| estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. | for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ... | 2011 | 22101334 |
| Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase. | The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ... | 2011 | 22128181 |
| Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase. | The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ... | 2011 | 22128181 |
| mass spectrometry of intact v-type atpases reveals bound lipids and the effects of nucleotide binding. | the ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. much less clear is the fate of membrane-embedded molecular machines in the gas phase. here we show that rotary adenosine triphosphatases (atpases)/synthases from thermus thermophilus and enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. mass spectra reveal subuni ... | 2011 | 22021858 |
| translational diffusion of macromolecular assemblies measured using transverse-relaxation-optimized pulsed field gradient nmr. | in structural biology, pulsed field gradient (pfg) nmr spectroscopy for the characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution conditions as used for nmr structure determination or for crystallization trials. this paper describes two transverse-relaxation-optimized (tro) (15)n-filtered pfg stimulated-echo (ste) experiments for studies of macromolecular translational d ... | 2011 | 21919531 |
| Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. | The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ... | 2011 | 22179038 |
| Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. | The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ... | 2011 | 22179038 |
| Structure and Function of the Small MutS-Related Domain. | MutS family proteins are widely distributed in almost all organisms from bacteria to human and play central roles in various DNA transactions such as DNA mismatch repair and recombinational events. The small MutS-related (Smr) domain was originally found in the C-terminal domain of an antirecombination protein, MutS2, a member of the MutS family. MutS2 is thought to suppress homologous recombination by endonucleolytic resolution of early intermediates in the process. The endonuclease activity of ... | 2011 | 22091410 |
| Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. | Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkh ... | 2011 | 21904051 |
| structural basis of free reduced flavin generation by flavin reductase from thermus thermophilus hb8. | free reduced flavins are involved in a variety of biological functions. they are generated from nad(p)h by flavin reductase via co-factor flavin bound to the enzyme. although recent findings on the structure and function of flavin reductase provide new information about co-factor fad and substrate nad, there have been no reports on the substrate flavin binding site. here we report the structure of ttha0420 from thermus thermophilus hb8, which belongs to flavin reductase, and describe the dual bi ... | 2011 | 22052907 |
| Molecular basis of dihydrouridine formation on tRNA. | Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes ... | 2011 | 22123979 |
| Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus. | Methyltransferases form a major class of tRNA-modifying enzymes that are needed for the proper functioning of tRNA. Here, the expression, purification and crystallization of two related putative tRNA methyltransferases from two kingdoms of life are reported. The protein encoded by the gene pf1002 from the archaeon Pyrococcus furiosus was crystallized in the monoclinic space group P2(1). A complete data set was collected to 2.2 Å resolution. The protein encoded by the gene ttc1157 from the eubact ... | 2011 | 22102250 |
| Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation. | Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted ... | 2011 | 22007758 |
| type-2 isopentenyl diphosphate isomerase: evidence for a stepwise mechanism. | isopentenyl diphosphate isomerase (idi) catalyzes the interconversion of isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp). these two molecules are the building blocks for construction of isoprenoid carbon skeletons in nature. two structurally unrelated forms of idi are known. a variety of studies support a proton addition/proton elimination mechanism for both enzymes. during studies with thermus thermophilus idi-2, we discovered that the olefinic hydrogens of a vinyl thiomethy ... | 2011 | 22047048 |
| adaptation to trna acceptor stem structure by flexible adjustment in the catalytic domain of class i trna synthetases. | class i aminoacyl-trna synthetases (aarss) use a rossmann-fold domain to catalyze the synthesis of aminoacyl-trnas required for decoding genetic information. while the rossmann-fold domain is conserved in evolution, the acceptor stem near the aminoacylation site varies among trna substrates, raising the question of how the conserved protein fold adapts to rna sequence variations. of interest is the existence of an unpaired c-a mismatch at the 1-72 position unique to bacterial initiator trna(fmet ... | 2011 | 22184460 |
| Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity. | The bacterium Myxococcus xanthus uses a G protein cycle to dynamically regulate the leading/lagging pole polarity axis. The G protein MglA is regulated by its GTPase-activating protein (GAP) MglB, thus resembling Ras family proteins. Here, we show structurally and biochemically that MglA undergoes a dramatic, GDP-GTP-dependent conformational change involving a screw-type forward movement of the central ß2-strand, never observed in any other G protein. This movement and complex formation with Mgl ... | 2011 | 21847100 |
| termination of protein synthesis in mammalian mitochondria. | all mechanisms of protein synthesis can be considered in four stages: initiation, elongation, termination, and ribosome recycling. remarkable progress has been made in understanding how these processes are mediated in the cytosol of many species; however, details of organellar protein synthesis remain sketchy. this is an important omission, as defects in human mitochondrial translation are known to cause disease and may contribute to the aging process itself. in this minireview, we focus on the ... | 2011 | 21873426 |
| structural basis for leucine-induced allosteric activation of glutamate dehydrogenase. | glutamate dehydrogenase (gdh) catalyzes reversible conversion between glutamate and 2-oxoglutarate using nad(p)(h) as a coenzyme. although mammalian gdh is regulated by gtp through the antenna domain, little is known about the mechanism of allosteric activation by leucine. an extremely thermophilic bacterium, thermus thermophilus, possesses gdh with a unique subunit configuration composed of two different subunits, gdha (regulatory subunit) and gdhb (catalytic subunit). t. thermophilus gdh is un ... | 2011 | 21900230 |
| crystal structure of the central axis df complex of the prokaryotic v-atpase. | v-atpases function as atp-dependent ion pumps in various membrane systems of living organisms. atp hydrolysis causes rotation of the central rotor complex, which is composed of the central axis d subunit and a membrane c ring that are connected by f and d subunits. here we determined the crystal structure of the df complex of the prokaryotic v-atpase of enterococcus hirae at 2.0-å resolution. the structure of the d subunit comprised a long left-handed coiled coil with a unique short β-hairpin re ... | 2011 | 22114184 |
| Crystal structure of the NurA-dAMP-Mn2+ complex. | Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ... | 2011 | 22064858 |
| Crystal structure of the NurA-dAMP-Mn2+ complex. | Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ... | 2011 | 22064858 |
| structure and activity of the cas3 hd nuclease mj0384, an effector enzyme of the crispr interference. | clustered regularly interspaced short palindromic repeats (crisprs) and cas proteins represent an adaptive microbial immunity system against viruses and plasmids. cas3 proteins have been proposed to play a key role in the crispr mechanism through the direct cleavage of invasive dna. here, we show that the cas3 hd domain protein mj0384 from methanocaldococcus jannaschii cleaves endonucleolytically and exonucleolytically (3'-5') single-stranded dnas and rnas, as well as 3'-flaps, splayed arms, and ... | 2011 | 22009198 |
| Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus. | The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ... | 2011 | 22079199 |
| Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus. | The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ... | 2011 | 22079199 |
| Profile of Venkatraman Ramakrishnan. Interview by Prashant Nair. | | 2011 | 21914843 |
| kinetic studies of the reactions of o(2) and no with reduced thermus thermophilus ba(3) and bovine aa(3) using photolabile carriers. | the reactions of molecular oxygen (o(2)) and nitric oxide (no) with reduced thermus thermophilus (tt) ba(3) and bovine heart aa(3) were investigated by time-resolved optical absorption spectroscopy to establish possible relationships between the structural diversity of these enzymes and their reaction dynamics. to determine whether the photodissociated carbon monoxide (co) in the co flow-flash experiment affects the ligand binding dynamics, we monitored the reactions in the absence and presence ... | 2011 | 22201543 |
| the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna. | the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ... | 2011 | 22079365 |
| the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna. | the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ... | 2011 | 22079365 |
