| functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. | targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ... | 2013 | 24062736 |
| a comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes. | the lipid cubic phase or in meso method is a robust approach for crystallizing membrane proteins for structure determination. the uptake of the method is such that it is experiencing what can only be described as explosive growth. this timely, comprehensive and up-to-date review introduces the reader to the practice of in meso crystallogenesis, to the associated challenges and to their solutions. a model of how crystallization comes about mechanistically is presented for a more rational approach ... | 2015 | 25615961 |
| insertion sequences. | insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ... | 1998 | 9729608 |
| the tyra family of aromatic-pathway dehydrogenases in phylogenetic context. | the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. | 2005 | 15888209 |
| protrepeatsdb: a database of amino acid repeats in genomes. | genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. innate protein repeats constitute vital functional and structural regions in proteins. repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. in the post genomic era, availability of protein sequences encoded in different genomes provides a unique ... | 2006 | 16827924 |
| the path to next generation biofuels: successes and challenges in the era of synthetic biology. | volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for con ... | 2010 | 20089184 |
| stable isotope peptide mass spectrometry to decipher amino acid metabolism in dehalococcoides strain cbdb1. | dehalococcoides species are key players in the anaerobic transformation of halogenated solvents at contaminated sites. here, we analyze isotopologue distributions in amino acid pools from peptides of dehalococcoides strain cbdb1 after incubation with (13)c-labeled acetate or bicarbonate as a carbon source. the resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. in addition to using gas chromatography-mass spectrometry (gc-ms) for analyz ... | 2012 | 22661690 |
| structure, function and inhibition of the two- and three-domain 4fe-4s ispg proteins. | ispg is a 4fe4s protein involved in isoprenoid biosynthesis. most bacterial ispgs contain two domains: a tim barrel (a) and a 4fe4s domain (b), but in plants and malaria parasites, there is a large insert domain (a*) whose structure and function are unknown. we show that bacterial ispgs function in solution as (ab)(2) dimers and that mutations in either both a or both b domains block activity. chimeras harboring an a-mutation in one chain and a b-mutation in the other have 50% of the activity se ... | 2012 | 22586085 |
| in silico analysis of a therapeutic target in leishmania infantum: the guanosine-diphospho-d-mannose pyrophosphorylase. | leishmaniases are tropical and sub-tropical diseases for which classical drugs (i.e. antimonials) exhibit toxicity and drug resistance. such a situation requires to find new chemical series with antileishmanial activity. this work consists in analyzing the structure of a validated target in leishmania: the gdp-mannose pyrophosphorylase (gdp-mp), an enzyme involved in glycosylation and essential for amastigote survival. by comparing both human and l. infantum gdp-mp 3d homology models, we identif ... | 2012 | 22314241 |
| veillonella, firmicutes: microbes disguised as gram negatives. | the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ... | 2013 | 24976898 |
| bacterial transfer rnas. | transfer rna is an essential adapter molecule that is found across all three domains of life. the primary role of transfer rna resides in its critical involvement in the accurate translation of messenger rna codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. this review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer rn ... | 2015 | 25796611 |
| novel type ii and monomeric nad+ specific isocitrate dehydrogenases: phylogenetic affinity, enzymatic characterization, and evolutionary implication. | nad(+) use is an ancestral trait of isocitrate dehydrogenase (idh), and the nadp(+) phenotype arose through evolution as an ancient adaptation event. however, no nad(+)-specific idhs have been found among type ii idhs and monomeric idhs. in this study, novel type ii homodimeric nad-idhs from ostreococcus lucimarinus cce9901 idh (olidh) and micromonas sp. rcc299 (miidh), and novel monomeric nad-idhs from campylobacter sp. fobrc14 idh (caidh) and campylobacter curvus (ccidh) were reported for the ... | 2015 | 25775177 |
| 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 |
| 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 |
