinery, an underexploited drug target. | new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ... | 2012 | 22206257 |
| molecular mechanisms of crispr-mediated microbial immunity. | bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ... | 2013 | 23959171 |