| simultaneous polyhydroxyalkanoates and rhamnolipids production by thermus thermophilus hb8. | abstract: the ability of thermus thermophilus hb8 to produce simultaneously two environmentally-friendly biodegradable products, polyhydroxyalkanoates (phas) and rhamnolipids (rls), using either sodium gluconate or glucose as sole carbon source, was demonstrated. the utilization of sodium gluconate resulted in higher levels of phas and rls production than when glucose was used as sole carbon source. the initial phosphate concentration (as po43-) influences both phas and rls productions that were ... | 2011 | 21906373 |
| Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8. | Methylenetetrahydrofolate reductase (MTHFR) is one of the enzymes involved in homocysteine metabolism. Despite considerable genetic and clinical attention, the reaction mechanism and regulation of this enzyme are not fully understood because of difficult production and poor stability. While recombinant enzymes from thermophilic organisms are often stable and easy to prepare, properties of thermostable MTHFRs have not yet been reported. | 2011 | 21858212 |
| bioinformatic analysis of leishmania donovani long-chain fatty acid-coa ligase as a novel drug target. | fatty acyl-coa synthetase (fatty acid: coa ligase, amp-forming; (ec 6.2.1.3)) catalyzes the formation of fatty acyl-coa by a two-step process that proceeds through the hydrolysis of pyrophosphate. fatty acyl-coa represents bioactive compounds that are involved in protein transport, enzyme activation, protein acylation, cell signaling, and transcriptional control in addition to serving as substrates for beta oxidation and phospholipid biosynthesis. fatty acyl-coa synthetase occupies a pivotal rol ... | 2011 | 22091399 |
| Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized. | In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ... | 2011 | 22122402 |
| Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized. | In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ... | 2011 | 22122402 |
| Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs. | The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ... | 2011 | 22105070 |
| Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs. | The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ... | 2011 | 22105070 |
| Loss of elongation factor p disrupts bacterial outer membrane integrity. | Elongation factor P (EF-P) is posttranslationally modified at a conserved lysyl residue by the coordinated action of two enzymes, PoxA and YjeK. We have previously established the importance of this modification in Salmonella stress resistance. Here we report that, like poxA and yjeK mutants, Salmonella strains lacking EF-P display increased susceptibility to hypoosmotic conditions, antibiotics, and detergents and enhanced resistance to the compound S-nitrosoglutathione. The susceptibility pheno ... | 2012 | 22081389 |
| pseudomonas aeruginosa 4-amino-4-deoxychorismate lyase: spatial conservation of an active site tyrosine and classification of two types of enzyme. | 4-amino-4-deoxychorismate lyase (pabc) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. this is an essential activity for the growth of gram-negative bacteria, including important pathogens such as pseudomonas aeruginosa. a high-resolution (1.75 å) crystal structure of pabc from p. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. residues around the pyridoxal 5'-phosphate cofactor are high ... | 2011 | 21935381 |
| Crystal structures of an archaeal class II DNA photolyase and its complex with UV-damaged duplex DNA. | Class II photolyases ubiquitously occur in plants, animals, prokaryotes and some viruses. Like the distantly related microbial class I photolyases, these enzymes repair UV-induced cyclobutane pyrimidine dimer (CPD) lesions within duplex DNA using blue/near-UV light. Methanosarcina mazei Mm0852 is a class II photolyase of the archaeal order of Methanosarcinales, and is closely related to plant and metazoan counterparts. Mm0852 catalyses light-driven DNA repair and photoreduction, but in contrast ... | 2011 | 21892138 |
| structures of phosphopantetheine adenylyltransferase from burkholderia pseudomallei. | phosphopantetheine adenylyltransferase (ppat) catalyzes the fourth of five steps in the coenzyme a biosynthetic pathway, reversibly transferring an adenylyl group from atp onto 4'-phosphopantetheine to yield dephospho-coenzyme a and pyrophosphate. burkholderia pseudomallei is a soil- and water-borne pathogenic bacterium and the etiologic agent of melioidosis, a potentially fatal systemic disease present in southeast asia. two crystal structures are presented of the ppat from b. pseudomallei with ... | 2011 | 21904046 |
| Overexpression, crystallization and preliminary X-ray crystallographic analysis of shikimate dehydrogenase from Archaeoglobus fulgidus. | Shikimate dehydrogenase (SDH), which catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway, is an attractive target for the development of herbicides and antimicrobial agents. Previous structural studies have shown that SDH exists in two conformations, an open and a closed form, and it is believed that the conformational state is crucial to understanding its catalytic mechanism. In order to facilitate further structural comparisons among SDHs, includ ... | 2011 | 22139165 |