| rna secondary structure prediction by centroids in a boltzmann weighted ensemble. | prediction of rna secondary structure by free energy minimization has been the standard for over two decades. here we describe a novel method that forsakes this paradigm for predictions based on boltzmann-weighted structure ensemble. we introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. in comparison with the minimum free energy (mfe) structure using diverse types of structural rnas, the centroid of the ensemb ... | 2005 | 16043502 |
| defense islands in bacterial and archaeal genomes and prediction of novel defense systems. | the arms race between cellular life forms and viruses is a major driving force of evolution. a substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. we analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. the defense islands are enriched ... | 2011 | 21908672 |
| the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. | ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ... | 2006 | 16859499 |
| evolution of prokaryotic spfh proteins. | the spfh protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. recently the origin of the spfh proteins has been questioned. instead, convergent evolution has been proposed. however, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution patt ... | 2009 | 19138386 |
| lipoic acid metabolism in microbial pathogens. | lipoic acid [(r)-5-(1,2-dithiolan-3-yl)pentanoic acid] is an enzyme cofactor required for intermediate metabolism in free-living cells. lipoic acid was discovered nearly 60 years ago and was shown to be covalently attached to proteins in several multicomponent dehydrogenases. cells can acquire lipoate (the deprotonated charge form of lipoic acid that dominates at physiological ph) through either scavenging or de novo synthesis. microbial pathogens implement these basic lipoylation strategies wit ... | 2010 | 20508247 |
| the genome of pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. | the bacterium pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. the genome of p. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing geobacter species. | 2012 | 23227809 |
| oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways. | in the universe, oxygen is the third most widespread element, while on earth it is the most abundant one. moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. besides o(2), reactive oxygen species (ros), among them hydrogen peroxide (h(2)o(2)), are also important reactants in the present aerobic metabolism. according to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving o(2) appeared after the evolution of oxygenic ... | 2012 | 22970865 |
| the crispr-associated gene cas2 of legionella pneumophila is required for intracellular infection of amoebae. | recent studies have shown that the clustered regularly interspaced palindromic repeats (crispr) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. upon analysis of the legionella pneumophila strain 130b chromosome, we detected a subtype ii-b crispr-cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. reverse transcription (rt)-pcr analysis demonstrated that the entire crispr-cas locus is expres ... | 2013 | 23481601 |
| bacterial genome instability. | bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ... | 2014 | 24600039 |
| quantification of 16s rrnas in complex bacterial communities by multiple competitive reverse transcription-pcr in temperature gradient gel electrophoresis fingerprints. | a novel approach was developed to quantify rrna sequences in complex bacterial communities. the main bacterial 16s rrnas in drentse a grassland soils (the netherlands) were amplified by reverse transcription (rt)-pcr with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (tgge). the primer pair used (primers u968-gc and l1401) was found to amplify with the same efficiency 16s rrnas from bacterial cultures containing different taxa and cloned 16s ribosomal ... | 1998 | 9797325 |
| bacterial cell-envelope glycoconjugates. | prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. the scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. this article a ... | 2013 | 24274370 |
| time-dependent transcriptional changes in axenic giardia duodenalis trophozoites. | giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. although g. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. the present study employed rna sequencing to characterize the mrna transcriptome of g. duodenalis trophozoites in axenic culture, at log (48 h of g ... | 2015 | 26636323 |
| a conserved histidine in switch-ii of ef-g moderates release of inorganic phosphate. | elongation factor g (ef-g), a translational gtpase responsible for trna-mrna translocation possesses a conserved histidine (h91 in escherichia coli) at the apex of switch-ii, which has been implicated in gtpase activation and gtp hydrolysis. while h91a, h91r and h91e mutants showed different degrees of defect in ribosome associated gtp hydrolysis, h91q behaved like the wt. however, all these mutants, including h91q, are much more defective in inorganic phosphate (pi) release, thereby suggesting ... | 2015 | 26264741 |
| bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. | fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within bacteria. in this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and fou ... | 2011 | 22022440 |
| s-layer proteins. | | 2000 | 10648507 |
| s-layers: principles and applications. | monomolecular arrays of protein or glycoprotein subunits forming surface layers (s-layers) are one of the most commonly observed prokaryotic cell envelope components. s-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. the isoporous lattices completely covering the cell surface provide organisms with various selection advantages including ... | 2014 | 24483139 |
| enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria. | the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ... | 2005 | 16269773 |
| the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin. | the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i. | 2007 | 18021395 |
| bacterial heme-transport proteins and their heme-coordination modes. | efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ... | 2008 | 18977196 |
| bacterial heme-transport proteins and their heme-coordination modes. | efficient iron acquisition is critical for an invading microbe's survival and virulence. most of the iron in mammals is incorporated into heme, which can be plundered by certain bacterial pathogens as a nutritional iron source. utilization of exogenous heme by bacteria involves the binding of heme or hemoproteins to the cell surface receptors, followed by the transport of heme into cells. once taken into the cytosol, heme is presented to heme oxygenases where the tetrapyrrole ring is cleaved in ... | 2008 | 18977196 |
| the elusive object of desire--interactions of bacteriophages and their hosts. | bacteria and their viruses (phages) are locked in an evolutionary contest, with each side producing constantly changing mechanisms of attack and defense that are aimed to increase the odds of survival. as a result, phages play central roles in a great variety of genetic processes and increase the rate of evolutionary change of the bacterial host, which could ultimately work to the benefit of the host in a long run. | 2008 | 18400552 |
| structural biology of proline catabolism. | the proline catabolic enzymes proline dehydrogenase and delta(1)-pyrroline-5-carboxylate dehydrogenase catalyze the 4-electron oxidation of proline to glutamate. these enzymes play important roles in cellular redox control, superoxide generation, apoptosis and cancer. in some bacteria, the two enzymes are fused into the bifunctional enzyme, proline utilization a. here we review the three-dimensional structural information that is currently available for proline catabolic enzymes. crystal structu ... | 2008 | 18369526 |
| assessing the quality of whole genome alignments in bacteria. | comparing genomes is an essential preliminary step to solve many problems in biology. matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. the first measure is based o ... | 2009 | 20049164 |
| genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements. | the mobility of restriction-modification (rm) gene complexes and their association with genome rearrangements is a subject of active investigation. here we conducted systematic genome comparisons and genome context analysis on fully sequenced prokaryotic genomes to detect rm-linked genome rearrangements. rm genes were frequently found to be linked to mobility-related genes such as integrase and transposase homologs. they were flanked by direct and inverted repeats at a significantly high frequen ... | 2010 | 20071371 |
| learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications. | the emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. the bacteria causing both hospital and community-acquired infections are most often multidrug resistant. in view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. the presented review focuses on the major characteristics of bacteriophages and phage-en ... | 2012 | 23305359 |
| characterization and structure of the aquifex aeolicus protein duf752: a bacterial trna-methyltransferase (mnmc2) functioning without the usually fused oxidase domain (mnmc1). | post-transcriptional modifications of the wobble uridine (u34) of trnas play a critical role in reading nna/g codons belonging to split codon boxes. in a subset of escherichia coli trna, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)u34) through sequential enzymatic reactions. uridine 34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)u34) by the mnme-mnmg enzyme complex. the cmnm(5)u34 is further modified to mnm(5)u by the bifunctional mnmc protein. in the ... | 2012 | 23091054 |