| Systematic chromosomal deletion of bacterial ribosomal protein genes. | Detailed studies of ribosomal proteins (RPs), essential components of the protein biosynthetic machinery, have been hampered by the lack of readily accessible chromosomal deletions of the corresponding genes. Here, we report the systematic genomic deletion of 41 individual RP genes in Escherichia coli, which are not included in the Keio collection. Chromosomal copies of these genes were replaced by an antibiotic resistance gene in the presence of an inducible, easy-to-exchange plasmid-born allel ... | 2011 | 21945294 |
| antimutator variants of dna polymerases. | evolution balances dna replication speed and accuracy to optimize replicative fitness and genetic stability. there is no selective pressure to improve dna replication fidelity beyond the background mutation rate from other sources, such as dna damage. however, dna polymerases remain amenable to amino acid substitutions that lower intrinsic error rates. here, we review these 'antimutagenic' changes in dna polymerases and discuss what they reveal about mechanisms of replication fidelity. pioneerin ... | 2011 | 21977975 |
| Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage. | Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ... | 2011 | 22167184 |
| Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage. | Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ... | 2011 | 22167184 |
| The role of E. coli Nus-factors in transcription regulation and transcription:translation coupling: From structure to mechanism. | Bacterial transcription mediated by RNA polymerase (RNAP) is a highly regulated process and RNAP action is modulated during the different phases of initiation, elongation and termination by proteins such as the Escherichia coli Nus transcription-factors. Here we discuss the structural interplay and the mechanistic role of the Nus-factors that are directly involved in the processivity of elongation, transcription:translation coupling and termination, as well as the varying effects of these protei ... | 2011 | 21922055 |
| neutrons, magnets, and photons: a career in structural biology. | the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ... | 2011 | 22086921 |
| neutrons, magnets, and photons: a career in structural biology. | the purpose of reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. they enjoy this activity so much that your editor, martha fedor, must have known that i would accept her invitation to write such an article, no matter how much i demurred at first. as everyone knows, flattery will get you everywhere. it may comfort the apprehensive reader to learn that there is not going to be much walking to schoo ... | 2011 | 22086921 |
| a photolyase-like protein from agrobacterium tumefaciens with an iron-sulfur cluster. | photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. while photolyases can repair uv-induced dna lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. here we report about two photolyase-related proteins, named phra and phrb, found in the phytopathogen agrobacterium tumefaciens. phra belongs to the class iii cyclobutane pyrimidine dimer (cpd) photolyases, the sister class of plant ... | 2011 | 22066008 |
| Functional characterization of the RuvB homologs from Mycoplasma pneumoniae and Mycoplasma genitalium. | Homologous recombination between repeated DNA elements in the genomes of Mycoplasma species has been hypothesized to be a crucial causal factor in sequence variation of antigenic proteins at the bacterial surface. To investigate this notion, studies were initiated to identify and characterize the proteins that form part of the homologous DNA recombination machinery in Mycoplasma pneumoniae as well as Mycoplasma genitalium. Among the most likely participants of this machinery are homologs of the ... | 2011 | 21949077 |
| Biosynthesis of the Pseudomonas aeruginosa Extracellular Polysaccharides, Alginate, Pel, and Psl. | Pseudomonas aeruginosa thrives in many aqueous environments and is an opportunistic pathogen that can cause both acute and chronic infections. Environmental conditions and host defenses cause differing stresses on the bacteria, and to survive in vastly different environments, P. aeruginosa must be able to adapt to its surroundings. One strategy for bacterial adaptation is to self-encapsulate with matrix material, primarily composed of secreted extracellular polysaccharides. P. aeruginosa has the ... | 2011 | 21991261 |
| Probing the mechanistic role of the long a-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis. | The C-terminus of the NuoL subunit of Complex I includes a long amphipathic a-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the ... | 2011 | 22060017 |
| Identification, tissue distribution, and molecular modeling of novel human isoforms of the key enzyme in sialic acid synthesis, UDP-GlcNAc 2-epimerase/ManNAc kinase. | UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) catalyzes the first two committed steps in sialic acid synthesis. In addition to the three previously described human GNE isoforms (hGNE1-hGNE3), our database and polymerase chain reaction analysis yielded five additional human isoforms (hGNE4-hGNE8). hGNE1 is the ubiquitously expressed major isoform, while the hGNE2-hGNE8 isoforms are differentially expressed and may act as tissue-specific regulators of sialylation. hGNE2 and hGNE7 display a 31-residue ... | 2011 | 21910480 |
| Is the sequence-specific binding of aminoacyl-tRNAs by EF-Tu universal among bacteria? | Three base pairs in the T-stem are primarily responsible for the sequence-specific interaction of tRNA with Escherichia coli and Thermus thermophilus EF-Tu. While the amino acids on the surface of EF-Tu that contact aminoacyl-tRNA (aa-tRNA) are highly conserved among bacteria, the T-stem sequences of individual tRNA are variable, making it unclear whether or not this protein-nucleic acid interaction is also sequence specific in other bacteria. We propose and validate a thermodynamic model that p ... | 2011 | 21893586 |
| insights into folate/fad-dependent trna methyltransferase mechanism: role of two highly conserved cysteines in catalysis. | the flavoprotein trmfo methylates specifically the c5 carbon of the highly conserved uridine 54 in trnas. contrary to most methyltransferases, the 1-carbon unit transferred by trmfo derives from 5,10-methylenetetrahydrofolate and not from s-adenosyl-l-methionine. the enzyme also employs the fad hydroquinone as a reducing agent of the c5 methylene u54-trna intermediate in vitro. by analogy with the catalytic mechanism of thymidylate synthase thya, a conserved cysteine located near the fad isoallo ... | 2011 | 21846722 |
| crystallization and preliminary x-ray diffraction of the first periplasmic domain of secdf, a translocon-associated membrane protein, from thermus thermophilus. | a membrane-integrated sec component, secdf, associates with the secyeg protein-conducting channel and facilitates protein secretion and membrane-protein integration. secdf contains 12 transmembrane helices and two periplasmic domains. the first periplasmic domain (p1) plays an important role in protein translocation. here, the overexpression, purification and crystallization of the p1 domain of thermus thermophilus secdf are reported. the crystals diffracted x-rays to 2.3 å resolution and belong ... | 2011 | 22102233 |
| initiation factor eif2γ promotes eif2-gtp-met-trnai(met) ternary complex binding to the 40s ribosome. | in contrast to prokaryotic elongation factor ef-tu, which delivers aminoacyl-trnas to the ribosomal a-site, eukaryotic initiation factor eif2 binds methionyl initiator transfer rna (met-trna(i)(met)) to the p-site of the 40s ribosomal subunit. the results of directed hydroxyl radical probing experiments to map binding of saccharomyces cerevisiae eif2 on the ribosome and on met-trna(i)(met) revealed that eif2γ primarily contacts the acceptor stem of met-trna(i)(met) and identified a key binding i ... | 2011 | 22002225 |
| expression and cellular localization of inducible nitric oxide synthase in lipopolysaccharide-treated rat kidneys. | | 2012 | 22260992 |
| physiology of resistant deinococcus geothermalis bacterium aerobically cultivated in low manganese medium. | this dynamic proteome study describes the physiology of growth and survival of deinococcus geothermalis, in conditions simulating paper machine waters being aerobic, warm, and low in carbon and manganese. industrial environment of this species differ from its natural habitats, geothermal springs and deep ocean subsurfaces, by being highly exposed to oxygen. quantitative proteome analysis using two-dimensional gel electrophoresis and bioinformatic tools showed expression change for 165 proteins f ... | 2012 | 22228732 |
| construction and transformation of a thermotoga-e. coli shuttle vector. | abstract: background: thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. they may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. a lack of genetic tools has hampered the investigation and application of these organisms. this study aims to develop a genetic transfer system for thermotoga spp.. results: methods for preparing and handling thermotoga solid cultures under aerobic condi ... | 2012 | 22225774 |
| key role of two ftsa terminal domains in its bidirectional polymerization. | the effect of two different truncations involving either the 1c domain or the simultaneous absence of the s12-13 β-strands of the ftsa protein from streptococcus pneumoniae, located at opposite terminal sides in the molecular structure, suggests that they are essential for atp-dependent polymerization. these two truncated proteins are not able to polymerize themselves but can be incorporated to some extent into the ftsa+ polymers during the assembling process. consequently, they block the growth ... | 2012 | 22247552 |