| redundancy and modularity in membrane-associated dissimilatory nitrate reduction in bacillus. | the genomes of two phenotypically denitrifying type strains of the genus bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. a considerable degree of functional redundancy was observed with marked differences between b. azotoforman ... | 2012 | 23087684 |
| the crystal structures of the α-subunit of the α(2)β (2) tetrameric glycyl-trna synthetase. | aminoacyl-trna synthetases (aarss) are ligases (ec.6.1.1.-) that catalyze the acylation of amino acids to their cognate trnas in the process of translating genetic information from mrna to protein. their amino acid and trna specificity are crucial for correctly translating the genetic code. glycine is the smallest amino acid and the glycyl-trna synthetase (glyrs) belongs to class ii aarss. the enzyme is unusual because it can assume different quaternary structures. in eukaryotes, archaebacteria ... | 2012 | 23054484 |
| specific metal recognition in nickel trafficking. | nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. as with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. because there are few enzymes (targets) that require nickel for activi ... | 2012 | 22970729 |
| the role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. | bacterial enhancer binding proteins (bebps) are transcriptional activators that assemble as hexameric rings in their active forms and utilize atp hydrolysis to remodel the conformation of rna polymerase containing the alternative sigma factor σ(54). we present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. the review is structured by introducing each of the three domains in turn: the central catalytic domain, the ... | 2012 | 22933558 |
| double-stranded endonuclease activity in bacillus halodurans clustered regularly interspaced short palindromic repeats (crispr)-associated cas2 protein. | the crispr (clustered regularly interspaced short palindromic repeats) system is a prokaryotic rna-based adaptive immune system against extrachromosomal genetic elements. cas2 is a universally conserved core crispr-associated protein required for the acquisition of new spacers for crispr adaptation. it was previously characterized as an endoribonuclease with preference for single-stranded (ss)rna. here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the bac ... | 2012 | 22942283 |
| phylogenetic position of aquificales based on the whole genome sequences of six aquificales species. | species belonging to the order aquificales are believed to be an early branching lineage within the bacteria. however, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the aquificales should be grouped with ε-proteobacteria. to investigate the phylogenetic position of aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six aquificales species based on the co ... | 2012 | 22844640 |
| structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase. | leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ... | 2012 | 22683997 |
| rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor. | protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ... | 2012 | 22661575 |
| structure of escherichia coli aspartate α-decarboxylase asn72ala: probing the role of asn72 in pyruvoyl cofactor formation. | the crystal structure of the asn72ala site-directed mutant of escherichia coli aspartate α-decarboxylase (adc) has been determined at 1.7 å resolution. the refined structure is consistent with the presence of a hydrolysis product serine in the active site in place of the pyruvoyl group required for catalysis, which suggests that the role of asn72 is to protect the ester formed during adc activation from hydrolysis. in previously determined structures of activated adc, including the wild type and ... | 2012 | 22505409 |
| chemoinformatic identification of novel inhibitors against mycobacterium tuberculosis l-aspartate α-decarboxylase. | l-aspartate α-decarboxylase (adc) belongs to a class of pyruvoyl dependent enzymes and catalyzes the conversion of aspartate to β-alanine in the pantothenate pathway, which is critical for the growth of several micro-organisms, including mycobacterium tuberculosis (mtb). its presence only in micro-organisms, fungi and plants and its absence in animals, particularly human, make it a promising drug target. we have followed a chemoinformatics-based approach to identify potential drug-like inhibitor ... | 2012 | 22470451 |
| genetic recombination in bacillus subtilis: a division of labor between two single-strand dna-binding proteins. | we have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) dna-binding proteins from bacillus subtilis, ssba and ssbb. during transformation, ssbb localizes at the dna entry pole where it binds and protects internalized ssdna. the 2.8-å resolution structure of ssbb bound to ssdna reveals a similar overall protein architecture and ssdna-binding surface to that of escherichia coli ssb. ssba, which binds ssdna with higher affinity than ssbb, co-assembles ont ... | 2012 | 22373918 |
| new insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine. | transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (cp) to an amine. although aspartate transcarbamylase and ornithine transcarbamylase (otc) are well characterized, little was known about putrescine transcarbamylase (ptc), the enzyme that generates cp for atp production in the fermentative catabolism of agmatine. we demonstrate that ptc (from enterococcus faecalis), in addition to using putrescine, can utilize l-ornithine as a poor substrate. crystal structures at 2.5 ... | 2012 | 22363663 |
| substrate channeling in proline metabolism. | proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. one intermediate is pyrroline-5-carboxylate (p5c), which upon hydrolysis opens to glutamic semialdehyde (gsa). recent structural and kinetic evidence indicate substrate channeling of p5c/gsa occurs in the proline catabol ... | 2012 | 22201749 |
| in planta mutagenesis of src homology 3 domain-like fold of ndhs, a ferredoxin-binding subunit of the chloroplast nadh dehydrogenase-like complex in arabidopsis: a conserved arg-193 plays a critical role in ferredoxin binding. | chloroplast nadh dehydrogenase-like (ndh) complex mediates cyclic electron transport around photosystem i and chlororespiration in angiosperms. the src homology 3 domain (sh3)-like fold protein ndhs/crr31 is an ndh subunit that is necessary for high affinity binding of ferredoxin, indicating that chloroplast ndh functions as a ferredoxin:plastoquinone oxidoreductase. however, the mechanism of the interaction between ndhs and ferredoxin is unclear. in this study, we analyzed their interaction in ... | 2013 | 24225949 |
| a novel type of n-acetylglutamate synthase is involved in the first step of arginine biosynthesis in corynebacterium glutamicum. | arginine biosynthesis in corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by n-acetylglutamate synthase (nags). there are different kinds of known nagss, for example, "classical" arga, bifunctional argj, argo, and s-nags. however, since c. glutamicum possesses a monofunctional argj, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown nags gene. | 2013 | 24138314 |
| archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in sulfolobus acidocaldarius. | in this study, the in vitro and in vivo functions of the only two identified protein phosphatases, saci-ptp and saci-pp2a, in the crenarchaeal model organism sulfolobus acidocaldarius were investigated. biochemical characterization revealed that saci-ptp is a dual-specific phosphatase (against pser/pthr and ptyr), whereas saci-pp2a exhibited specific pser/pthr activity and inhibition by okadaic acid. deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, wh ... | 2013 | 24078887 |
| the tetr family of regulators. | the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ... | 2013 | 24006471 |
| cloning and characterization of ef-tu and ef-ts from pseudomonas aeruginosa. | we have cloned genes encoding elongation factors ef-tu and ef-ts from pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. sequence analysis indicated that p. aeruginosa ef-tu and ef-ts are 84% and 55% identical to e. coli counterparts, respectively. p. aeruginosa ef-tu was active when assayed in gdp exchange assays. kinetic parameters for the interaction of ef-tu with gdp in the absence of ef-ts were observed to be k m = 33 μm, k cat (obs) = 0.003 s(-1 ... | 2013 | 23984384 |
| the glove-like structure of the conserved membrane protein tatc provides insight into signal sequence recognition in twin-arginine translocation. | in bacteria, two signal-sequence-dependent secretion pathways translocate proteins across the cytoplasmic membrane. although the mechanism of the ubiquitous general secretory pathway is becoming well understood, that of the twin-arginine translocation pathway, responsible for translocation of folded proteins across the bilayer, is more mysterious. tatc, the largest and most conserved of three integral membrane components, provides the initial binding site of the signal sequence prior to pore ass ... | 2013 | 23583035 |
| determination of the structure of the catabolic n-succinylornithine transaminase (astc) from escherichia coli. | escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (astc) and the other anabolic (argd), that participate in l-arginine metabolism. although only 58% identical, the enzymes have been shown to be functionally interchangeable. here we have purified astc and have obtained x-ray crystal structures of apo and holo-astc and of the enzyme complexed with its physiological substrate, succinylornithine. we compare the structures obtained in this study with those of argd from sa ... | 2013 | 23484010 |