| structural changes that occur upon photolysis of the fe(ii)(a3)-co complex in the cytochrome ba(3)-oxidase of thermus thermophilus: a combined x-ray crystallographic and infrared spectral study demonstrates co binding to cu(b). | the purpose of the work was to provide a crystallographic demonstration of the venerable idea that co photolyzed from ferrous heme-a(3) moves to the nearby cuprous ion in the cytochrome c oxidases. crystal structures of co-bound cytochrome ba(3)-oxidase from thermus thermophilus, determined at ~2.8-3.2å resolution, reveal a fe-c distance of ~2.0å, a cu-o distance of 2.4å and a fe-c-o angle of ~126°. upon photodissociation at 100k, x-ray structures indicate loss of fe(a3)-co and appearance of cu( ... | 2011 | 22226917 |
| structural and biochemical characterization of hp0315 from helicobacter pylori as a vapd protein with an endoribonuclease activity. | vapd-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3d structure of these proteins. recently, a relationship between the cas2 family of ribonucleases associated with the crispr system of microbial immunity and vapd was suggested. here, we show for the first time the structure of a member of the vapd family and present a relationship of vapd with cas2 family and toxin-antitoxin (ta) systems. the crystal structure o ... | 2012 | 22241770 |
| structure of the pilus assembly protein tadz from eubacterium rectale: implications for polar localization. | the tad (tight adherence) locus encodes a protein translocation system that produces a novel variant of type iv pili. the pilus assembly protein tadz (called cpae in caulobacter crescentus) is ubiquitous in tad loci, but is absent in other type iv pilus biogenesis systems. the crystal structure of tadz from eubacterium rectale (ertadz), in complex with atp and mg(2+) , was determined to 2.1 å resolution. ertadz contains an atypical atpase domain with a variant of a deviant walker-a motif that re ... | 2011 | 22211578 |
| structure of n-formylglycinamide ribonucleotide amidotransferase ii (purl) from thermus thermophilus hb8. | the crystal structure of purl from thermus thermophilus hb8 (ttpurl; ttha1519) was determined in complex with an adenine nucleotide, po(4)(3-) and mg(2+) at 2.35 å resolution. ttpurl consists of 29 α-helices and 28 β-strands, and one loop is disordered. ttpurl consists of four domains, a1, a2, b1 and b2, and the structures of the a1-b1 and a2-b2 domains were almost identical to each other. although the sequence identity between ttpurl and purl from thermotoga maritima (tmpurl) is higher than tha ... | 2012 | 22232163 |
| an unusual n-terminal ααβαββα fold of pilq from t. thermophilus mediates ring formation and is essential for piliation. | dna translocators of natural transformation systems are complex systems critical for the uptake of free dna and provide a powerful mechanism for adaptation to changing environmental conditions. in natural transformation machineries, outer membrane secretins are suggested to form a multimeric pore for the uptake of external dna. recently, we reported on a novel structure of the dna translocator secretin complex, pilq, in thermus thermophilus hb27 comprising a stable cone and cup structure and six ... | 2012 | 22253437 |
| mycobacterium tuberculosis rv2419c, the missing glucosyl-3-phosphoglycerate phosphatase for the second step in methylglucose lipopolysaccharide biosynthesis. | mycobacteria synthesize intracellular methylglucose lipopolysaccharides (mglp) proposed to regulate fatty acid synthesis. although their structures have been elucidated, the identity of most biosynthetic genes remains unknown. the first step in mglp biosynthesis is catalyzed by a glucosyl-3-phosphoglycerate synthase (gpgs, rv1208 in mycobacterium tuberculosis h37rv). however, a typical glucosyl-3-phosphoglycerate phosphatase (gpgp, ec3.1.3.70) for dephosphorylation of glucosyl-3-phosphoglycerate ... | 2011 | 22355692 |
| crystallization and preliminary neutron diffraction studies of adp-ribose pyrophosphatase-i from thermus thermophilus hb8. | adp-ribose pyrophosphatase-i from thermus thermophilus hb8 (ttadprase-i) prevents the intracellular accumulation of adp-ribose by hydrolyzing it to amp and ribose 5'-phosphate. to understand the catalytic mechanism of ttadprase-i, it is necessary to investigate the role of glutamates and metal ions as well as the coordination of water molecules located at the active site. a macroseeding method was developed in order to obtain a large ttadprase-i crystal which was suitable for a neutron diffracti ... | 2011 | 22232170 |
| characterization of the alkaline laccase ssl1 from streptomyces sviceus with unusual properties discovered by genome mining. | fungal laccases are well investigated enzymes with high potential in diverse applications like bleaching of waste waters and textiles, cellulose delignification, and organic synthesis. however, they are limited to acidic reaction conditions and require eukaryotic expression systems. this raises a demand for novel laccases without these constraints. we have taken advantage of the laccase engineering database lcced derived from genome mining to identify and clone the laccase ssl1 from streptomyces ... | 2012 | 23285009 |
| engineering the substrate specificity of a thermophilic penicillin acylase from thermus thermophilus. | a homologue of the escherichia coli penicillin acylase is encoded in the genomes of several thermophiles, including in different thermus thermophilus strains. although the natural substrate of this enzyme is not known, this acylase shows a marked preference for penicillin k over penicillin g. three-dimensional models were created in which the catalytic residues and the substrate binding pocket were identified. through rational redesign, residues were replaced to mimic the aromatic binding site o ... | 2012 | 23263966 |
| simultaneous quantification of mitochondrial dna damage and copy number in circulating blood: a sensitive approach to systemic oxidative stress. | systemic oxidative stress is associated with a wide range of pathological conditions. oxidative dna damage is frequently measured in circulating lymphocytes. mitochondrial dna (mtdna) is known to be more sensitive to oxidative damage than nuclear dna but is rarely used for direct measurement of dna damage in clinical studies. based on the supercoiling-sensitive real-time pcr method, we propose a new approach for the noninvasive monitoring of systemic oxidative stress by quantifying the mtdna str ... | 2012 | 23484085 |
| simultaneous quantification of mitochondrial dna damage and copy number in circulating blood: a sensitive approach to systemic oxidative stress. | systemic oxidative stress is associated with a wide range of pathological conditions. oxidative dna damage is frequently measured in circulating lymphocytes. mitochondrial dna (mtdna) is known to be more sensitive to oxidative damage than nuclear dna but is rarely used for direct measurement of dna damage in clinical studies. based on the supercoiling-sensitive real-time pcr method, we propose a new approach for the noninvasive monitoring of systemic oxidative stress by quantifying the mtdna str ... | 2012 | 23484085 |
| effect of lecithin on d-galactosamine induced hepatotoxicity through mitochondrial pathway involving bcl-2 and bax. | twenty four wistar strain albino rats were used for the investigations. lecithin 50 and 100 mg/kg b wt was administered for 1 week by oral route. liver damage was induced by intra peritoneal administration of 400 mg/kg b wt d-galactosamine on the last day. at the end of the study animals were sacrificed and liver enzyme levels, histopathology, mitochondrial integrity, expression of p53, bax and bcl-2 mrna levels were studied. increases in the liver enzyme levels by d-galn were significantly inhi ... | 2011 | 23024474 |
| a universal method for the identification of bacteria based on general pcr primers. | the universal method (um) described here will allow the detection of any bacterial rdna leading to the identification of that bacterium. the method should allow prompt and accurate identification of bacteria. the principle of the method is simple; when a pure pcr product of the 16s gene is obtained, sequenced, and aligned against bacterial dna data base, then the bacterium can be identified. confirmation of identity may follow. in this work, several general 16s primers were designed, mixed and a ... | 2011 | 23024404 |
| multiple conversion between the genes encoding bacterial class-i release factors. | bacteria require two class-i release factors, rf1 and rf2, that recognize stop codons and promote peptide release from the ribosome. rf1 and rf2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. this scenario expects that the two rf gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. however, we here report two independent cases of conversion b ... | 2015 | 26257102 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families. | the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ... | 2014 | 24931479 |
| intrastrand triplex dna repeats in bacteria: a source of genomic instability. | repetitive nucleic acid sequences are often prone to form secondary structures distinct from b-dna. prominent examples of such structures are dna triplexes. we observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. a systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the itxf database available online at http://bioinformatics.uni-konstanz.de/utils/itxf/ ... | 2015 | 26450966 |
| molecular mechanism and evolution of guanylate kinase regulation by (p)ppgpp. | the nucleotide (p)ppgpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. here, we characterize the molecular interaction between (p)ppgpp and guanylate kinase (gmk), revealing the importance of this interaction in adaptation to starvation. combining structural and kinetic analyses, we show that (p)ppgpp binds the gmk active site and competitively inhibits the enzyme. the (p)ppgpp-gmk interact ... | 2015 | 25661490 |
| horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein s4. | the universal ribosomal protein s4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. being part of the information processing machinery of the cell, the gene for s4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. here we report the evolution of ribosomal protein s4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (hgt) of s4 duri ... | 2009 | 19640295 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| the dynamic nature of genomes across the tree of life. | genomes are dynamic in lineages across the tree of life. among bacteria and archaea, for example, dna content varies throughout life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. these observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. here, we synthesize information on three aspects o ... | 2014 | 24500971 |
| the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015. | | 2015 | 26452528 |
| comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages. | genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples. | 2012 | 22676492 |
| dcia is an ancestral replicative helicase operator essential for bacterial replication initiation. | delivery of the replicative helicase onto dna is an essential step in the initiation of replication. in bacteria, dnac (in escherichia coli) and dnai (in bacillus subtilis) are representative of the two known mechanisms that assist the replicative helicase at this stage. here, we establish that these two strategies cannot be regarded as prototypical of the bacterial domain since dnac and dnai (dna[ci]) are present in only a few bacterial phyla. we show that dna[ci] was domesticated at least seve ... | 2016 | 27830752 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| determination of rna polymerase binding surfaces of transcription factors by nmr spectroscopy. | in bacteria, rna polymerase (rnap), the central enzyme of transcription, is regulated by n-utilization substance (nus) transcription factors. several of these factors interact directly, and only transiently, with rnap to modulate its function. as details of these interactions are largely unknown, we probed the rnap binding surfaces of escherichia coli (e. coli) nus factors by nuclear magnetic resonance (nmr) spectroscopy. perdeuterated factors with [(1)h,(13)c]-labeled methyl groups of val, leu, ... | 2015 | 26560741 |
| the eukaryotic translation initiation regulator cdc123 defines a divergent clade of atp-grasp enzymes with a predicted role in novel protein modifications. | deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. one such feature is the highly conserved, but poorly understood, eukaryotic protein cdc123, which regulates the abundance of the eukaryotic translation initiation eif2 complex and binds one of its components eif2γ. we show that the eukaryotic protein cdc123 defines a novel clade of atp-grasp enzymes distinguished from all other members o ... | 2015 | 25976611 |
| a novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. | domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. | 2007 | 17250770 |
| two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. | several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ... | 2010 | 20459678 |
| type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. | pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ... | 2013 | 24148833 |
| molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers. | highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ... | 2014 | 26019546 |
| genome signature difference between deinococcus radiodurans and thermus thermophilus. | the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ... | 2012 | 22500246 |
| phylogenomics of prokaryotic ribosomal proteins. | archaeal and bacterial ribosomes contain more than 50 proteins, including 34 that are universally conserved in the three domains of cellular life (bacteria, archaea, and eukaryotes). despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. we developed an automated computational pipeline for identification of r-protein genes and applied it to 995 completely sequenced bacterial and 87 arch ... | 2012 | 22615861 |
| evolution of mitochondria reconstructed from the energy metabolism of living bacteria. | the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ... | 2014 | 24804722 |
| calibrating bacterial evolution. | attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal applica ... | 1999 | 10535975 |
| two c or not two c: recurrent disruption of zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. | ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. in prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. howe ... | 2001 | 11574053 |