| shallow breathing: bacterial life at low o(2). | competition for molecular oxygen (o(2)) among respiratory microorganisms is intense because o(2) is a potent electron acceptor. this competition leads to the formation of microoxic environments wherever microorganisms congregate in aquatic, terrestrial and host-associated communities. bacteria can harvest o(2) present at low, even nanomolar, concentrations using high-affinity terminal oxidases. here, we report the results of surveys searching for high-affinity terminal oxidase genes in sequenced ... | 2013 | 23411864 |
| the variability of the 16s rrna gene in bacterial genomes and its consequences for bacterial community analyses. | 16s ribosomal rna currently represents the most important target of study in bacterial ecology. its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. here we use the information from sequenced bacterial genomes to explore the variability of 16s rrna sequences and copy numbers at various taxonomic levels and apply it to estimate bacterial genome an ... | 2013 | 23460914 |
| functional dissection of the multi-domain di-heme cytochrome c(550) from thermus thermophilus. | in bacteria, oxidation of sulfite to sulfate, the most common strategy for sulfite detoxification, is mainly accomplished by the molybdenum-containing sulfite:acceptor oxidoreductases (sors). bacterial sors are very diverse proteins; they can exist as monomers or homodimers of their core subunit, as well as heterodimers with an additional cytochrome c subunit. we have previously described the homodimeric sor from thermus thermophilus hb8 (sor(tthb8)), identified its physiological electron accept ... | 2013 | 23383080 |
| mechanism of tetracycline resistance by ribosomal protection protein tet(o). | tetracycline resistance protein tet(o), which protects the bacterial ribosome from binding the antibiotic tetracycline, is a translational gtpase with significant similarity in both sequence and structure to the elongation factor ef-g. here, we present an atomic model of the tet(o)-bound 70s ribosome based on our cryo-electron microscopic reconstruction at 9.6-å resolution. this atomic model allowed us to identify the tet(o)-ribosome binding sites, which involve three characteristic loops in dom ... | 2013 | 23403578 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| uracil-dna glycosylases-structural and functional perspectives on an essential family of dna repair enzymes. | uracil-dna glycosylases (udgs) are evolutionarily conserved dna repair enzymes that initiate the base excision repair pathway and remove uracil from dna. the udg superfamily is classified into six families based on their substrate specificity. this review focuses on the family i enzymes since these are the most extensively studied members of the superfamily. the structural basis for substrate specificity and base recognition as well as for dna binding, nucleotide flipping and catalytic mechanism ... | 2014 | 25252105 |
| effect of the l499m mutation of the ascomycetous botrytis aclada laccase on redox potential and catalytic properties. | laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. these enzymes contain four cu atoms per molecule organized into three sites: t1, t2 and t3. in all laccases, the t1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. the redox potential of ... | 2014 | 25372682 |
| structural and biochemical characterization of chlamydia trachomatis hypothetical protein ct263 supports that menaquinone synthesis occurs through the futalosine pathway. | the obligate intracellular human pathogen chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. genomic sequencing of chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. in order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). the sources or biosynthetic pathways requir ... | 2014 | 25253688 |
| cocrystal structures of glycyl-trna synthetase in complex with trna suggest multiple conformational states in glycylation. | aminoacyl-trna synthetases are an ancient enzyme family that specifically charges trna molecules with cognate amino acids for protein synthesis. glycyl-trna synthetase (glyrs) is one of the most intriguing aminoacyl-trna synthetases due to its divergent quaternary structure and abnormal charging properties. in the past decade, mutations of human glyrs (hglyrs) were also found to be associated with charcot-marie-tooth disease. however, the mechanisms of traditional and alternative functions of hg ... | 2014 | 24898252 |
| metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. | | 2014 | 24758379 |
| natural competence and the evolution of dna uptake specificity. | many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ... | 2014 | 24488316 |
| chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence. | we previously proposed that in chlamydiaceae rapid vegetative growth and a quiescent state of survival (persistence) depend upon alternative protein translational profiles dictated by host tryptophan (trp) availability. these alternative profiles correspond, respectively, with a set of chlamydial proteins having higher-than-predicted contents of trp ("up-trp" selection), or with another set exhibiting lower-than-predicted contents of trp ("down-trp" selection). a comparative evaluation of chlamy ... | 2014 | 24616884 |
| crystal structure and putative substrate identification for the entamoeba histolytica low molecular weight tyrosine phosphatase. | entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. we have characterized the e. histolytica putative low molecular weight protein tyrosine phosphatase (lmw-ptp). the structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. in amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. a mutant lm ... | 2014 | 24548880 |
| origin and evolution of the peptidyl transferase center from proto-trnas. | we tested the hypothesis of tamura (2011) [3] that molecules of trna gave origin to ribosomes, particularly to the peptidyl transferase center (ptc) of the 23s ribosomal rna. we reconstructed the ancestral sequences from all types of trna and compared them in their sequences with the current ptc of 23s ribosomal rna from different organisms. we built an ancestral sequence of proto-trnas that showed a remarkable overall identity of 50.53% with the catalytic site of ptc. we conclude that the pepti ... | 2014 | 24649398 |
| radical s-adenosylmethionine enzymes. | | 2014 | 24476342 |
| x-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and o2-reduction states. | during x-ray data collection from a multicopper oxidase (mco) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the x-ray-induced reduction of o2 to 2h2o at the trinuclear copper cluster (tnc) of the enzyme. in this work, 12 crystallographic structures of thermus thermophilus hb27 multicopper oxidase (tth-mco) in holo, apo and hg-bound forms and with different x-ray absorbed doses have been determined. in holo tth-mco structures w ... | 2015 | 26627648 |
| colombos v3.0: leveraging gene expression compendia for cross-species analyses. | colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ... | 2015 | 26586805 |
| colombos v3.0: leveraging gene expression compendia for cross-species analyses. | colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ... | 2015 | 26586805 |
| high-resolution structures of lactobacillus salivarius transketolase in the presence and absence of thiamine pyrophosphate. | probiotic bacterial strains have been shown to enhance the health of the host through a range of mechanisms including colonization, resistance against pathogens, secretion of antimicrobial compounds and modulation of the activity of the innate immune system. lactobacillus salivarius ucc118 is a well characterized probiotic strain which survives intestinal transit and has many desirable host-interaction properties. probiotic bacteria display a wide range of catabolic activities, which determine t ... | 2015 | 26457526 |
| structural basis of transcription inhibition by cbr hydroxamidines and cbr pyrazoles. | cbr hydroxamidines are small-molecule inhibitors of bacterial rna polymerase (rnap) discovered through high-throughput screening of synthetic-compound libraries. cbr pyrazoles are structurally related rnap inhibitors discovered through scaffold hopping from cbr hydroxamidines. cbr hydroxamidines and pyrazoles selectively inhibit gram-negative bacterial rnap and exhibit selective antibacterial activity against gram-negative bacteria. here, we report crystal structures of the prototype cbr hydroxa ... | 2015 | 26190576 |
| structural biology of bacterial rna polymerase. | since its discovery and characterization in the early 1960s (hurwitz, j. the discovery of rna polymerase. j. biol. chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial rna polymerase (rnap). in the late 1990s, structural information pertaining to bacterial rnap has emerged that provided unprecedented insights into the function and mechanism of rna transcription. in this review, i list all structures related to bacterial rn ... | 2015 | 25970587 |
| 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 |
| filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates. | chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ... | 2010 | 20042599 |
| filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates. | chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ... | 2010 | 20042599 |
| tmrdb (tmrna database). | the tmrna database (tmrdb) is maintained at the university of texas health science center at tyler, texas, and is accessible on the www at url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.++ +html. a tmrdb mirror site is located on the campus of auburn university, auburn, alabama, reachable at the url http://www.ag.auburn.edu/mirror/tmrdb/. since april 1997, the tmrdb has provided sequences of tmrna (previously called 10sa rna), a molecule present in most bacteria and some organelles. this release ad ... | 2000 | 10592214 |
| the renaissance of aminoacyl-trna synthesis. | the role of trna as the adaptor in protein synthesis has held an enduring fascination for molecular biologists. over four decades of study, taking in numerous milestones in molecular biology, led to what was widely held to be a fairly complete picture of how trnas and amino acids are paired prior to protein synthesis. however, recent developments in genomics and structural biology have revealed an unexpected array of new enzymes, pathways and mechanisms involved in aminoacyl-trna synthesis. as a ... | 2001 | 11375928 |
| modularity and specialization in superfamily 1 and 2 helicases. | | 2002 | 11889086 |
| the trna world. | | 2004 | 14970379 |
| the acetate switch. | to succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. one such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. this review explains why, when, and how cells excrete or dissimilate acetate. the central components of the "switch" (phos ... | 2005 | 15755952 |
| secretion by numbers: protein traffic in prokaryotes. | almost all aspects of protein traffic in bacteria were covered at the asm-fems meeting on the topic in iraklio, crete in may 2006. the studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. among the highlights from the meeting that are reviewed here are the molecular dynamics of seca protein, membrane protein insertion, type iii secretion needles and chaperones, type iv secretion, th ... | 2006 | 17020575 |
| crystal structure of rlmm, the 2'o-ribose methyltransferase for c2498 of escherichia coli 23s rrna. | rlmm (ygde) catalyzes the s-adenosyl methionine (adomet)-dependent 2'o methylation of c2498 in 23s ribosomal rna (rrna) of escherichia coli. previous experiments have shown that rlmm is active on 23s rrna from an rlmm knockout strain but not on mature 50s subunits from the same strain. here, we demonstrate rlmm methyltransferase (mtase) activity on in vitro transcribed 23s rrna and its domain v. we have solved crystal structures of e. coli rlmm at 1.9 å resolution and of an rlmm-adomet complex a ... | 2012 | 22923526 |
| low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition. | previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. however, the relationship between high and low temperature adaptations remains unclear. to investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substit ... | 2015 | 26614525 |
| tie me up, tie me down: inhibiting rna polymerase. | mechanistic understanding of antibiotic action can yield crucial insights that aid in the design of new antibiotics. in this issue, mukhopadhyay et al. (2008) uncover the mechanism by which the antibiotic myxopyronin inhibits bacterial rna polymerase, suggesting a new target region in rna polymerase for inhibitor design. | 2008 | 18957193 |
| new target for inhibition of bacterial rna polymerase: 'switch region'. | a new drug target - the 'switch region' - has been identified within bacterial rna polymerase (rnap), the enzyme that mediates bacterial rna synthesis. the new target serves as the binding site for compounds that inhibit bacterial rna synthesis and kill bacteria. since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. since the new target is different from targets of other antibacterial agents, com ... | 2011 | 21862392 |
| structure-based ligand design of novel bacterial rna polymerase inhibitors. | bacterial rna polymerase (rnap) is essential for transcription and is an antibacterial target for small molecule inhibitors. the binding region of myxopyronin b (myxb), a bacterial rnap inhibitor, offers the possibility of new inhibitor design. the molecular design program sprout has been used in conjunction with the x-ray cocrystal structure of thermus thermophilus rnap with myxb to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. a series of molecules, with molecular ... | 2011 | 24900260 |
| frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in staphylococcus aureus. | the antibiotic myxopyronin (myx) functions by inhibiting bacterial rna polymerase (rnap). the binding site on rnap for myx-the rnap "switch region sw1/sw2 subregion"-is different from the binding site on rnap for the rnap inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (rif). here, we report the frequency, spectrum, and fitness costs of myx resistance in staphylococcus aureus. the resistance rate for myx is 4 × 10(-8) to 7 × 10(-8) per generation, which is equal within ... | 2012 | 23006749 |
| new mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. | the acel_2062 protein from acidothermus cellulolyticus is a protein of unknown function. initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (hexxhxxgxxd). the acel_2062 protein was chosen by the joint center for structural genomics for crystal structure determination to explore novel protein seq ... | 2014 | 24383880 |
| 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 |